diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..fa2a100 --- /dev/null +++ b/.gitignore @@ -0,0 +1,110 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +env/ +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +#lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +*.egg-info/ +.installed.cfg +*.egg + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +.hypothesis/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# pyenv +.python-version + +# celery beat schedule file +celerybeat-schedule + +# SageMath parsed files +*.sage.py + +# dotenv +.env + +# virtualenv +.venv +venv/ +ENV/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ + +# ninja specification +*.nja + +# temp files +*/.download/ + +# pycharm files +.idea/ \ No newline at end of file diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..9cecc1d --- /dev/null +++ b/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +the GNU General Public License is intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. We, the Free Software Foundation, use the +GNU General Public License for most of our software; it applies also to +any other work released this way by its authors. You can apply it to +your programs, too. + + When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +them if you wish), that you receive source code or can get it if you +want it, that you can change the software or use pieces of it in new +free programs, and that you know you can do these things. + + To protect your rights, we need to prevent others from denying you +these rights or asking you to surrender the rights. Therefore, you have +certain responsibilities if you distribute copies of the software, or if +you modify it: responsibilities to respect the freedom of others. + + For example, if you distribute copies of such a program, whether +gratis or for a fee, you must pass on to the recipients the same +freedoms that you received. You must make sure that they, too, receive +or can get the source code. And you must show them these terms so they +know their rights. + + Developers that use the GNU GPL protect your rights with two steps: +(1) assert copyright on the software, and (2) offer you this License +giving you legal permission to copy, distribute and/or modify it. + + For the developers' and authors' protection, the GPL clearly explains +that there is no warranty for this free software. For both users' and +authors' sake, the GPL requires that modified versions be marked as +changed, so that their problems will not be attributed erroneously to +authors of previous versions. + + Some devices are designed to deny users access to install or run +modified versions of the software inside them, although the manufacturer +can do so. This is fundamentally incompatible with the aim of +protecting users' freedom to change the software. The systematic +pattern of such abuse occurs in the area of products for individuals to +use, which is precisely where it is most unacceptable. Therefore, we +have designed this version of the GPL to prohibit the practice for those +products. If such problems arise substantially in other domains, we +stand ready to extend this provision to those domains in future versions +of the GPL, as needed to protect the freedom of users. + + Finally, every program is threatened constantly by software patents. +States should not allow patents to restrict development and use of +software on general-purpose computers, but in those that do, we wish to +avoid the special danger that patents applied to a free program could +make it effectively proprietary. To prevent this, the GPL assures that +patents cannot be used to render the program non-free. + + The precise terms and conditions for copying, distribution and +modification follow. + + TERMS AND CONDITIONS + + 0. Definitions. + + "This License" refers to version 3 of the GNU General Public License. + + "Copyright" also means copyright-like laws that apply to other kinds of +works, such as semiconductor masks. + + "The Program" refers to any copyrightable work licensed under this +License. Each licensee is addressed as "you". "Licensees" and +"recipients" may be individuals or organizations. + + To "modify" a work means to copy from or adapt all or part of the work +in a fashion requiring copyright permission, other than the making of an +exact copy. The resulting work is called a "modified version" of the +earlier work or a work "based on" the earlier work. + + A "covered work" means either the unmodified Program or a work based +on the Program. + + To "propagate" a work means to do anything with it that, without +permission, would make you directly or secondarily liable for +infringement under applicable copyright law, except executing it on a +computer or modifying a private copy. Propagation includes copying, +distribution (with or without modification), making available to the +public, and in some countries other activities as well. + + To "convey" a work means any kind of propagation that enables other +parties to make or receive copies. Mere interaction with a user through +a computer network, with no transfer of a copy, is not conveying. + + An interactive user interface displays "Appropriate Legal Notices" +to the extent that it includes a convenient and prominently visible +feature that (1) displays an appropriate copyright notice, and (2) +tells the user that there is no warranty for the work (except to the +extent that warranties are provided), that licensees may convey the +work under this License, and how to view a copy of this License. If +the interface presents a list of user commands or options, such as a +menu, a prominent item in the list meets this criterion. + + 1. Source Code. + + The "source code" for a work means the preferred form of the work +for making modifications to it. "Object code" means any non-source +form of a work. + + A "Standard Interface" means an interface that either is an official +standard defined by a recognized standards body, or, in the case of +interfaces specified for a particular programming language, one that +is widely used among developers working in that language. + + The "System Libraries" of an executable work include anything, other +than the work as a whole, that (a) is included in the normal form of +packaging a Major Component, but which is not part of that Major +Component, and (b) serves only to enable use of the work with that +Major Component, or to implement a Standard Interface for which an +implementation is available to the public in source code form. A +"Major Component", in this context, means a major essential component +(kernel, window system, and so on) of the specific operating system +(if any) on which the executable work runs, or a compiler used to +produce the work, or an object code interpreter used to run it. + + The "Corresponding Source" for a work in object code form means all +the source code needed to generate, install, and (for an executable +work) run the object code and to modify the work, including scripts to +control those activities. However, it does not include the work's +System Libraries, or general-purpose tools or generally available free +programs which are used unmodified in performing those activities but +which are not part of the work. For example, Corresponding Source +includes interface definition files associated with source files for +the work, and the source code for shared libraries and dynamically +linked subprograms that the work is specifically designed to require, +such as by intimate data communication or control flow between those +subprograms and other parts of the work. + + The Corresponding Source need not include anything that users +can regenerate automatically from other parts of the Corresponding +Source. + + The Corresponding Source for a work in source code form is that +same work. + + 2. Basic Permissions. + + All rights granted under this License are granted for the term of +copyright on the Program, and are irrevocable provided the stated +conditions are met. This License explicitly affirms your unlimited +permission to run the unmodified Program. The output from running a +covered work is covered by this License only if the output, given its +content, constitutes a covered work. This License acknowledges your +rights of fair use or other equivalent, as provided by copyright law. + + You may make, run and propagate covered works that you do not +convey, without conditions so long as your license otherwise remains +in force. You may convey covered works to others for the sole purpose +of having them make modifications exclusively for you, or provide you +with facilities for running those works, provided that you comply with +the terms of this License in conveying all material for which you do +not control copyright. Those thus making or running the covered works +for you must do so exclusively on your behalf, under your direction +and control, on terms that prohibit them from making any copies of +your copyrighted material outside their relationship with you. + + Conveying under any other circumstances is permitted solely under +the conditions stated below. Sublicensing is not allowed; section 10 +makes it unnecessary. + + 3. Protecting Users' Legal Rights From Anti-Circumvention Law. + + No covered work shall be deemed part of an effective technological +measure under any applicable law fulfilling obligations under article +11 of the WIPO copyright treaty adopted on 20 December 1996, or +similar laws prohibiting or restricting circumvention of such +measures. + + When you convey a covered work, you waive any legal power to forbid +circumvention of technological measures to the extent such circumvention +is effected by exercising rights under this License with respect to +the covered work, and you disclaim any intention to limit operation or +modification of the work as a means of enforcing, against the work's +users, your or third parties' legal rights to forbid circumvention of +technological measures. + + 4. Conveying Verbatim Copies. + + You may convey verbatim copies of the Program's source code as you +receive it, in any medium, provided that you conspicuously and +appropriately publish on each copy an appropriate copyright notice; +keep intact all notices stating that this License and any +non-permissive terms added in accord with section 7 apply to the code; +keep intact all notices of the absence of any warranty; and give all +recipients a copy of this License along with the Program. + + You may charge any price or no price for each copy that you convey, +and you may offer support or warranty protection for a fee. + + 5. Conveying Modified Source Versions. + + You may convey a work based on the Program, or the modifications to +produce it from the Program, in the form of source code under the +terms of section 4, provided that you also meet all of these conditions: + + a) The work must carry prominent notices stating that you modified + it, and giving a relevant date. + + b) The work must carry prominent notices stating that it is + released under this License and any conditions added under section + 7. This requirement modifies the requirement in section 4 to + "keep intact all notices". + + c) You must license the entire work, as a whole, under this + License to anyone who comes into possession of a copy. This + License will therefore apply, along with any applicable section 7 + additional terms, to the whole of the work, and all its parts, + regardless of how they are packaged. This License gives no + permission to license the work in any other way, but it does not + invalidate such permission if you have separately received it. + + d) If the work has interactive user interfaces, each must display + Appropriate Legal Notices; however, if the Program has interactive + interfaces that do not display Appropriate Legal Notices, your + work need not make them do so. + + A compilation of a covered work with other separate and independent +works, which are not by their nature extensions of the covered work, +and which are not combined with it such as to form a larger program, +in or on a volume of a storage or distribution medium, is called an +"aggregate" if the compilation and its resulting copyright are not +used to limit the access or legal rights of the compilation's users +beyond what the individual works permit. Inclusion of a covered work +in an aggregate does not cause this License to apply to the other +parts of the aggregate. + + 6. Conveying Non-Source Forms. + + You may convey a covered work in object code form under the terms +of sections 4 and 5, provided that you also convey the +machine-readable Corresponding Source under the terms of this License, +in one of these ways: + + a) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by the + Corresponding Source fixed on a durable physical medium + customarily used for software interchange. + + b) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by a + written offer, valid for at least three years and valid for as + long as you offer spare parts or customer support for that product + model, to give anyone who possesses the object code either (1) a + copy of the Corresponding Source for all the software in the + product that is covered by this License, on a durable physical + medium customarily used for software interchange, for a price no + more than your reasonable cost of physically performing this + conveying of source, or (2) access to copy the + Corresponding Source from a network server at no charge. + + c) Convey individual copies of the object code with a copy of the + written offer to provide the Corresponding Source. This + alternative is allowed only occasionally and noncommercially, and + only if you received the object code with such an offer, in accord + with subsection 6b. + + d) Convey the object code by offering access from a designated + place (gratis or for a charge), and offer equivalent access to the + Corresponding Source in the same way through the same place at no + further charge. You need not require recipients to copy the + Corresponding Source along with the object code. If the place to + copy the object code is a network server, the Corresponding Source + may be on a different server (operated by you or a third party) + that supports equivalent copying facilities, provided you maintain + clear directions next to the object code saying where to find the + Corresponding Source. Regardless of what server hosts the + Corresponding Source, you remain obligated to ensure that it is + available for as long as needed to satisfy these requirements. + + e) Convey the object code using peer-to-peer transmission, provided + you inform other peers where the object code and Corresponding + Source of the work are being offered to the general public at no + charge under subsection 6d. + + A separable portion of the object code, whose source code is excluded +from the Corresponding Source as a System Library, need not be +included in conveying the object code work. + + A "User Product" is either (1) a "consumer product", which means any +tangible personal property which is normally used for personal, family, +or household purposes, or (2) anything designed or sold for incorporation +into a dwelling. In determining whether a product is a consumer product, +doubtful cases shall be resolved in favor of coverage. For a particular +product received by a particular user, "normally used" refers to a +typical or common use of that class of product, regardless of the status +of the particular user or of the way in which the particular user +actually uses, or expects or is expected to use, the product. A product +is a consumer product regardless of whether the product has substantial +commercial, industrial or non-consumer uses, unless such uses represent +the only significant mode of use of the product. + + "Installation Information" for a User Product means any methods, +procedures, authorization keys, or other information required to install +and execute modified versions of a covered work in that User Product from +a modified version of its Corresponding Source. The information must +suffice to ensure that the continued functioning of the modified object +code is in no case prevented or interfered with solely because +modification has been made. + + If you convey an object code work under this section in, or with, or +specifically for use in, a User Product, and the conveying occurs as +part of a transaction in which the right of possession and use of the +User Product is transferred to the recipient in perpetuity or for a +fixed term (regardless of how the transaction is characterized), the +Corresponding Source conveyed under this section must be accompanied +by the Installation Information. But this requirement does not apply +if neither you nor any third party retains the ability to install +modified object code on the User Product (for example, the work has +been installed in ROM). + + The requirement to provide Installation Information does not include a +requirement to continue to provide support service, warranty, or updates +for a work that has been modified or installed by the recipient, or for +the User Product in which it has been modified or installed. Access to a +network may be denied when the modification itself materially and +adversely affects the operation of the network or violates the rules and +protocols for communication across the network. + + Corresponding Source conveyed, and Installation Information provided, +in accord with this section must be in a format that is publicly +documented (and with an implementation available to the public in +source code form), and must require no special password or key for +unpacking, reading or copying. + + 7. Additional Terms. + + "Additional permissions" are terms that supplement the terms of this +License by making exceptions from one or more of its conditions. +Additional permissions that are applicable to the entire Program shall +be treated as though they were included in this License, to the extent +that they are valid under applicable law. If additional permissions +apply only to part of the Program, that part may be used separately +under those permissions, but the entire Program remains governed by +this License without regard to the additional permissions. + + When you convey a copy of a covered work, you may at your option +remove any additional permissions from that copy, or from any part of +it. (Additional permissions may be written to require their own +removal in certain cases when you modify the work.) You may place +additional permissions on material, added by you to a covered work, +for which you have or can give appropriate copyright permission. + + Notwithstanding any other provision of this License, for material you +add to a covered work, you may (if authorized by the copyright holders of +that material) supplement the terms of this License with terms: + + a) Disclaiming warranty or limiting liability differently from the + terms of sections 15 and 16 of this License; or + + b) Requiring preservation of specified reasonable legal notices or + author attributions in that material or in the Appropriate Legal + Notices displayed by works containing it; or + + c) Prohibiting misrepresentation of the origin of that material, or + requiring that modified versions of such material be marked in + reasonable ways as different from the original version; or + + d) Limiting the use for publicity purposes of names of licensors or + authors of the material; or + + e) Declining to grant rights under trademark law for use of some + trade names, trademarks, or service marks; or + + f) Requiring indemnification of licensors and authors of that + material by anyone who conveys the material (or modified versions of + it) with contractual assumptions of liability to the recipient, for + any liability that these contractual assumptions directly impose on + those licensors and authors. + + All other non-permissive additional terms are considered "further +restrictions" within the meaning of section 10. If the Program as you +received it, or any part of it, contains a notice stating that it is +governed by this License along with a term that is a further +restriction, you may remove that term. If a license document contains +a further restriction but permits relicensing or conveying under this +License, you may add to a covered work material governed by the terms +of that license document, provided that the further restriction does +not survive such relicensing or conveying. + + If you add terms to a covered work in accord with this section, you +must place, in the relevant source files, a statement of the +additional terms that apply to those files, or a notice indicating +where to find the applicable terms. + + Additional terms, permissive or non-permissive, may be stated in the +form of a separately written license, or stated as exceptions; +the above requirements apply either way. + + 8. Termination. + + You may not propagate or modify a covered work except as expressly +provided under this License. Any attempt otherwise to propagate or +modify it is void, and will automatically terminate your rights under +this License (including any patent licenses granted under the third +paragraph of section 11). + + However, if you cease all violation of this License, then your +license from a particular copyright holder is reinstated (a) +provisionally, unless and until the copyright holder explicitly and +finally terminates your license, and (b) permanently, if the copyright +holder fails to notify you of the violation by some reasonable means +prior to 60 days after the cessation. + + Moreover, your license from a particular copyright holder is +reinstated permanently if the copyright holder notifies you of the +violation by some reasonable means, this is the first time you have +received notice of violation of this License (for any work) from that +copyright holder, and you cure the violation prior to 30 days after +your receipt of the notice. + + Termination of your rights under this section does not terminate the +licenses of parties who have received copies or rights from you under +this License. If your rights have been terminated and not permanently +reinstated, you do not qualify to receive new licenses for the same +material under section 10. + + 9. Acceptance Not Required for Having Copies. + + You are not required to accept this License in order to receive or +run a copy of the Program. Ancillary propagation of a covered work +occurring solely as a consequence of using peer-to-peer transmission +to receive a copy likewise does not require acceptance. However, +nothing other than this License grants you permission to propagate or +modify any covered work. These actions infringe copyright if you do +not accept this License. Therefore, by modifying or propagating a +covered work, you indicate your acceptance of this License to do so. + + 10. Automatic Licensing of Downstream Recipients. + + Each time you convey a covered work, the recipient automatically +receives a license from the original licensors, to run, modify and +propagate that work, subject to this License. You are not responsible +for enforcing compliance by third parties with this License. + + An "entity transaction" is a transaction transferring control of an +organization, or substantially all assets of one, or subdividing an +organization, or merging organizations. If propagation of a covered +work results from an entity transaction, each party to that +transaction who receives a copy of the work also receives whatever +licenses to the work the party's predecessor in interest had or could +give under the previous paragraph, plus a right to possession of the +Corresponding Source of the work from the predecessor in interest, if +the predecessor has it or can get it with reasonable efforts. + + You may not impose any further restrictions on the exercise of the +rights granted or affirmed under this License. For example, you may +not impose a license fee, royalty, or other charge for exercise of +rights granted under this License, and you may not initiate litigation +(including a cross-claim or counterclaim in a lawsuit) alleging that +any patent claim is infringed by making, using, selling, offering for +sale, or importing the Program or any portion of it. + + 11. Patents. + + A "contributor" is a copyright holder who authorizes use under this +License of the Program or a work on which the Program is based. The +work thus licensed is called the contributor's "contributor version". + + A contributor's "essential patent claims" are all patent claims +owned or controlled by the contributor, whether already acquired or +hereafter acquired, that would be infringed by some manner, permitted +by this License, of making, using, or selling its contributor version, +but do not include claims that would be infringed only as a +consequence of further modification of the contributor version. For +purposes of this definition, "control" includes the right to grant +patent sublicenses in a manner consistent with the requirements of +this License. + + Each contributor grants you a non-exclusive, worldwide, royalty-free +patent license under the contributor's essential patent claims, to +make, use, sell, offer for sale, import and otherwise run, modify and +propagate the contents of its contributor version. + + In the following three paragraphs, a "patent license" is any express +agreement or commitment, however denominated, not to enforce a patent +(such as an express permission to practice a patent or covenant not to +sue for patent infringement). To "grant" such a patent license to a +party means to make such an agreement or commitment not to enforce a +patent against the party. + + If you convey a covered work, knowingly relying on a patent license, +and the Corresponding Source of the work is not available for anyone +to copy, free of charge and under the terms of this License, through a +publicly available network server or other readily accessible means, +then you must either (1) cause the Corresponding Source to be so +available, or (2) arrange to deprive yourself of the benefit of the +patent license for this particular work, or (3) arrange, in a manner +consistent with the requirements of this License, to extend the patent +license to downstream recipients. "Knowingly relying" means you have +actual knowledge that, but for the patent license, your conveying the +covered work in a country, or your recipient's use of the covered work +in a country, would infringe one or more identifiable patents in that +country that you have reason to believe are valid. + + If, pursuant to or in connection with a single transaction or +arrangement, you convey, or propagate by procuring conveyance of, a +covered work, and grant a patent license to some of the parties +receiving the covered work authorizing them to use, propagate, modify +or convey a specific copy of the covered work, then the patent license +you grant is automatically extended to all recipients of the covered +work and works based on it. + + A patent license is "discriminatory" if it does not include within +the scope of its coverage, prohibits the exercise of, or is +conditioned on the non-exercise of one or more of the rights that are +specifically granted under this License. You may not convey a covered +work if you are a party to an arrangement with a third party that is +in the business of distributing software, under which you make payment +to the third party based on the extent of your activity of conveying +the work, and under which the third party grants, to any of the +parties who would receive the covered work from you, a discriminatory +patent license (a) in connection with copies of the covered work +conveyed by you (or copies made from those copies), or (b) primarily +for and in connection with specific products or compilations that +contain the covered work, unless you entered into that arrangement, +or that patent license was granted, prior to 28 March 2007. + + Nothing in this License shall be construed as excluding or limiting +any implied license or other defenses to infringement that may +otherwise be available to you under applicable patent law. + + 12. No Surrender of Others' Freedom. + + If conditions are imposed on you (whether by court order, agreement or +otherwise) that contradict the conditions of this License, they do not +excuse you from the conditions of this License. If you cannot convey a +covered work so as to satisfy simultaneously your obligations under this +License and any other pertinent obligations, then as a consequence you may +not convey it at all. For example, if you agree to terms that obligate you +to collect a royalty for further conveying from those to whom you convey +the Program, the only way you could satisfy both those terms and this +License would be to refrain entirely from conveying the Program. + + 13. Use with the GNU Affero General Public License. + + Notwithstanding any other provision of this License, you have +permission to link or combine any covered work with a work licensed +under version 3 of the GNU Affero General Public License into a single +combined work, and to convey the resulting work. The terms of this +License will continue to apply to the part which is the covered work, +but the special requirements of the GNU Affero General Public License, +section 13, concerning interaction through a network will apply to the +combination as such. + + 14. Revised Versions of this License. + + The Free Software Foundation may publish revised and/or new versions of +the GNU General Public License from time to time. Such new versions will +be similar in spirit to the present version, but may differ in detail to +address new problems or concerns. + + Each version is given a distinguishing version number. If the +Program specifies that a certain numbered version of the GNU General +Public License "or any later version" applies to it, you have the +option of following the terms and conditions either of that numbered +version or of any later version published by the Free Software +Foundation. If the Program does not specify a version number of the +GNU General Public License, you may choose any version ever published +by the Free Software Foundation. + + If the Program specifies that a proxy can decide which future +versions of the GNU General Public License can be used, that proxy's +public statement of acceptance of a version permanently authorizes you +to choose that version for the Program. + + Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + + 15. Disclaimer of Warranty. + + THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY +OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, +THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM +IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF +ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + + 16. Limitation of Liability. + + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS +THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY +GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE +USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF +DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD +PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), +EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF +SUCH DAMAGES. + + 17. Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + {one line to give the program's name and a brief idea of what it does.} + Copyright (C) {year} {name of author} + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + {project} Copyright (C) {year} {fullname} + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/README.md b/README.md index 01ebf4d..9ba08bf 100644 --- a/README.md +++ b/README.md @@ -1 +1,134 @@ -# MIDS \ No newline at end of file + +
+ +
+

+ +

Medical Imaging Bank Valencia Region 1

+ +

Medical Imaging Data Structure

+

BIDS Extension Proposal xx (BEP0xx)

+ +

+In order to add to the scientific knowledge, methods that yield reliable and reproducible results must be used. +High test-retest reliability of the methods applied is the foundation of research irrespective of the scientific discipline and it is in the prime interest of every scientist that results are reproducible. While such reproducibility was considered of utmost importance in the positron emitting tomography (PET) field [Adams et al., 2010], the quantitative assessment of reproducibility has largely been neglected in the fMRI community, +or as Bennett and Miller described it: “Reliability is not a typical topic of conversation” between fMRI investigators [Bennett and Miller, 2010]. This situation changed significantly in 2016, following the establishment of the Committee on Best Practices in Data Analysis and Sharing ([COBIDAS](www.humanbrainmapping.org/cobidas/)) by the most important neuroimaging society - the Organisation for Human Brain Mapping (OHBM). +

+ +

+The objective of BIMCV (Medical Imaging Bank Valencia Region) is that all this scientific knowledge be colected in a correct and efficient way. More concretely, all that knowledge is refered to data imaging. Find a way to organize this information is necesary. +

+ +

+Currently, distinc forms to store images and medical information exist, but there is not a standard that indicates how this information should be organized and shared. The CEIB idea is to use a simple organisation that any researcher can understand the distribution of data. +

+ +

+This desing is called MIDS (Medical Imaging Data Structure). MIDS is a new standard that contains every type of medical information and images in simple hierarchy folders. This is born as an extension of the standard BIDS (Brain Imaging Data Structure). BIDS [Gorgolewski et al.] is a structure that collect medical brain images, but MIDS pretend to extend it far away and not limit it the use to medical brain images. the idea is to create the same structure with both brain, column images or torso,... whether Resonance magnetic, Computed tomography, ecography,... This structure will definitely follow the same process regardless of the type and shape of the image. +

+ + +## Index + +>[1. Introduction: Medical Imaging Data Structure](#loading) + +>[2. MIDS structural format](#mids) + +>[3. Aplications](#aplications) + +>[4. future lines](#future) + +>[5. References](#references) + + + + +## 1. Introduction + +

+At present, many studies based on obtaining a dataset of medical images for its process of study. the qualitative improvement has been enormous for these studies since its use. Management and control all images and metadata added to them is a extra hard work. Furthermore, during the study, more data is generated where it is necessary to relocate. Each study search the way to organize these data in the way that best suits. this makes it more difficult to understand the data collected and results. +

+ +

+There are any studies that proposal a standar to store this type of data. One of them is BIDS ([Brain Imaging Data Structure](http://bids.neuroimaging.io/),[1]). BIDS is a proposal standar to store a magnetic resonance imaging and data in a structural folder hierarchy. This structure is very clear and easy to use. This standard is supported by several programs and libraries dedicated to the study of medical images (i.e. c-pacs, freesurfer, xnat, BIDSValidator...) and it is very used in the comunity researchers. In te Figure 1, a example of structure in BIDS is presented,the left directory is a folder with dicom images (Mildenberger, Eichelberg & Martin,2002) and the right directory is a BIDS structure +

+ + + +

+ +

+
+figure 1: DICOM to BIDS conversion with the tool Dcm2Bids +
+ + +

+However, BIDS only suports RM imaging and only brain images. For example, if a project need lumbar RM imaging, BIDS would not given support to these images. Nevertheless, this structure has not limits to store other anatomy parts. Without going into further, other acquisition images can be implemented. To that end, MIDS has been created. +

+ + +## 2. MIDS structural format + + +

+Currently, MIDS tries to stablish yourself like a BIDS ampliation. the structural format is highly similar like BIDS in magnetic resonance.The paper of [standar BIDS](http://www.nature.com/articles/sdata201644) or [BIDS specification](http://bids.neuroimaging.io/bids_spec1.0.2.pdf) can be read for more detail. +

+ +

+One proposal to extend and include BIDS into MIDS is create new variable in named specification of files. For example the estructure in one file is **sub-*id*[*obtative\_list\_variables*]\_*modality*.nii.gz** the proposal is add in this obtative variables the term \_bop-*body\_part\_dicom* which refers to the part of the body collected in the label dicom [(0018,0015)](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0015). The absence of the bop variable is set as the default skull.Thus, any BIDS structure is included in MIDS. The folder **data** shows a one exemple of input directory and output directory in MIDS structure.

+ + +# Aplications + +## XNAT2MIDS +This sorfware allow the user to Download one project into XNAT platform (--version XNAT <= 1.7.4.1) of BIMCV and convert the XNAT directory images in a directory MIDS. The aplication execution need Python --version >= 3.5. + +An example of execution is: + +```sh +python3.5 main.py -w Project_id -i dirXNAT -o dirOutput +``` + +### Options + +there are 2 funtions in this code: + + Download one project from xnat aplicatión: + + download one project from xnat aplicatión: + + arguments: + + + Prefix -w --web PAGE_WEB 1) The ULR page where XNAT is. + + Prefix -p --project [PROJECTS] 2) The project name to download + + Prefix -i --input PATH 3) the directfory where the files + will be downloaded + + Prefix -u --user [USER] 4) The username to loggin in XNAT + If not write a username, It + loggin as guest. + + Convert the xnat directories of the project in MIDS format: + arguments: + + + Prefix -i --input PATH 1) the directfory where the files will + be downloaded + + Prefix -o --output PATH 2) Directory where the MIDS model + is applied. + +## 4. Future Lines + +Now, BIDS is a potential standard to store images of RM and there is a little diference between BIDS and MIDS. However,MIDS pretend to incorporate, within epidemiological studies based on Population Image (BIMCV), any type of [modality](http://dicomlookup.com/modalities.asp) of medical image (i.e. Computed Radiography,Computed Tomography, Ultrasound, Mammography, ...). + +Taking in count, all images in BIMCV come from clinical imaging protocols in RM. these imaging don't ajust to labels in BIDS and, for that reason, one proposal is to extend and specify format label in MIDS. this format structure is "\_OriModSeq" where "Ori" is the orientation (**ax**->axial,**sag**->sagital,**cor**->coronal), "Mod" is the modality of image (T1,T2,Stir,angio,...) and "Seq" is the scaning sequence (**SE**->Spin Echo,**FSE**->Fast Spin Echo,**GR**->Gradiente,...). For more information, see the table in ./MIDS/XNAT2MIDS/.python\_objects/dictionary\_scan.csv in the column _Modality\_label_. + + +## 5. References + +Adams MC., Turkington TG., Wilson JM., Wong TZ. (2010). A systematic review of the factors affecting accuracy of SUV measurements. AJR American journal of roentgenology 195:310-320. + +Bennett CM., Miller MB. (2010) How reliable are the results from functional magnetic resonance imaging? Annals of the New York Academy of Sciences 1191:133-155. + +Mildenberger, P., Eichelberg, M., & Martin, E. (2002). Introduction to the DICOM standard. European radiology, 12(4), 920-927. + +Gorgolewski, K. J., Auer, T., Calhoun, V. D., Craddock, R. C., Das, S., Duff, E. P., ... & Handwerker, D. A. (2016). The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments. Scientific Data, 3, 160044. diff --git a/data/examples/MRI_Head/CHANGES.txt b/data/examples/MRI_Head/CHANGES.txt new file mode 100644 index 0000000..6280197 --- /dev/null +++ b/data/examples/MRI_Head/CHANGES.txt @@ -0,0 +1,9 @@ +1.0.1 2017-08-27 + - DICOM information. +1.0.0 2016-05-26 + - Initial release. + +AUTHOR + - Jose Manuel Saborit Torres + +COPYRIGHT AND LICENSE \ No newline at end of file diff --git a/data/examples/MRI_Head/README.txt b/data/examples/MRI_Head/README.txt new file mode 100644 index 0000000..e69de29 diff --git a/data/examples/MRI_Head/dataset_description.json b/data/examples/MRI_Head/dataset_description.json new file mode 100644 index 0000000..3a1866f --- /dev/null +++ b/data/examples/MRI_Head/dataset_description.json @@ -0,0 +1,12 @@ +{ + "Name": "MRI_Head", + "BIDSVersion": "1.1.0", + "MIDSVersion": "0.10.23", + "License": "CC BY 4.0" + "Authors": ["Jose Manuel Saborit Torres","CEIB-CSUSP"], + "Acknowledgements": "A special thanks to Jhon Jairo Saenz Gamboa for the help to format this data set in MIDS, to Joaquim Montell for the management of the XNAT platform, to María de la Iglesia Vayá head of Lab. for her support; Thanks to the CEIB-SUSP team of scientists, who developed the download, anonymization and scientific knowledge processes necessary to carry out this data set, and to the Public Health Department of Valencia for providing the data.", + "HowToAcknowledge": "Please cite this paper: ", + "Funding": ["Centre of Excellence and Technological Innovation in Bioimaging, Health Regional Ministry of Valencia and Public Health(CEIB-CSUSP), http://ceib.san.gva.es/ceib-cs", "Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), http://fisabio.san.gva.es/","Conselleria de Sanitat Universal i Salut Pública, http://www.san.gva.es"], + "ReferencesAndLinks": ["http://bimcv.cipf.es/2_projects/mids/", "http://bimcv.cipf.es/2_projects/10k-bdbi-4-cv/"], + "DatasetDOI": "" +} diff --git a/data/examples/MRI_Head/participants.tsv b/data/examples/MRI_Head/participants.tsv new file mode 100644 index 0000000..c45a48b --- /dev/null +++ b/data/examples/MRI_Head/participants.tsv @@ -0,0 +1,4 @@ +participant_id age gender control +sub-3 8 M 191 +sub-2 76 M 191 +sub-1 91 F 191 \ No newline at end of file diff --git a/data/examples/MRI_Head/sub-1/ses-1/anat/sub-1_ses-1_T1w.json b/data/examples/MRI_Head/sub-1/ses-1/anat/sub-1_ses-1_T1w.json new file mode 100644 index 0000000..a79b043 --- /dev/null +++ b/data/examples/MRI_Head/sub-1/ses-1/anat/sub-1_ses-1_T1w.json @@ -0,0 +1 @@ +[{"tag1": "(0002,0001)", "vr": "OB", "value": "00\\01", "tag2": "", "desc": "File Meta Information Version"}, {"tag1": "(0002,0002)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "", "desc": "Media Storage SOP Class UID"}, {"tag1": "(0002,0003)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1616754.9228.1430200133.557", "tag2": "", "desc": "Media Storage SOP Instance UID"}, {"tag1": "(0002,0010)", "vr": "UI", "value": "1.2.840.10008.1.2.1", "tag2": "", "desc": "Transfer Syntax UID"}, {"tag1": "(0002,0012)", "vr": "UI", "value": "1.2.40.0.13.1.1", "tag2": "", "desc": "Implementation Class UID"}, {"tag1": "(0002,0013)", "vr": "SH", "value": "dcm4che-2.0", "tag2": "", "desc": "Implementation Version Name"}, {"tag1": "(0002,0016)", "vr": "AE", "value": "CTP", "tag2": "", "desc": "Source Application Entity Title"}, {"tag1": "(0008,0005)", "vr": "CS", "value": "ISO_IR 100", "tag2": "", "desc": "Specific Character Set"}, {"tag1": "(0008,0008)", "vr": "CS", "value": "ORIGINAL\\PRIMARY\\OTHER", "tag2": "", "desc": "Image Type"}, {"tag1": "(0008,0016)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "", "desc": "SOP Class UID"}, {"tag1": "(0008,0018)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1616754.9228.1430200133.557", "tag2": "", "desc": "SOP Instance UID"}, {"tag1": "(0008,0020)", "vr": "DA", "value": "20150428", "tag2": "", "desc": "Study Date"}, {"tag1": "(0008,0021)", "vr": "DA", "value": "20150428", "tag2": "", "desc": "Series Date"}, {"tag1": "(0008,0022)", "vr": "DA", "value": "20150428", "tag2": "", "desc": "Acquisition Date"}, {"tag1": "(0008,0023)", "vr": "DA", "value": "20150428", "tag2": "", "desc": "Content Date"}, {"tag1": "(0008,0030)", "vr": "TM", "value": "090707.000000", "tag2": "", "desc": "Study Time"}, {"tag1": "(0008,0031)", "vr": "TM", "value": "092930.000000", "tag2": "", "desc": "Series Time"}, {"tag1": "(0008,0032)", "vr": "TM", "value": "092930.000000", "tag2": "", "desc": "Acquisition Time"}, {"tag1": "(0008,0033)", "vr": "TM", "value": "092930.000000", "tag2": "", "desc": "Content Time"}, {"tag1": "(0008,0050)", "vr": "SH", "value": "", "tag2": "", "desc": "Accession Number"}, {"tag1": "(0008,0060)", "vr": "CS", "value": "MR", "tag2": "", "desc": "Modality"}, {"tag1": "(0008,0061)", "vr": "CS", "value": "MR", "tag2": "", "desc": "Modalities in Study"}, {"tag1": "(0008,0070)", "vr": "LO", "value": "GE MEDICAL SYSTEMS", "tag2": "", "desc": "Manufacturer"}, {"tag1": "(0008,0090)", "vr": "PN", "value": "", "tag2": "", "desc": "Referring Physician’s Name"}, {"tag1": "(0008,1010)", "vr": "SH", "value": "CASTMRI", "tag2": "", "desc": "Station Name"}, {"tag1": "(0008,1030)", "vr": "LO", "value": "RMI_head", "tag2": "", "desc": "Study Description"}, {"tag1": "(0008,1032)", "vr": "SQ", "value": "", "tag2": "(0008,1032)", "desc": "Procedure Code Sequence"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "015031_RM111B", "tag2": "(0008,0100)", "desc": "Code Value"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "GEIIS", "tag2": "(0008,0102)", "desc": "Coding Scheme Designator"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "0", "tag2": "(0008,0103)", "desc": "Coding Scheme Version"}, {"tag1": "(0008,1032)", "vr": "LO", "value": "RM ESPECTROSCOPICA CEREBRAL", "tag2": "(0008,0104)", "desc": "Code Meaning"}, {"tag1": "(0008,103E)", "vr": "LO", "value": "AXIALT1", "tag2": "", "desc": "Series Description"}, {"tag1": "(0008,1090)", "vr": "LO", "value": "SIGNA EXCITE", "tag2": "", "desc": "Manufacturer’s Model Name"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1616754.9228.1430200132.795", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1616754.9228.1430200132.798", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0009,0010)", "vr": "LO", "value": "GEMS_IDEN_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0009,0011)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0010,0010)", "vr": "PN", "value": "304229696761426913368206915776875392104", "tag2": "", "desc": "Patient’s Name"}, {"tag1": "(0010,0020)", "vr": "LO", "value": "239996943502289713192853049918686757778", "tag2": "", "desc": "Patient ID"}, {"tag1": "(0010,0030)", "vr": "DA", "value": "19240302", "tag2": "", "desc": "Patient’s Birth Date"}, {"tag1": "(0010,0040)", "vr": "CS", "value": "F", "tag2": "", "desc": "Patient’s Sex"}, {"tag1": "(0010,1010)", "vr": "AS", "value": "091Y", "tag2": "", "desc": "Patient’s Age"}, {"tag1": "(0010,1030)", "vr": "DS", "value": "41", "tag2": "", "desc": "Patient’s Weight"}, {"tag1": "(0011,0010)", "vr": "LO", "value": "GEMS_PATI_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0018,0020)", "vr": "CS", "value": "SE", "tag2": "", "desc": "Scanning Sequence"}, {"tag1": "(0018,0021)", "vr": "CS", "value": "NONE", "tag2": "", "desc": "Sequence Variant"}, {"tag1": "(0018,0022)", "vr": "CS", "value": "VB_GEMS\\EDR_GEMS\\FILTERED_GEMS", "tag2": "", "desc": "Scan Options"}, {"tag1": "(0018,0023)", "vr": "CS", "value": "2D", "tag2": "", "desc": "MR Acquisition Type"}, {"tag1": "(0018,0025)", "vr": "CS", "value": "N", "tag2": "", "desc": "Angio Flag"}, {"tag1": "(0018,0050)", "vr": "DS", "value": "5", "tag2": "", "desc": "Slice Thickness"}, {"tag1": "(0018,0080)", "vr": "DS", "value": "480", "tag2": "", "desc": "Repetition Time"}, {"tag1": "(0018,0081)", "vr": "DS", "value": "12", "tag2": "", "desc": "Echo Time"}, {"tag1": "(0018,0082)", "vr": "DS", "value": "0", "tag2": "", "desc": "Inversion Time"}, {"tag1": "(0018,0083)", "vr": "DS", "value": "1", "tag2": "", "desc": "Number of Averages"}, {"tag1": "(0018,0084)", "vr": "DS", "value": "63.868208", "tag2": "", "desc": "Imaging Frequency"}, {"tag1": "(0018,0085)", "vr": "SH", "value": "1H", "tag2": "", "desc": "Imaged Nucleus"}, {"tag1": "(0018,0086)", "vr": "IS", "value": "1", "tag2": "", "desc": "Echo Number(s)"}, {"tag1": "(0018,0087)", "vr": "DS", "value": "1.5", "tag2": "", "desc": "Magnetic Field Strength"}, {"tag1": "(0018,0088)", "vr": "DS", "value": "6", "tag2": "", "desc": "Spacing Between Slices"}, {"tag1": "(0018,0091)", "vr": "IS", "value": "1", "tag2": "", "desc": "Echo Train Length"}, {"tag1": "(0018,0093)", "vr": "DS", "value": "100", "tag2": "", "desc": "Percent Sampling"}, {"tag1": "(0018,0094)", "vr": "DS", "value": "75", "tag2": "", "desc": "Percent Phase Field of View"}, {"tag1": "(0018,0095)", "vr": "DS", "value": "81.3672", "tag2": "", "desc": "Pixel Bandwidth"}, {"tag1": "(0018,1000)", "vr": "LO", "value": "00000000NPV24200", "tag2": "", "desc": "Device Serial Number"}, {"tag1": "(0018,1020)", "vr": "LO", "value": "11\\LX\\MR Software release:11.1_M4_0818.a", "tag2": "", "desc": "Software Version(s)"}, {"tag1": "(0018,1030)", "vr": "LO", "value": "4436599", "tag2": "", "desc": "Protocol Name"}, {"tag1": "(0018,1088)", "vr": "IS", "value": "0", "tag2": "", "desc": "Heart Rate"}, {"tag1": "(0018,1090)", "vr": "IS", "value": "0", "tag2": "", "desc": "Cardiac Number of Images"}, {"tag1": "(0018,1094)", "vr": "IS", "value": "0", "tag2": "", "desc": "Trigger Window"}, {"tag1": "(0018,1100)", "vr": "DS", "value": "240", "tag2": "", "desc": "Reconstruction Diameter"}, {"tag1": "(0018,1250)", "vr": "SH", "value": "8HRBRAIN", "tag2": "", "desc": "Receive Coil Name"}, {"tag1": "(0018,1310)", "vr": "US", "value": "0\\256\\192\\0", "tag2": "", "desc": "Acquisition Matrix"}, {"tag1": "(0018,1312)", "vr": "CS", "value": "ROW", "tag2": "", "desc": "In-plane Phase Encoding Direction"}, {"tag1": "(0018,1314)", "vr": "DS", "value": "90", "tag2": "", "desc": "Flip Angle"}, {"tag1": "(0018,1315)", "vr": "CS", "value": "N", "tag2": "", "desc": "Variable Flip Angle Flag"}, {"tag1": "(0018,1316)", "vr": "DS", "value": "1.168009", "tag2": "", "desc": "SAR"}, {"tag1": "(0018,5100)", "vr": "CS", "value": "HFS", "tag2": "", "desc": "Patient Position"}, {"tag1": "(0019,0010)", "vr": "LO", "value": "GEMS_ACQU_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0019,10BB)", "vr": "DS", "value": "0", "tag2": "", "desc": "?"}, {"tag1": "(0019,10BC)", "vr": "DS", "value": "0", "tag2": "", "desc": "?"}, {"tag1": "(0019,10BD)", "vr": "DS", "value": "0", "tag2": "", "desc": "?"}, {"tag1": "(0019,10D9)", "vr": "DS", "value": "0", "tag2": "", "desc": "?"}, {"tag1": "(0019,10DF)", "vr": "DS", "value": "0", "tag2": "", "desc": "?"}, {"tag1": "(0019,10E0)", "vr": "DS", "value": "0", "tag2": "", "desc": "?"}, {"tag1": "(0020,000D)", "vr": "UI", "value": "1.2.124.113532.10.192.138.26.20150427.140750.4893596", "tag2": "", "desc": "Study Instance UID"}, {"tag1": "(0020,000E)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1616754.9228.1430200133.472", "tag2": "", "desc": "Series Instance UID"}, {"tag1": "(0020,0010)", "vr": "SH", "value": "", "tag2": "", "desc": "Study ID"}, {"tag1": "(0020,0011)", "vr": "IS", "value": "9", "tag2": "", "desc": "Series Number"}, {"tag1": "(0020,0012)", "vr": "IS", "value": "1", "tag2": "", "desc": "Acquisition Number"}, {"tag1": "(0020,0013)", "vr": "IS", "value": "20", "tag2": "", "desc": "Instance Number"}, {"tag1": "(0020,0032)", "vr": "DS", "value": "-122.107\\-135.4\\50", "tag2": "", "desc": "Image Position (Patient)"}, {"tag1": "(0020,0037)", "vr": "DS", "value": "1\\0\\0\\0\\1\\0", "tag2": "", "desc": "Image Orientation (Patient)"}, {"tag1": "(0020,0052)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1616754.9298.1430199842.154", "tag2": "", "desc": "Frame of Reference UID"}, {"tag1": "(0020,0110)", "vr": "DS", "value": "0", "tag2": "", "desc": "Temporal Resolution"}, {"tag1": "(0020,1040)", "vr": "LO", "value": "", "tag2": "", "desc": "Position Reference Indicator"}, {"tag1": "(0020,1041)", "vr": "DS", "value": "50", "tag2": "", "desc": "Slice Location"}, {"tag1": "(0020,1208)", "vr": "IS", "value": "1102", "tag2": "", "desc": "Number of Study Related Instances"}, {"tag1": "(0021,0010)", "vr": "LO", "value": "GEMS_RELA_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0021,105A)", "vr": "SL", "value": "0", "tag2": "", "desc": "?"}, {"tag1": "(0023,0010)", "vr": "LO", "value": "GEMS_STDY_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0025,0010)", "vr": "LO", "value": "GEMS_SERS_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0027,0010)", "vr": "LO", "value": "GEMS_IMAG_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0028,0002)", "vr": "US", "value": "1", "tag2": "", "desc": "Samples per Pixel"}, {"tag1": "(0028,0004)", "vr": "CS", "value": "MONOCHROME2", "tag2": "", "desc": "Photometric Interpretation"}, {"tag1": "(0028,0010)", "vr": "US", "value": "512", "tag2": "", "desc": "Rows"}, {"tag1": "(0028,0011)", "vr": "US", "value": "512", "tag2": "", "desc": "Columns"}, {"tag1": "(0028,0030)", "vr": "DS", "value": "0.46875\\0.46875", "tag2": "", "desc": "Pixel Spacing"}, {"tag1": "(0028,0100)", "vr": "US", "value": "16", "tag2": "", "desc": "Bits Allocated"}, {"tag1": "(0028,0101)", "vr": "US", "value": "16", "tag2": "", "desc": "Bits Stored"}, {"tag1": "(0028,0102)", "vr": "US", "value": "15", "tag2": "", "desc": "High Bit"}, {"tag1": "(0028,0103)", "vr": "US", "value": "1", "tag2": "", "desc": "Pixel Representation"}, {"tag1": "(0028,0303)", "vr": "CS", "value": "", "tag2": "", "desc": "Longitudinal Temporal Information Modified"}, {"tag1": "(0028,1050)", "vr": "DS", "value": "295", "tag2": "", "desc": "Window Center"}, {"tag1": "(0028,1051)", "vr": "DS", "value": "591", "tag2": "", "desc": "Window Width"}, {"tag1": "(0029,0010)", "vr": "LO", "value": "GEMS_IMPS_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0043,0010)", "vr": "LO", "value": "GEMS_PARM_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0043,1039)", "vr": "IS", "value": "0\\32\\0\\0", "tag2": "", "desc": "?"}, {"tag1": "(07A1,0010)", "vr": "LO", "value": "ELSCINT1", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(07A3,0010)", "vr": "LO", "value": "ELSCINT1", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(07A5,0010)", "vr": "LO", "value": "ELSCINT1", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0903,0010)", "vr": "LO", "value": "GEIIS PACS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0905,0010)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(7FD1,0010)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}] \ No newline at end of file diff --git a/data/examples/MRI_Head/sub-1/ses-1/anat/sub-1_ses-1_T1w.nii.gz b/data/examples/MRI_Head/sub-1/ses-1/anat/sub-1_ses-1_T1w.nii.gz new file mode 100644 index 0000000..278e2c2 Binary files /dev/null and b/data/examples/MRI_Head/sub-1/ses-1/anat/sub-1_ses-1_T1w.nii.gz differ diff --git a/data/examples/MRI_Head/sub-1/ses-1/dwi/sub-1_ses-1_acq-b1000_dwi.bval b/data/examples/MRI_Head/sub-1/ses-1/dwi/sub-1_ses-1_acq-b1000_dwi.bval new file mode 100644 index 0000000..a72be1b --- /dev/null +++ b/data/examples/MRI_Head/sub-1/ses-1/dwi/sub-1_ses-1_acq-b1000_dwi.bval @@ -0,0 +1 @@ +1000 0 diff --git a/data/examples/MRI_Head/sub-1/ses-1/dwi/sub-1_ses-1_acq-b1000_dwi.bvec b/data/examples/MRI_Head/sub-1/ses-1/dwi/sub-1_ses-1_acq-b1000_dwi.bvec new file mode 100644 index 0000000..41c02d7 --- /dev/null +++ b/data/examples/MRI_Head/sub-1/ses-1/dwi/sub-1_ses-1_acq-b1000_dwi.bvec @@ -0,0 +1,3 @@ +0 0 +0 0 +0 0 diff --git a/data/examples/MRI_Head/sub-1/ses-1/dwi/sub-1_ses-1_acq-b1000_dwi.json b/data/examples/MRI_Head/sub-1/ses-1/dwi/sub-1_ses-1_acq-b1000_dwi.json new file mode 100644 index 0000000..92f17f1 --- /dev/null +++ b/data/examples/MRI_Head/sub-1/ses-1/dwi/sub-1_ses-1_acq-b1000_dwi.json @@ -0,0 +1 @@ +[{"tag1": "(0002,0001)", "vr": "OB", "value": "00\\01", "tag2": "", "desc": "File Meta Information Version"}, {"tag1": "(0002,0002)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "", "desc": "Media Storage SOP Class UID"}, {"tag1": "(0002,0003)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1616754.9228.1430200133.180", "tag2": "", "desc": "Media Storage SOP Instance UID"}, {"tag1": "(0002,0010)", "vr": "UI", "value": "1.2.840.10008.1.2.1", "tag2": "", "desc": "Transfer Syntax UID"}, {"tag1": "(0002,0012)", "vr": "UI", "value": "1.2.40.0.13.1.1", "tag2": "", "desc": "Implementation Class UID"}, {"tag1": "(0002,0013)", "vr": "SH", "value": "dcm4che-2.0", "tag2": "", "desc": "Implementation Version Name"}, {"tag1": "(0002,0016)", "vr": "AE", "value": "CTP", "tag2": "", "desc": "Source Application Entity Title"}, {"tag1": "(0008,0005)", "vr": "CS", "value": "ISO_IR 100", "tag2": "", "desc": "Specific Character Set"}, {"tag1": "(0008,0008)", "vr": "CS", "value": "ORIGINAL\\PRIMARY\\OTHER", "tag2": "", "desc": "Image Type"}, {"tag1": "(0008,0016)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "", "desc": "SOP Class UID"}, {"tag1": "(0008,0018)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1616754.9228.1430200133.180", "tag2": "", "desc": "SOP Instance UID"}, {"tag1": "(0008,0020)", "vr": "DA", "value": "20150428", "tag2": "", "desc": "Study Date"}, {"tag1": "(0008,0021)", "vr": "DA", "value": "20150428", "tag2": "", "desc": "Series Date"}, {"tag1": "(0008,0022)", "vr": "DA", "value": "20150428", "tag2": "", "desc": "Acquisition Date"}, {"tag1": "(0008,0023)", "vr": "DA", "value": "20150428", "tag2": "", "desc": "Content Date"}, {"tag1": "(0008,0030)", "vr": "TM", "value": "090707.000000", "tag2": "", "desc": "Study Time"}, {"tag1": "(0008,0031)", "vr": "TM", "value": "091710.000000", "tag2": "", "desc": "Series Time"}, {"tag1": "(0008,0032)", "vr": "TM", "value": "091711.000000", "tag2": "", "desc": "Acquisition Time"}, {"tag1": "(0008,0033)", "vr": "TM", "value": "091711.000000", "tag2": "", "desc": "Content Time"}, {"tag1": "(0008,0050)", "vr": "SH", "value": "", "tag2": "", "desc": "Accession Number"}, {"tag1": "(0008,0060)", "vr": "CS", "value": "MR", "tag2": "", "desc": "Modality"}, {"tag1": "(0008,0070)", "vr": "LO", "value": "GE MEDICAL SYSTEMS", "tag2": "", "desc": "Manufacturer"}, {"tag1": "(0008,0090)", "vr": "PN", "value": "", "tag2": "", "desc": "Referring Physician’s Name"}, {"tag1": "(0008,1010)", "vr": "SH", "value": "CASTMRI", "tag2": "", "desc": "Station Name"}, {"tag1": "(0008,1030)", "vr": "LO", "value": "RMI_head", "tag2": "", "desc": "Study Description"}, {"tag1": "(0008,1032)", "vr": "SQ", "value": "", "tag2": "(0008,1032)", "desc": "Procedure Code Sequence"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "015031_RM111B", "tag2": "(0008,0100)", "desc": "Code Value"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "GEIIS", "tag2": "(0008,0102)", "desc": "Coding Scheme Designator"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "0", "tag2": "(0008,0103)", "desc": "Coding Scheme Version"}, {"tag1": "(0008,1032)", "vr": "LO", "value": "RM ESPECTROSCOPICA CEREBRAL", "tag2": "(0008,0104)", "desc": "Code Meaning"}, {"tag1": "(0008,103E)", "vr": "LO", "value": "DIFUSIONB1000", "tag2": "", "desc": "Series Description"}, {"tag1": "(0008,1090)", "vr": "LO", "value": "SIGNA EXCITE", "tag2": "", "desc": "Manufacturer’s Model Name"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1616754.9228.1430200132.795", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1616754.9228.1430200132.798", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0009,0010)", "vr": "LO", "value": "GEMS_IDEN_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0009,0011)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0010,0010)", "vr": "PN", "value": "304229696761426913368206915776875392104", "tag2": "", "desc": "Patient’s Name"}, {"tag1": "(0010,0020)", "vr": "LO", "value": "239996943502289713192853049918686757778", "tag2": "", "desc": "Patient ID"}, {"tag1": "(0010,0030)", "vr": "DA", "value": "19240302", "tag2": "", "desc": "Patient’s Birth Date"}, {"tag1": "(0010,0040)", "vr": "CS", "value": "F", "tag2": "", "desc": "Patient’s Sex"}, {"tag1": "(0010,1010)", "vr": "AS", "value": "091Y", "tag2": "", "desc": "Patient’s Age"}, {"tag1": "(0010,1030)", "vr": "DS", "value": "41", "tag2": "", "desc": "Patient’s Weight"}, {"tag1": "(0011,0010)", "vr": "LO", "value": "GEMS_PATI_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0018,0020)", "vr": "CS", "value": "EP\\SE", "tag2": "", "desc": "Scanning Sequence"}, {"tag1": "(0018,0021)", "vr": "CS", "value": "NONE", "tag2": "", "desc": "Sequence Variant"}, {"tag1": "(0018,0022)", "vr": "CS", "value": "VB_GEMS\\EPI_GEMS\\PFF", "tag2": "", "desc": "Scan Options"}, {"tag1": "(0018,0023)", "vr": "CS", "value": "2D", "tag2": "", "desc": "MR Acquisition Type"}, {"tag1": "(0018,0025)", "vr": "CS", "value": "N", "tag2": "", "desc": "Angio Flag"}, {"tag1": "(0018,0050)", "vr": "DS", "value": "5", "tag2": "", "desc": "Slice Thickness"}, {"tag1": "(0018,0080)", "vr": "DS", "value": "8100", "tag2": "", "desc": "Repetition Time"}, {"tag1": "(0018,0081)", "vr": "DS", "value": "78.2", "tag2": "", "desc": "Echo Time"}, {"tag1": "(0018,0082)", "vr": "DS", "value": "0", "tag2": "", "desc": "Inversion Time"}, {"tag1": "(0018,0083)", "vr": "DS", "value": "1", "tag2": "", "desc": "Number of Averages"}, {"tag1": "(0018,0084)", "vr": "DS", "value": "63.868212", "tag2": "", "desc": "Imaging Frequency"}, {"tag1": "(0018,0085)", "vr": "SH", "value": "1H", "tag2": "", "desc": "Imaged Nucleus"}, {"tag1": "(0018,0086)", "vr": "IS", "value": "1", "tag2": "", "desc": "Echo Number(s)"}, {"tag1": "(0018,0087)", "vr": "DS", "value": "1.5", "tag2": "", "desc": "Magnetic Field Strength"}, {"tag1": "(0018,0088)", "vr": "DS", "value": "6", "tag2": "", "desc": "Spacing Between Slices"}, {"tag1": "(0018,0091)", "vr": "IS", "value": "1", "tag2": "", "desc": "Echo Train Length"}, {"tag1": "(0018,0093)", "vr": "DS", "value": "100", "tag2": "", "desc": "Percent Sampling"}, {"tag1": "(0018,0094)", "vr": "DS", "value": "100", "tag2": "", "desc": "Percent Phase Field of View"}, {"tag1": "(0018,0095)", "vr": "DS", "value": "1953.12", "tag2": "", "desc": "Pixel Bandwidth"}, {"tag1": "(0018,1000)", "vr": "LO", "value": "00000000NPV24200", "tag2": "", "desc": "Device Serial Number"}, {"tag1": "(0018,1020)", "vr": "LO", "value": "11\\LX\\MR Software release:11.1_M4_0818.a", "tag2": "", "desc": "Software Version(s)"}, {"tag1": "(0018,1030)", "vr": "LO", "value": "4436599", "tag2": "", "desc": "Protocol Name"}, {"tag1": "(0018,1088)", "vr": "IS", "value": "0", "tag2": "", "desc": "Heart Rate"}, {"tag1": "(0018,1090)", "vr": "IS", "value": "0", "tag2": "", "desc": "Cardiac Number of Images"}, {"tag1": "(0018,1094)", "vr": "IS", "value": "0", "tag2": "", "desc": "Trigger Window"}, {"tag1": "(0018,1100)", "vr": "DS", "value": "240", "tag2": "", "desc": "Reconstruction Diameter"}, {"tag1": "(0018,1250)", "vr": "SH", "value": "8HRBRAIN", "tag2": "", "desc": "Receive Coil Name"}, {"tag1": "(0018,1310)", "vr": "US", "value": "128\\0\\0\\128", "tag2": "", "desc": "Acquisition Matrix"}, {"tag1": "(0018,1312)", "vr": "CS", "value": "COL", "tag2": "", "desc": "In-plane Phase Encoding Direction"}, {"tag1": "(0018,1314)", "vr": "DS", "value": "90", "tag2": "", "desc": "Flip Angle"}, {"tag1": "(0018,1315)", "vr": "CS", "value": "N", "tag2": "", "desc": "Variable Flip Angle Flag"}, {"tag1": "(0018,1316)", "vr": "DS", "value": "0.064779", "tag2": "", "desc": "SAR"}, {"tag1": "(0018,5100)", "vr": "CS", "value": "HFS", "tag2": "", "desc": "Patient Position"}, {"tag1": "(0019,0010)", "vr": "LO", "value": "GEMS_ACQU_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0019,10BB)", "vr": "DS", "value": "0", "tag2": "", "desc": "?"}, {"tag1": "(0019,10BC)", "vr": "DS", "value": "0", "tag2": "", "desc": "?"}, {"tag1": "(0019,10BD)", "vr": "DS", "value": "0", "tag2": "", "desc": "?"}, {"tag1": "(0019,10D9)", "vr": "DS", "value": "0", "tag2": "", "desc": "?"}, {"tag1": "(0019,10DF)", "vr": "DS", "value": "0", "tag2": "", "desc": "?"}, {"tag1": "(0019,10E0)", "vr": "DS", "value": "0", "tag2": "", "desc": "?"}, {"tag1": "(0020,000D)", "vr": "UI", "value": "1.2.124.113532.10.192.138.26.20150427.140750.4893596", "tag2": "", "desc": "Study Instance UID"}, {"tag1": "(0020,000E)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1616754.9228.1430200133.94", "tag2": "", "desc": "Series Instance UID"}, {"tag1": "(0020,0010)", "vr": "SH", "value": "", "tag2": "", "desc": "Study ID"}, {"tag1": "(0020,0011)", "vr": "IS", "value": "5", "tag2": "", "desc": "Series Number"}, {"tag1": "(0020,0012)", "vr": "IS", "value": "1", "tag2": "", "desc": "Acquisition Number"}, {"tag1": "(0020,0013)", "vr": "IS", "value": "21", "tag2": "", "desc": "Instance Number"}, {"tag1": "(0020,0032)", "vr": "DS", "value": "-121.873\\-135.165\\56", "tag2": "", "desc": "Image Position (Patient)"}, {"tag1": "(0020,0037)", "vr": "DS", "value": "1\\0\\0\\0\\1\\0", "tag2": "", "desc": "Image Orientation (Patient)"}, {"tag1": "(0020,0052)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1616754.9298.1430199842.154", "tag2": "", "desc": "Frame of Reference UID"}, {"tag1": "(0020,0110)", "vr": "DS", "value": "0", "tag2": "", "desc": "Temporal Resolution"}, {"tag1": "(0020,1040)", "vr": "LO", "value": "", "tag2": "", "desc": "Position Reference Indicator"}, {"tag1": "(0020,1041)", "vr": "DS", "value": "56", "tag2": "", "desc": "Slice Location"}, {"tag1": "(0021,0010)", "vr": "LO", "value": "GEMS_RELA_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0021,105A)", "vr": "SL", "value": "7", "tag2": "", "desc": "?"}, {"tag1": "(0023,0010)", "vr": "LO", "value": "GEMS_STDY_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0025,0010)", "vr": "LO", "value": "GEMS_SERS_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0027,0010)", "vr": "LO", "value": "GEMS_IMAG_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0028,0002)", "vr": "US", "value": "1", "tag2": "", "desc": "Samples per Pixel"}, {"tag1": "(0028,0004)", "vr": "CS", "value": "MONOCHROME2", "tag2": "", "desc": "Photometric Interpretation"}, {"tag1": "(0028,0010)", "vr": "US", "value": "256", "tag2": "", "desc": "Rows"}, {"tag1": "(0028,0011)", "vr": "US", "value": "256", "tag2": "", "desc": "Columns"}, {"tag1": "(0028,0030)", "vr": "DS", "value": "0.9375\\0.9375", "tag2": "", "desc": "Pixel Spacing"}, {"tag1": "(0028,0100)", "vr": "US", "value": "16", "tag2": "", "desc": "Bits Allocated"}, {"tag1": "(0028,0101)", "vr": "US", "value": "16", "tag2": "", "desc": "Bits Stored"}, {"tag1": "(0028,0102)", "vr": "US", "value": "15", "tag2": "", "desc": "High Bit"}, {"tag1": "(0028,0103)", "vr": "US", "value": "1", "tag2": "", "desc": "Pixel Representation"}, {"tag1": "(0028,0303)", "vr": "CS", "value": "", "tag2": "", "desc": "Longitudinal Temporal Information Modified"}, {"tag1": "(0028,1050)", "vr": "DS", "value": "101", "tag2": "", "desc": "Window Center"}, {"tag1": "(0028,1051)", "vr": "DS", "value": "203", "tag2": "", "desc": "Window Width"}, {"tag1": "(0029,0010)", "vr": "LO", "value": "GEMS_IMPS_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0043,0010)", "vr": "LO", "value": "GEMS_PARM_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0043,1039)", "vr": "IS", "value": "1000\\8\\0\\0", "tag2": "", "desc": "?"}, {"tag1": "(0903,0010)", "vr": "LO", "value": "GEIIS PACS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0905,0010)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(7FD1,0010)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}] \ No newline at end of file diff --git a/data/examples/MRI_Head/sub-1/ses-1/dwi/sub-1_ses-1_acq-b1000_dwi.nii.gz b/data/examples/MRI_Head/sub-1/ses-1/dwi/sub-1_ses-1_acq-b1000_dwi.nii.gz new file mode 100644 index 0000000..e9aeedb Binary files /dev/null and b/data/examples/MRI_Head/sub-1/ses-1/dwi/sub-1_ses-1_acq-b1000_dwi.nii.gz differ diff --git a/data/examples/MRI_Head/sub-1/ses-1/dwi/sub-1_ses-1_acq-b3000_dwi.bval b/data/examples/MRI_Head/sub-1/ses-1/dwi/sub-1_ses-1_acq-b3000_dwi.bval new file mode 100644 index 0000000..0d2e681 --- /dev/null +++ b/data/examples/MRI_Head/sub-1/ses-1/dwi/sub-1_ses-1_acq-b3000_dwi.bval @@ -0,0 +1 @@ +3000 0 diff --git a/data/examples/MRI_Head/sub-1/ses-1/dwi/sub-1_ses-1_acq-b3000_dwi.bvec b/data/examples/MRI_Head/sub-1/ses-1/dwi/sub-1_ses-1_acq-b3000_dwi.bvec new file mode 100644 index 0000000..41c02d7 --- /dev/null +++ b/data/examples/MRI_Head/sub-1/ses-1/dwi/sub-1_ses-1_acq-b3000_dwi.bvec @@ -0,0 +1,3 @@ +0 0 +0 0 +0 0 diff --git a/data/examples/MRI_Head/sub-1/ses-1/dwi/sub-1_ses-1_acq-b3000_dwi.json b/data/examples/MRI_Head/sub-1/ses-1/dwi/sub-1_ses-1_acq-b3000_dwi.json new file mode 100644 index 0000000..dfdfcd5 --- /dev/null +++ b/data/examples/MRI_Head/sub-1/ses-1/dwi/sub-1_ses-1_acq-b3000_dwi.json @@ -0,0 +1 @@ +[{"tag1": "(0002,0001)", "vr": "OB", "value": "00\\01", "tag2": "", "desc": "File Meta Information Version"}, {"tag1": "(0002,0002)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "", "desc": "Media Storage SOP Class UID"}, {"tag1": "(0002,0003)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1616754.9228.1430200133.91", "tag2": "", "desc": "Media Storage SOP Instance UID"}, {"tag1": "(0002,0010)", "vr": "UI", "value": "1.2.840.10008.1.2.1", "tag2": "", "desc": "Transfer Syntax UID"}, {"tag1": "(0002,0012)", "vr": "UI", "value": "1.2.40.0.13.1.1", "tag2": "", "desc": "Implementation Class UID"}, {"tag1": "(0002,0013)", "vr": "SH", "value": "dcm4che-2.0", "tag2": "", "desc": "Implementation Version Name"}, {"tag1": "(0002,0016)", "vr": "AE", "value": "CTP", "tag2": "", "desc": "Source Application Entity Title"}, {"tag1": "(0008,0005)", "vr": "CS", "value": "ISO_IR 100", "tag2": "", "desc": "Specific Character Set"}, {"tag1": "(0008,0008)", "vr": "CS", "value": "ORIGINAL\\PRIMARY\\OTHER", "tag2": "", "desc": "Image Type"}, {"tag1": "(0008,0016)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "", "desc": "SOP Class UID"}, {"tag1": "(0008,0018)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1616754.9228.1430200133.91", "tag2": "", "desc": "SOP Instance UID"}, {"tag1": "(0008,0020)", "vr": "DA", "value": "20150428", "tag2": "", "desc": "Study Date"}, {"tag1": "(0008,0021)", "vr": "DA", "value": "20150428", "tag2": "", "desc": "Series Date"}, {"tag1": "(0008,0022)", "vr": "DA", "value": "20150428", "tag2": "", "desc": "Acquisition Date"}, {"tag1": "(0008,0023)", "vr": "DA", "value": "20150428", "tag2": "", "desc": "Content Date"}, {"tag1": "(0008,0030)", "vr": "TM", "value": "090707.000000", "tag2": "", "desc": "Study Time"}, {"tag1": "(0008,0031)", "vr": "TM", "value": "091421.000000", "tag2": "", "desc": "Series Time"}, {"tag1": "(0008,0032)", "vr": "TM", "value": "091421.000000", "tag2": "", "desc": "Acquisition Time"}, {"tag1": "(0008,0033)", "vr": "TM", "value": "091421.000000", "tag2": "", "desc": "Content Time"}, {"tag1": "(0008,0050)", "vr": "SH", "value": "", "tag2": "", "desc": "Accession Number"}, {"tag1": "(0008,0060)", "vr": "CS", "value": "MR", "tag2": "", "desc": "Modality"}, {"tag1": "(0008,0070)", "vr": "LO", "value": "GE MEDICAL SYSTEMS", "tag2": "", "desc": "Manufacturer"}, {"tag1": "(0008,0090)", "vr": "PN", "value": "", "tag2": "", "desc": "Referring Physician’s Name"}, {"tag1": "(0008,1010)", "vr": "SH", "value": "CASTMRI", "tag2": "", "desc": "Station Name"}, {"tag1": "(0008,1030)", "vr": "LO", "value": "RMI_head", "tag2": "", "desc": "Study Description"}, {"tag1": "(0008,1032)", "vr": "SQ", "value": "", "tag2": "(0008,1032)", "desc": "Procedure Code Sequence"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "015031_RM111B", "tag2": "(0008,0100)", "desc": "Code Value"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "GEIIS", "tag2": "(0008,0102)", "desc": "Coding Scheme Designator"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "0", "tag2": "(0008,0103)", "desc": "Coding Scheme Version"}, {"tag1": "(0008,1032)", "vr": "LO", "value": "RM ESPECTROSCOPICA CEREBRAL", "tag2": "(0008,0104)", "desc": "Code Meaning"}, {"tag1": "(0008,103E)", "vr": "LO", "value": "AxDIFb3000", "tag2": "", "desc": "Series Description"}, {"tag1": "(0008,1090)", "vr": "LO", "value": "SIGNA EXCITE", "tag2": "", "desc": "Manufacturer’s Model Name"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1616754.9228.1430200132.795", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1616754.9228.1430200132.798", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0009,0010)", "vr": "LO", "value": "GEMS_IDEN_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0009,0011)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0010,0010)", "vr": "PN", "value": "304229696761426913368206915776875392104", "tag2": "", "desc": "Patient’s Name"}, {"tag1": "(0010,0020)", "vr": "LO", "value": "239996943502289713192853049918686757778", "tag2": "", "desc": "Patient ID"}, {"tag1": "(0010,0030)", "vr": "DA", "value": "19240302", "tag2": "", "desc": "Patient’s Birth Date"}, {"tag1": "(0010,0040)", "vr": "CS", "value": "F", "tag2": "", "desc": "Patient’s Sex"}, {"tag1": "(0010,1010)", "vr": "AS", "value": "091Y", "tag2": "", "desc": "Patient’s Age"}, {"tag1": "(0010,1030)", "vr": "DS", "value": "41", "tag2": "", "desc": "Patient’s Weight"}, {"tag1": "(0011,0010)", "vr": "LO", "value": "GEMS_PATI_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0018,0020)", "vr": "CS", "value": "EP\\SE", "tag2": "", "desc": "Scanning Sequence"}, {"tag1": "(0018,0021)", "vr": "CS", "value": "NONE", "tag2": "", "desc": "Sequence Variant"}, {"tag1": "(0018,0022)", "vr": "CS", "value": "VB_GEMS\\EPI_GEMS\\PFF", "tag2": "", "desc": "Scan Options"}, {"tag1": "(0018,0023)", "vr": "CS", "value": "2D", "tag2": "", "desc": "MR Acquisition Type"}, {"tag1": "(0018,0025)", "vr": "CS", "value": "N", "tag2": "", "desc": "Angio Flag"}, {"tag1": "(0018,0050)", "vr": "DS", "value": "5", "tag2": "", "desc": "Slice Thickness"}, {"tag1": "(0018,0080)", "vr": "DS", "value": "9000", "tag2": "", "desc": "Repetition Time"}, {"tag1": "(0018,0081)", "vr": "DS", "value": "101.8", "tag2": "", "desc": "Echo Time"}, {"tag1": "(0018,0082)", "vr": "DS", "value": "0", "tag2": "", "desc": "Inversion Time"}, {"tag1": "(0018,0083)", "vr": "DS", "value": "4", "tag2": "", "desc": "Number of Averages"}, {"tag1": "(0018,0084)", "vr": "DS", "value": "63.868212", "tag2": "", "desc": "Imaging Frequency"}, {"tag1": "(0018,0085)", "vr": "SH", "value": "1H", "tag2": "", "desc": "Imaged Nucleus"}, {"tag1": "(0018,0086)", "vr": "IS", "value": "1", "tag2": "", "desc": "Echo Number(s)"}, {"tag1": "(0018,0087)", "vr": "DS", "value": "1.5", "tag2": "", "desc": "Magnetic Field Strength"}, {"tag1": "(0018,0088)", "vr": "DS", "value": "6", "tag2": "", "desc": "Spacing Between Slices"}, {"tag1": "(0018,0091)", "vr": "IS", "value": "1", "tag2": "", "desc": "Echo Train Length"}, {"tag1": "(0018,0093)", "vr": "DS", "value": "100", "tag2": "", "desc": "Percent Sampling"}, {"tag1": "(0018,0094)", "vr": "DS", "value": "100", "tag2": "", "desc": "Percent Phase Field of View"}, {"tag1": "(0018,0095)", "vr": "DS", "value": "1953.12", "tag2": "", "desc": "Pixel Bandwidth"}, {"tag1": "(0018,1000)", "vr": "LO", "value": "00000000NPV24200", "tag2": "", "desc": "Device Serial Number"}, {"tag1": "(0018,1020)", "vr": "LO", "value": "11\\LX\\MR Software release:11.1_M4_0818.a", "tag2": "", "desc": "Software Version(s)"}, {"tag1": "(0018,1030)", "vr": "LO", "value": "4436599", "tag2": "", "desc": "Protocol Name"}, {"tag1": "(0018,1088)", "vr": "IS", "value": "0", "tag2": "", "desc": "Heart Rate"}, {"tag1": "(0018,1090)", "vr": "IS", "value": "0", "tag2": "", "desc": "Cardiac Number of Images"}, {"tag1": "(0018,1094)", "vr": "IS", "value": "0", "tag2": "", "desc": "Trigger Window"}, {"tag1": "(0018,1100)", "vr": "DS", "value": "240", "tag2": "", "desc": "Reconstruction Diameter"}, {"tag1": "(0018,1250)", "vr": "SH", "value": "8HRBRAIN", "tag2": "", "desc": "Receive Coil Name"}, {"tag1": "(0018,1310)", "vr": "US", "value": "128\\0\\0\\128", "tag2": "", "desc": "Acquisition Matrix"}, {"tag1": "(0018,1312)", "vr": "CS", "value": "COL", "tag2": "", "desc": "In-plane Phase Encoding Direction"}, {"tag1": "(0018,1314)", "vr": "DS", "value": "90", "tag2": "", "desc": "Flip Angle"}, {"tag1": "(0018,1315)", "vr": "CS", "value": "N", "tag2": "", "desc": "Variable Flip Angle Flag"}, {"tag1": "(0018,1316)", "vr": "DS", "value": "0.058301", "tag2": "", "desc": "SAR"}, {"tag1": "(0018,5100)", "vr": "CS", "value": "HFS", "tag2": "", "desc": "Patient Position"}, {"tag1": "(0019,0010)", "vr": "LO", "value": "GEMS_ACQU_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0019,10BB)", "vr": "DS", "value": "0", "tag2": "", "desc": "?"}, {"tag1": "(0019,10BC)", "vr": "DS", "value": "0", "tag2": "", "desc": "?"}, {"tag1": "(0019,10BD)", "vr": "DS", "value": "0", "tag2": "", "desc": "?"}, {"tag1": "(0019,10D9)", "vr": "DS", "value": "0", "tag2": "", "desc": "?"}, {"tag1": "(0019,10DF)", "vr": "DS", "value": "0", "tag2": "", "desc": "?"}, {"tag1": "(0019,10E0)", "vr": "DS", "value": "0", "tag2": "", "desc": "?"}, {"tag1": "(0020,000D)", "vr": "UI", "value": "1.2.124.113532.10.192.138.26.20150427.140750.4893596", "tag2": "", "desc": "Study Instance UID"}, {"tag1": "(0020,000E)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1616754.9228.1430200132.980", "tag2": "", "desc": "Series Instance UID"}, {"tag1": "(0020,0010)", "vr": "SH", "value": "", "tag2": "", "desc": "Study ID"}, {"tag1": "(0020,0011)", "vr": "IS", "value": "4", "tag2": "", "desc": "Series Number"}, {"tag1": "(0020,0012)", "vr": "IS", "value": "1", "tag2": "", "desc": "Acquisition Number"}, {"tag1": "(0020,0013)", "vr": "IS", "value": "46", "tag2": "", "desc": "Instance Number"}, {"tag1": "(0020,0032)", "vr": "DS", "value": "-121.873\\-135.165\\62", "tag2": "", "desc": "Image Position (Patient)"}, {"tag1": "(0020,0037)", "vr": "DS", "value": "1\\0\\0\\0\\1\\0", "tag2": "", "desc": "Image Orientation (Patient)"}, {"tag1": "(0020,0052)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1616754.9298.1430199842.154", "tag2": "", "desc": "Frame of Reference UID"}, {"tag1": "(0020,0110)", "vr": "DS", "value": "0", "tag2": "", "desc": "Temporal Resolution"}, {"tag1": "(0020,1040)", "vr": "LO", "value": "", "tag2": "", "desc": "Position Reference Indicator"}, {"tag1": "(0020,1041)", "vr": "DS", "value": "62", "tag2": "", "desc": "Slice Location"}, {"tag1": "(0021,0010)", "vr": "LO", "value": "GEMS_RELA_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0021,105A)", "vr": "SL", "value": "7", "tag2": "", "desc": "?"}, {"tag1": "(0023,0010)", "vr": "LO", "value": "GEMS_STDY_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0025,0010)", "vr": "LO", "value": "GEMS_SERS_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0027,0010)", "vr": "LO", "value": "GEMS_IMAG_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0028,0002)", "vr": "US", "value": "1", "tag2": "", "desc": "Samples per Pixel"}, {"tag1": "(0028,0004)", "vr": "CS", "value": "MONOCHROME2", "tag2": "", "desc": "Photometric Interpretation"}, {"tag1": "(0028,0010)", "vr": "US", "value": "256", "tag2": "", "desc": "Rows"}, {"tag1": "(0028,0011)", "vr": "US", "value": "256", "tag2": "", "desc": "Columns"}, {"tag1": "(0028,0030)", "vr": "DS", "value": "0.9375\\0.9375", "tag2": "", "desc": "Pixel Spacing"}, {"tag1": "(0028,0100)", "vr": "US", "value": "16", "tag2": "", "desc": "Bits Allocated"}, {"tag1": "(0028,0101)", "vr": "US", "value": "16", "tag2": "", "desc": "Bits Stored"}, {"tag1": "(0028,0102)", "vr": "US", "value": "15", "tag2": "", "desc": "High Bit"}, {"tag1": "(0028,0103)", "vr": "US", "value": "1", "tag2": "", "desc": "Pixel Representation"}, {"tag1": "(0028,0303)", "vr": "CS", "value": "", "tag2": "", "desc": "Longitudinal Temporal Information Modified"}, {"tag1": "(0028,1050)", "vr": "DS", "value": "605", "tag2": "", "desc": "Window Center"}, {"tag1": "(0028,1051)", "vr": "DS", "value": "1210", "tag2": "", "desc": "Window Width"}, {"tag1": "(0029,0010)", "vr": "LO", "value": "GEMS_IMPS_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0043,0010)", "vr": "LO", "value": "GEMS_PARM_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0043,1039)", "vr": "IS", "value": "0\\8\\0\\0", "tag2": "", "desc": "?"}, {"tag1": "(0903,0010)", "vr": "LO", "value": "GEIIS PACS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0905,0010)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(7FD1,0010)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}] \ No newline at end of file diff --git a/data/examples/MRI_Head/sub-1/ses-1/dwi/sub-1_ses-1_acq-b3000_dwi.nii.gz b/data/examples/MRI_Head/sub-1/ses-1/dwi/sub-1_ses-1_acq-b3000_dwi.nii.gz new file mode 100644 index 0000000..ed7dedc Binary files /dev/null and b/data/examples/MRI_Head/sub-1/ses-1/dwi/sub-1_ses-1_acq-b3000_dwi.nii.gz differ diff --git a/data/examples/MRI_Head/sub-1/ses-1/sub-1_ses-1_scans.tsv b/data/examples/MRI_Head/sub-1/ses-1/sub-1_ses-1_scans.tsv new file mode 100644 index 0000000..5be71f1 --- /dev/null +++ b/data/examples/MRI_Head/sub-1/ses-1/sub-1_ses-1_scans.tsv @@ -0,0 +1,4 @@ +filename Manufacturer (0008,0070) Series Description (0008,103E) Manufacturer’s Model Name (0008,1090) Patient ID (0010,0020) Patient’s Sex (0010,0040) Patient’s Age (0010,1010) Patient’s Weight (0010,1030) Scanning Sequence (0018,0020) Sequence Variant (0018,0021) Scan Options (0018,0022) MR Acquisition Type (0018,0023) Slice Thickness (0018,0050) Repetition Time (0018,0080) Echo Time (0018,0081) Inversion Time (0018,0082) Imaging Frequency (0018,0084) Magnetic Field Strength (0018,0087) Manufacturer’s Model Name (0008,1090) Spacing Between Slices (0018,0088) Echo Train Length (0018,0091) Percent Sampling (0018,0093) Pixel Bandwidth (0018,0095) Flip Angle (0018,1314) Patient Position (0018,5100) Image Position (Patient) (0020,0032) Image Orientation (Patient) (0020,0037) Position Reference Indicator (0020,1040) Slice Location (0020,1041) Rows (0028,0010) Columns (0028,0011) Pixel Spacing (0028,0030) Bits Allocated (0028,0100) Number of Averages (0018,0083) Echo Number(s) (0018,0086) (0018,9461) +anat/sub-1_ses-1_T1w.nii.gz GE MEDICAL SYSTEMS AXIALT1 SIGNA EXCITE 239996943502289713192853049918686757778 F 091Y 41 SE n/a VB_GEMS\EDR_GEMS\FILTERED_GEMS 2D 5 480 12 0 63.868208 1.5 SIGNA EXCITE 6 1 100 81.3672 90 HFS -122.107\-135.4\50 1\0\0\0\1\0 n/a 50 512 512 0.46875\0.46875 16 1 1 n/a +dwi/sub-1_ses-1_acq-b3000_dwi.nii.gz GE MEDICAL SYSTEMS DIFUSIONB1000 SIGNA EXCITE 239996943502289713192853049918686757778 F 091Y 41 EP\SE n/a VB_GEMS\EPI_GEMS\PFF 2D 5 8100 78.2 0 63.868212 1.5 SIGNA EXCITE 6 1 100 1953.12 90 HFS -121.873\-135.165\56 1\0\0\0\1\0 n/a 56 256 256 0.9375\0.9375 16 1 1 n/a +dwi/sub-1_ses-1_acq-b1000_dwi.nii.gz GE MEDICAL SYSTEMS AxDIFb3000 SIGNA EXCITE 239996943502289713192853049918686757778 F 091Y 41 EP\SE n/a VB_GEMS\EPI_GEMS\PFF 2D 5 9000 101.8 0 63.868212 1.5 SIGNA EXCITE 6 1 100 1953.12 90 HFS -121.873\-135.165\62 1\0\0\0\1\0 n/a 62 256 256 0.9375\0.9375 16 4 1 n/a diff --git a/data/examples/MRI_Head/sub-2/ses-1/anat/sub-2_ses-1_run-1_T1w.json b/data/examples/MRI_Head/sub-2/ses-1/anat/sub-2_ses-1_run-1_T1w.json new file mode 100644 index 0000000..59eae03 --- /dev/null +++ b/data/examples/MRI_Head/sub-2/ses-1/anat/sub-2_ses-1_run-1_T1w.json @@ -0,0 +1 @@ +[{"tag1": "(0002,0001)", "vr": "OB", "value": "00\\01", "tag2": "", "desc": "File Meta Information Version"}, {"tag1": "(0002,0002)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "", "desc": "Media Storage SOP Class UID"}, {"tag1": "(0002,0003)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9529.1353572443.598", "tag2": "", "desc": "Media Storage SOP Instance UID"}, {"tag1": "(0002,0010)", "vr": "UI", "value": "1.2.840.10008.1.2.1", "tag2": "", "desc": "Transfer Syntax UID"}, {"tag1": "(0002,0012)", "vr": "UI", "value": "1.2.40.0.13.1.1", "tag2": "", "desc": "Implementation Class UID"}, {"tag1": "(0002,0013)", "vr": "SH", "value": "dcm4che-2.0", "tag2": "", "desc": "Implementation Version Name"}, {"tag1": "(0002,0016)", "vr": "AE", "value": "CTP", "tag2": "", "desc": "Source Application Entity Title"}, {"tag1": "(0008,0005)", "vr": "CS", "value": "ISO_IR 100", "tag2": "", "desc": "Specific Character Set"}, {"tag1": "(0008,0008)", "vr": "CS", "value": "ORIGINAL\\PRIMARY\\OTHER", "tag2": "", "desc": "Image Type"}, {"tag1": "(0008,0016)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "", "desc": "SOP Class UID"}, {"tag1": "(0008,0018)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9529.1353572443.598", "tag2": "", "desc": "SOP Instance UID"}, {"tag1": "(0008,0020)", "vr": "DA", "value": "20121122", "tag2": "", "desc": "Study Date"}, {"tag1": "(0008,0021)", "vr": "DA", "value": "20121122", "tag2": "", "desc": "Series Date"}, {"tag1": "(0008,0022)", "vr": "DA", "value": "20121122", "tag2": "", "desc": "Acquisition Date"}, {"tag1": "(0008,0023)", "vr": "DA", "value": "20121122", "tag2": "", "desc": "Content Date"}, {"tag1": "(0008,0030)", "vr": "TM", "value": "195032.000000", "tag2": "", "desc": "Study Time"}, {"tag1": "(0008,0031)", "vr": "TM", "value": "200539", "tag2": "", "desc": "Series Time"}, {"tag1": "(0008,0032)", "vr": "TM", "value": "200539", "tag2": "", "desc": "Acquisition Time"}, {"tag1": "(0008,0033)", "vr": "TM", "value": "200539", "tag2": "", "desc": "Content Time"}, {"tag1": "(0008,0050)", "vr": "SH", "value": "", "tag2": "", "desc": "Accession Number"}, {"tag1": "(0008,0060)", "vr": "CS", "value": "MR", "tag2": "", "desc": "Modality"}, {"tag1": "(0008,0070)", "vr": "LO", "value": "GE MEDICAL SYSTEMS", "tag2": "", "desc": "Manufacturer"}, {"tag1": "(0008,0090)", "vr": "PN", "value": "", "tag2": "", "desc": "Referring Physician’s Name"}, {"tag1": "(0008,1010)", "vr": "SH", "value": "I3-PIM02", "tag2": "", "desc": "Station Name"}, {"tag1": "(0008,1030)", "vr": "LO", "value": "MRI_Head", "tag2": "", "desc": "Study Description"}, {"tag1": "(0008,1032)", "vr": "SQ", "value": "", "tag2": "(0008,1032)", "desc": "Procedure Code Sequence"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "012071_30411", "tag2": "(0008,0100)", "desc": "Code Value"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "GEIIS", "tag2": "(0008,0102)", "desc": "Coding Scheme Designator"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "0", "tag2": "(0008,0103)", "desc": "Coding Scheme Version"}, {"tag1": "(0008,1032)", "vr": "LO", "value": "RM CRANEAL", "tag2": "(0008,0104)", "desc": "Code Meaning"}, {"tag1": "(0008,103E)", "vr": "LO", "value": "AXT1SE", "tag2": "", "desc": "Series Description"}, {"tag1": "(0008,1090)", "vr": "LO", "value": "SIGNA EXCITE", "tag2": "", "desc": "Manufacturer’s Model Name"}, {"tag1": "(0008,1110)", "vr": "SQ", "value": "", "tag2": "(0008,1110)", "desc": "Referenced Study Sequence"}, {"tag1": "(0008,1110)", "vr": "UI", "value": "1.2.840.10008.3.1.2.3.1", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1110)", "vr": "UI", "value": "1.2.124.113532.80.22179.580.20121122.72334.20932853", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1111)", "vr": "SQ", "value": "", "tag2": "(0008,1111)", "desc": "Referenced Performed Procedure Step Sequence"}, {"tag1": "(0008,1111)", "vr": "UI", "value": "1.2.840.10008.3.1.2.3.3", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1111)", "vr": "UI", "value": "1.2.40.0.13.1.1.172.18.97.166.20121122070006446.32927", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9529.1353572442.912", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9529.1353572442.913", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0009,0010)", "vr": "LO", "value": "GEMS_IDEN_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0009,0011)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0010,0010)", "vr": "PN", "value": "206420261264115296606936483329680842341", "tag2": "", "desc": "Patient’s Name"}, {"tag1": "(0010,0020)", "vr": "LO", "value": "309742868506857266318767310985292225200", "tag2": "", "desc": "Patient ID"}, {"tag1": "(0010,0030)", "vr": "DA", "value": "19360612", "tag2": "", "desc": "Patient’s Birth Date"}, {"tag1": "(0010,0040)", "vr": "CS", "value": "M", "tag2": "", "desc": "Patient’s Sex"}, {"tag1": "(0010,1010)", "vr": "AS", "value": "076Y", "tag2": "", "desc": "Patient’s Age"}, {"tag1": "(0010,1030)", "vr": "DS", "value": "68", "tag2": "", "desc": "Patient’s Weight"}, {"tag1": "(0010,21B0)", "vr": "LT", "value": "", "tag2": "", "desc": "Additional Patient History"}, {"tag1": "(0011,0010)", "vr": "LO", "value": "GEMS_PATI_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0018,0020)", "vr": "CS", "value": "SE", "tag2": "", "desc": "Scanning Sequence"}, {"tag1": "(0018,0021)", "vr": "CS", "value": "NONE", "tag2": "", "desc": "Sequence Variant"}, {"tag1": "(0018,0022)", "vr": "CS", "value": "VB_GEMS\\FILTERED_GEMS", "tag2": "", "desc": "Scan Options"}, {"tag1": "(0018,0023)", "vr": "CS", "value": "2D", "tag2": "", "desc": "MR Acquisition Type"}, {"tag1": "(0018,0025)", "vr": "CS", "value": "N", "tag2": "", "desc": "Angio Flag"}, {"tag1": "(0018,0050)", "vr": "DS", "value": "4.5", "tag2": "", "desc": "Slice Thickness"}, {"tag1": "(0018,0080)", "vr": "DS", "value": "560", "tag2": "", "desc": "Repetition Time"}, {"tag1": "(0018,0081)", "vr": "DS", "value": "14", "tag2": "", "desc": "Echo Time"}, {"tag1": "(0018,0082)", "vr": "DS", "value": "0", "tag2": "", "desc": "Inversion Time"}, {"tag1": "(0018,0083)", "vr": "DS", "value": "1", "tag2": "", "desc": "Number of Averages"}, {"tag1": "(0018,0084)", "vr": "DS", "value": "63.858879", "tag2": "", "desc": "Imaging Frequency"}, {"tag1": "(0018,0085)", "vr": "SH", "value": "1H", "tag2": "", "desc": "Imaged Nucleus"}, {"tag1": "(0018,0086)", "vr": "IS", "value": "1", "tag2": "", "desc": "Echo Number(s)"}, {"tag1": "(0018,0087)", "vr": "DS", "value": "1.5", "tag2": "", "desc": "Magnetic Field Strength"}, {"tag1": "(0018,0088)", "vr": "DS", "value": "5.5", "tag2": "", "desc": "Spacing Between Slices"}, {"tag1": "(0018,0091)", "vr": "IS", "value": "1", "tag2": "", "desc": "Echo Train Length"}, {"tag1": "(0018,0093)", "vr": "DS", "value": "100", "tag2": "", "desc": "Percent Sampling"}, {"tag1": "(0018,0094)", "vr": "DS", "value": "100", "tag2": "", "desc": "Percent Phase Field of View"}, {"tag1": "(0018,0095)", "vr": "DS", "value": "75.1172", "tag2": "", "desc": "Pixel Bandwidth"}, {"tag1": "(0018,1000)", "vr": "LO", "value": "00000000NPV24000", "tag2": "", "desc": "Device Serial Number"}, {"tag1": "(0018,1020)", "vr": "LO", "value": "11\\LX\\MR Software release:11.1_M4_0818.a", "tag2": "", "desc": "Software Version(s)"}, {"tag1": "(0018,1030)", "vr": "LO", "value": "CEREBRLAPURE", "tag2": "", "desc": "Protocol Name"}, {"tag1": "(0018,1088)", "vr": "IS", "value": "0", "tag2": "", "desc": "Heart Rate"}, {"tag1": "(0018,1090)", "vr": "IS", "value": "0", "tag2": "", "desc": "Cardiac Number of Images"}, {"tag1": "(0018,1094)", "vr": "IS", "value": "0", "tag2": "", "desc": "Trigger Window"}, {"tag1": "(0018,1100)", "vr": "DS", "value": "240", "tag2": "", "desc": "Reconstruction Diameter"}, {"tag1": "(0018,1250)", "vr": "SH", "value": "8NVHEAD_A", "tag2": "", "desc": "Receive Coil Name"}, {"tag1": "(0018,1310)", "vr": "US", "value": "0\\320\\224\\0", "tag2": "", "desc": "Acquisition Matrix"}, {"tag1": "(0018,1312)", "vr": "CS", "value": "ROW", "tag2": "", "desc": "In-plane Phase Encoding Direction"}, {"tag1": "(0018,1314)", "vr": "DS", "value": "90", "tag2": "", "desc": "Flip Angle"}, {"tag1": "(0018,1315)", "vr": "CS", "value": "N", "tag2": "", "desc": "Variable Flip Angle Flag"}, {"tag1": "(0018,1316)", "vr": "DS", "value": "1.275538", "tag2": "", "desc": "SAR"}, {"tag1": "(0018,5100)", "vr": "CS", "value": "HFS", "tag2": "", "desc": "Patient Position"}, {"tag1": "(0019,0010)", "vr": "LO", "value": "GEMS_ACQU_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0019,10BB)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10BC)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10BD)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10D9)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10DF)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10E0)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0020,000D)", "vr": "UI", "value": "1.2.124.113532.172.18.96.237.20121122.71447.1841208", "tag2": "", "desc": "Study Instance UID"}, {"tag1": "(0020,000E)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9529.1353572443.519", "tag2": "", "desc": "Series Instance UID"}, {"tag1": "(0020,0010)", "vr": "SH", "value": "", "tag2": "", "desc": "Study ID"}, {"tag1": "(0020,0011)", "vr": "IS", "value": "8", "tag2": "", "desc": "Series Number"}, {"tag1": "(0020,0012)", "vr": "IS", "value": "1", "tag2": "", "desc": "Acquisition Number"}, {"tag1": "(0020,0013)", "vr": "IS", "value": "14", "tag2": "", "desc": "Instance Number"}, {"tag1": "(0020,0032)", "vr": "DS", "value": "-118.251\\-128.961\\22.3567", "tag2": "", "desc": "Image Position (Patient)"}, {"tag1": "(0020,0037)", "vr": "DS", "value": "0.999808\\-0\\0.0195927\\0.000976557\\0.998774\\-0.0495007", "tag2": "", "desc": "Image Orientation (Patient)"}, {"tag1": "(0020,0052)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9591.1353572129.48", "tag2": "", "desc": "Frame of Reference UID"}, {"tag1": "(0020,0060)", "vr": "CS", "value": "", "tag2": "", "desc": "Laterality"}, {"tag1": "(0020,0110)", "vr": "DS", "value": "0", "tag2": "", "desc": "Temporal Resolution"}, {"tag1": "(0020,1040)", "vr": "LO", "value": "", "tag2": "", "desc": "Position Reference Indicator"}, {"tag1": "(0020,1041)", "vr": "DS", "value": "18.77477646", "tag2": "", "desc": "Slice Location"}, {"tag1": "(0021,0010)", "vr": "LO", "value": "GEMS_RELA_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0021,105A)", "vr": "UN", "value": "\\00\\00\\00\\00", "tag2": "", "desc": "?"}, {"tag1": "(0023,0010)", "vr": "LO", "value": "GEMS_STDY_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0025,0010)", "vr": "LO", "value": "GEMS_SERS_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0027,0010)", "vr": "LO", "value": "GEMS_IMAG_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0028,0002)", "vr": "US", "value": "1", "tag2": "", "desc": "Samples per Pixel"}, {"tag1": "(0028,0004)", "vr": "CS", "value": "MONOCHROME2", "tag2": "", "desc": "Photometric Interpretation"}, {"tag1": "(0028,0010)", "vr": "US", "value": "512", "tag2": "", "desc": "Rows"}, {"tag1": "(0028,0011)", "vr": "US", "value": "512", "tag2": "", "desc": "Columns"}, {"tag1": "(0028,0030)", "vr": "DS", "value": "0.468753\\0.468754", "tag2": "", "desc": "Pixel Spacing"}, {"tag1": "(0028,0100)", "vr": "US", "value": "16", "tag2": "", "desc": "Bits Allocated"}, {"tag1": "(0028,0101)", "vr": "US", "value": "16", "tag2": "", "desc": "Bits Stored"}, {"tag1": "(0028,0102)", "vr": "US", "value": "15", "tag2": "", "desc": "High Bit"}, {"tag1": "(0028,0103)", "vr": "US", "value": "1", "tag2": "", "desc": "Pixel Representation"}, {"tag1": "(0028,0120)", "vr": "SS", "value": "0", "tag2": "", "desc": "Pixel Padding Value"}, {"tag1": "(0028,0303)", "vr": "CS", "value": "", "tag2": "", "desc": "Longitudinal Temporal Information Modified"}, {"tag1": "(0028,1050)", "vr": "DS", "value": "1182", "tag2": "", "desc": "Window Center"}, {"tag1": "(0028,1051)", "vr": "DS", "value": "2364", "tag2": "", "desc": "Window Width"}, {"tag1": "(0029,0010)", "vr": "LO", "value": "GEMS_IMPS_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0032,000A)", "vr": "CS", "value": "READ", "tag2": "", "desc": "Study Status ID"}, {"tag1": "(0040,0241)", "vr": "AE", "value": "I3-PIM02", "tag2": "", "desc": "Performed Station AE Title"}, {"tag1": "(0040,0244)", "vr": "DA", "value": "20121122", "tag2": "", "desc": "Performed Procedure Step Start Date"}, {"tag1": "(0040,0245)", "vr": "TM", "value": "195032.000", "tag2": "", "desc": "Performed Procedure Step Start Time"}, {"tag1": "(0040,0254)", "vr": "LO", "value": "", "tag2": "", "desc": "Performed Procedure Step Description"}, {"tag1": "(0043,0010)", "vr": "LO", "value": "GEMS_PARM_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0043,1039)", "vr": "UN", "value": "0\\\\0\\\\0\\\\0 ", "tag2": "", "desc": "?"}, {"tag1": "(0903,0010)", "vr": "LO", "value": "GEIIS PACS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0905,0010)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(7FD1,0010)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}] \ No newline at end of file diff --git a/data/examples/MRI_Head/sub-2/ses-1/anat/sub-2_ses-1_run-1_T1w.nii.gz b/data/examples/MRI_Head/sub-2/ses-1/anat/sub-2_ses-1_run-1_T1w.nii.gz new file mode 100644 index 0000000..25ed4e9 Binary files /dev/null and b/data/examples/MRI_Head/sub-2/ses-1/anat/sub-2_ses-1_run-1_T1w.nii.gz differ diff --git a/data/examples/MRI_Head/sub-2/ses-1/anat/sub-2_ses-1_run-2_T1w.json b/data/examples/MRI_Head/sub-2/ses-1/anat/sub-2_ses-1_run-2_T1w.json new file mode 100644 index 0000000..97efe38 --- /dev/null +++ b/data/examples/MRI_Head/sub-2/ses-1/anat/sub-2_ses-1_run-2_T1w.json @@ -0,0 +1 @@ +[{"tag1": "(0002,0001)", "vr": "OB", "value": "00\\01", "tag2": "", "desc": "File Meta Information Version"}, {"tag1": "(0002,0002)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "", "desc": "Media Storage SOP Class UID"}, {"tag1": "(0002,0003)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9529.1353572443.497", "tag2": "", "desc": "Media Storage SOP Instance UID"}, {"tag1": "(0002,0010)", "vr": "UI", "value": "1.2.840.10008.1.2.1", "tag2": "", "desc": "Transfer Syntax UID"}, {"tag1": "(0002,0012)", "vr": "UI", "value": "1.2.40.0.13.1.1", "tag2": "", "desc": "Implementation Class UID"}, {"tag1": "(0002,0013)", "vr": "SH", "value": "dcm4che-2.0", "tag2": "", "desc": "Implementation Version Name"}, {"tag1": "(0002,0016)", "vr": "AE", "value": "CTP", "tag2": "", "desc": "Source Application Entity Title"}, {"tag1": "(0008,0005)", "vr": "CS", "value": "ISO_IR 100", "tag2": "", "desc": "Specific Character Set"}, {"tag1": "(0008,0008)", "vr": "CS", "value": "ORIGINAL\\PRIMARY\\OTHER", "tag2": "", "desc": "Image Type"}, {"tag1": "(0008,0016)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "", "desc": "SOP Class UID"}, {"tag1": "(0008,0018)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9529.1353572443.497", "tag2": "", "desc": "SOP Instance UID"}, {"tag1": "(0008,0020)", "vr": "DA", "value": "20121122", "tag2": "", "desc": "Study Date"}, {"tag1": "(0008,0021)", "vr": "DA", "value": "20121122", "tag2": "", "desc": "Series Date"}, {"tag1": "(0008,0022)", "vr": "DA", "value": "20121122", "tag2": "", "desc": "Acquisition Date"}, {"tag1": "(0008,0023)", "vr": "DA", "value": "20121122", "tag2": "", "desc": "Content Date"}, {"tag1": "(0008,0030)", "vr": "TM", "value": "195032.000000", "tag2": "", "desc": "Study Time"}, {"tag1": "(0008,0031)", "vr": "TM", "value": "200216", "tag2": "", "desc": "Series Time"}, {"tag1": "(0008,0032)", "vr": "TM", "value": "200216", "tag2": "", "desc": "Acquisition Time"}, {"tag1": "(0008,0033)", "vr": "TM", "value": "200216", "tag2": "", "desc": "Content Time"}, {"tag1": "(0008,0050)", "vr": "SH", "value": "", "tag2": "", "desc": "Accession Number"}, {"tag1": "(0008,0060)", "vr": "CS", "value": "MR", "tag2": "", "desc": "Modality"}, {"tag1": "(0008,0070)", "vr": "LO", "value": "GE MEDICAL SYSTEMS", "tag2": "", "desc": "Manufacturer"}, {"tag1": "(0008,0090)", "vr": "PN", "value": "", "tag2": "", "desc": "Referring Physician’s Name"}, {"tag1": "(0008,1010)", "vr": "SH", "value": "I3-PIM02", "tag2": "", "desc": "Station Name"}, {"tag1": "(0008,1030)", "vr": "LO", "value": "MRI_Head", "tag2": "", "desc": "Study Description"}, {"tag1": "(0008,1032)", "vr": "SQ", "value": "", "tag2": "(0008,1032)", "desc": "Procedure Code Sequence"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "012071_30411", "tag2": "(0008,0100)", "desc": "Code Value"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "GEIIS", "tag2": "(0008,0102)", "desc": "Coding Scheme Designator"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "0", "tag2": "(0008,0103)", "desc": "Coding Scheme Version"}, {"tag1": "(0008,1032)", "vr": "LO", "value": "RM CRANEAL", "tag2": "(0008,0104)", "desc": "Code Meaning"}, {"tag1": "(0008,103E)", "vr": "LO", "value": "CorT1FIR", "tag2": "", "desc": "Series Description"}, {"tag1": "(0008,1090)", "vr": "LO", "value": "SIGNA EXCITE", "tag2": "", "desc": "Manufacturer’s Model Name"}, {"tag1": "(0008,1110)", "vr": "SQ", "value": "", "tag2": "(0008,1110)", "desc": "Referenced Study Sequence"}, {"tag1": "(0008,1110)", "vr": "UI", "value": "1.2.840.10008.3.1.2.3.1", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1110)", "vr": "UI", "value": "1.2.124.113532.80.22179.580.20121122.72334.20932853", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1111)", "vr": "SQ", "value": "", "tag2": "(0008,1111)", "desc": "Referenced Performed Procedure Step Sequence"}, {"tag1": "(0008,1111)", "vr": "UI", "value": "1.2.840.10008.3.1.2.3.3", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1111)", "vr": "UI", "value": "1.2.40.0.13.1.1.172.18.97.166.20121122070006446.32927", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9529.1353572442.912", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9529.1353572442.911", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0009,0010)", "vr": "LO", "value": "GEMS_IDEN_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0009,0011)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0010,0010)", "vr": "PN", "value": "206420261264115296606936483329680842341", "tag2": "", "desc": "Patient’s Name"}, {"tag1": "(0010,0020)", "vr": "LO", "value": "309742868506857266318767310985292225200", "tag2": "", "desc": "Patient ID"}, {"tag1": "(0010,0030)", "vr": "DA", "value": "19360612", "tag2": "", "desc": "Patient’s Birth Date"}, {"tag1": "(0010,0040)", "vr": "CS", "value": "M", "tag2": "", "desc": "Patient’s Sex"}, {"tag1": "(0010,1010)", "vr": "AS", "value": "076Y", "tag2": "", "desc": "Patient’s Age"}, {"tag1": "(0010,1030)", "vr": "DS", "value": "68", "tag2": "", "desc": "Patient’s Weight"}, {"tag1": "(0010,21B0)", "vr": "LT", "value": "", "tag2": "", "desc": "Additional Patient History"}, {"tag1": "(0011,0010)", "vr": "LO", "value": "GEMS_PATI_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0018,0020)", "vr": "CS", "value": "IR", "tag2": "", "desc": "Scanning Sequence"}, {"tag1": "(0018,0021)", "vr": "CS", "value": "NONE", "tag2": "", "desc": "Sequence Variant"}, {"tag1": "(0018,0022)", "vr": "CS", "value": "VB_GEMS\\SEQ_GEMS\\TRF_GEMS\\FILTERED_GEMS", "tag2": "", "desc": "Scan Options"}, {"tag1": "(0018,0023)", "vr": "CS", "value": "2D", "tag2": "", "desc": "MR Acquisition Type"}, {"tag1": "(0018,0025)", "vr": "CS", "value": "N", "tag2": "", "desc": "Angio Flag"}, {"tag1": "(0018,0050)", "vr": "DS", "value": "5", "tag2": "", "desc": "Slice Thickness"}, {"tag1": "(0018,0080)", "vr": "DS", "value": "2537.07", "tag2": "", "desc": "Repetition Time"}, {"tag1": "(0018,0081)", "vr": "DS", "value": "28.56", "tag2": "", "desc": "Echo Time"}, {"tag1": "(0018,0082)", "vr": "DS", "value": "750", "tag2": "", "desc": "Inversion Time"}, {"tag1": "(0018,0083)", "vr": "DS", "value": "2", "tag2": "", "desc": "Number of Averages"}, {"tag1": "(0018,0084)", "vr": "DS", "value": "63.858867", "tag2": "", "desc": "Imaging Frequency"}, {"tag1": "(0018,0085)", "vr": "SH", "value": "1H", "tag2": "", "desc": "Imaged Nucleus"}, {"tag1": "(0018,0086)", "vr": "IS", "value": "1", "tag2": "", "desc": "Echo Number(s)"}, {"tag1": "(0018,0087)", "vr": "DS", "value": "1.5", "tag2": "", "desc": "Magnetic Field Strength"}, {"tag1": "(0018,0088)", "vr": "DS", "value": "6.5", "tag2": "", "desc": "Spacing Between Slices"}, {"tag1": "(0018,0091)", "vr": "IS", "value": "6", "tag2": "", "desc": "Echo Train Length"}, {"tag1": "(0018,0093)", "vr": "DS", "value": "100", "tag2": "", "desc": "Percent Sampling"}, {"tag1": "(0018,0094)", "vr": "DS", "value": "75", "tag2": "", "desc": "Percent Phase Field of View"}, {"tag1": "(0018,0095)", "vr": "DS", "value": "122.07", "tag2": "", "desc": "Pixel Bandwidth"}, {"tag1": "(0018,1000)", "vr": "LO", "value": "00000000NPV24000", "tag2": "", "desc": "Device Serial Number"}, {"tag1": "(0018,1020)", "vr": "LO", "value": "11\\LX\\MR Software release:11.1_M4_0818.a", "tag2": "", "desc": "Software Version(s)"}, {"tag1": "(0018,1030)", "vr": "LO", "value": "CEREBRLAPURE", "tag2": "", "desc": "Protocol Name"}, {"tag1": "(0018,1088)", "vr": "IS", "value": "0", "tag2": "", "desc": "Heart Rate"}, {"tag1": "(0018,1090)", "vr": "IS", "value": "0", "tag2": "", "desc": "Cardiac Number of Images"}, {"tag1": "(0018,1094)", "vr": "IS", "value": "0", "tag2": "", "desc": "Trigger Window"}, {"tag1": "(0018,1100)", "vr": "DS", "value": "240", "tag2": "", "desc": "Reconstruction Diameter"}, {"tag1": "(0018,1250)", "vr": "SH", "value": "8NVHEAD_A", "tag2": "", "desc": "Receive Coil Name"}, {"tag1": "(0018,1310)", "vr": "US", "value": "0\\320\\256\\0", "tag2": "", "desc": "Acquisition Matrix"}, {"tag1": "(0018,1312)", "vr": "CS", "value": "ROW", "tag2": "", "desc": "In-plane Phase Encoding Direction"}, {"tag1": "(0018,1314)", "vr": "DS", "value": "90", "tag2": "", "desc": "Flip Angle"}, {"tag1": "(0018,1315)", "vr": "CS", "value": "N", "tag2": "", "desc": "Variable Flip Angle Flag"}, {"tag1": "(0018,1316)", "vr": "DS", "value": "1.265900", "tag2": "", "desc": "SAR"}, {"tag1": "(0018,5100)", "vr": "CS", "value": "HFS", "tag2": "", "desc": "Patient Position"}, {"tag1": "(0019,0010)", "vr": "LO", "value": "GEMS_ACQU_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0019,10BB)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10BC)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10BD)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10D9)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10DF)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10E0)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0020,000D)", "vr": "UI", "value": "1.2.124.113532.172.18.96.237.20121122.71447.1841208", "tag2": "", "desc": "Study Instance UID"}, {"tag1": "(0020,000E)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9529.1353572443.429", "tag2": "", "desc": "Series Instance UID"}, {"tag1": "(0020,0010)", "vr": "SH", "value": "", "tag2": "", "desc": "Study ID"}, {"tag1": "(0020,0011)", "vr": "IS", "value": "7", "tag2": "", "desc": "Series Number"}, {"tag1": "(0020,0012)", "vr": "IS", "value": "1", "tag2": "", "desc": "Acquisition Number"}, {"tag1": "(0020,0013)", "vr": "IS", "value": "3", "tag2": "", "desc": "Instance Number"}, {"tag1": "(0020,0032)", "vr": "DS", "value": "-128.263\\-55.68\\115.683", "tag2": "", "desc": "Image Position (Patient)"}, {"tag1": "(0020,0037)", "vr": "DS", "value": "0.997749\\-0.0129399\\0.0657984\\0.0643033\\-0.0941203\\-0.993482", "tag2": "", "desc": "Image Orientation (Patient)"}, {"tag1": "(0020,0052)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9591.1353572129.48", "tag2": "", "desc": "Frame of Reference UID"}, {"tag1": "(0020,0060)", "vr": "CS", "value": "", "tag2": "", "desc": "Laterality"}, {"tag1": "(0020,0110)", "vr": "DS", "value": "0", "tag2": "", "desc": "Temporal Resolution"}, {"tag1": "(0020,1040)", "vr": "LO", "value": "", "tag2": "", "desc": "Position Reference Indicator"}, {"tag1": "(0020,1041)", "vr": "DS", "value": "68.5019455", "tag2": "", "desc": "Slice Location"}, {"tag1": "(0021,0010)", "vr": "LO", "value": "GEMS_RELA_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0021,105A)", "vr": "UN", "value": "\\00\\00\\00\\00", "tag2": "", "desc": "?"}, {"tag1": "(0023,0010)", "vr": "LO", "value": "GEMS_STDY_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0025,0010)", "vr": "LO", "value": "GEMS_SERS_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0027,0010)", "vr": "LO", "value": "GEMS_IMAG_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0028,0002)", "vr": "US", "value": "1", "tag2": "", "desc": "Samples per Pixel"}, {"tag1": "(0028,0004)", "vr": "CS", "value": "MONOCHROME2", "tag2": "", "desc": "Photometric Interpretation"}, {"tag1": "(0028,0010)", "vr": "US", "value": "512", "tag2": "", "desc": "Rows"}, {"tag1": "(0028,0011)", "vr": "US", "value": "512", "tag2": "", "desc": "Columns"}, {"tag1": "(0028,0030)", "vr": "DS", "value": "0.468744\\0.468747", "tag2": "", "desc": "Pixel Spacing"}, {"tag1": "(0028,0100)", "vr": "US", "value": "16", "tag2": "", "desc": "Bits Allocated"}, {"tag1": "(0028,0101)", "vr": "US", "value": "16", "tag2": "", "desc": "Bits Stored"}, {"tag1": "(0028,0102)", "vr": "US", "value": "15", "tag2": "", "desc": "High Bit"}, {"tag1": "(0028,0103)", "vr": "US", "value": "1", "tag2": "", "desc": "Pixel Representation"}, {"tag1": "(0028,0120)", "vr": "SS", "value": "0", "tag2": "", "desc": "Pixel Padding Value"}, {"tag1": "(0028,0303)", "vr": "CS", "value": "", "tag2": "", "desc": "Longitudinal Temporal Information Modified"}, {"tag1": "(0028,1050)", "vr": "DS", "value": "1047", "tag2": "", "desc": "Window Center"}, {"tag1": "(0028,1051)", "vr": "DS", "value": "2094", "tag2": "", "desc": "Window Width"}, {"tag1": "(0029,0010)", "vr": "LO", "value": "GEMS_IMPS_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0032,000A)", "vr": "CS", "value": "READ", "tag2": "", "desc": "Study Status ID"}, {"tag1": "(0040,0241)", "vr": "AE", "value": "I3-PIM02", "tag2": "", "desc": "Performed Station AE Title"}, {"tag1": "(0040,0244)", "vr": "DA", "value": "20121122", "tag2": "", "desc": "Performed Procedure Step Start Date"}, {"tag1": "(0040,0245)", "vr": "TM", "value": "195032.000", "tag2": "", "desc": "Performed Procedure Step Start Time"}, {"tag1": "(0040,0254)", "vr": "LO", "value": "", "tag2": "", "desc": "Performed Procedure Step Description"}, {"tag1": "(0043,0010)", "vr": "LO", "value": "GEMS_PARM_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0043,1039)", "vr": "UN", "value": "0\\\\0\\\\0\\\\0 ", "tag2": "", "desc": "?"}, {"tag1": "(0903,0010)", "vr": "LO", "value": "GEIIS PACS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0905,0010)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(7FD1,0010)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}] \ No newline at end of file diff --git a/data/examples/MRI_Head/sub-2/ses-1/anat/sub-2_ses-1_run-2_T1w.nii.gz b/data/examples/MRI_Head/sub-2/ses-1/anat/sub-2_ses-1_run-2_T1w.nii.gz new file mode 100644 index 0000000..bc56f59 Binary files /dev/null and b/data/examples/MRI_Head/sub-2/ses-1/anat/sub-2_ses-1_run-2_T1w.nii.gz differ diff --git a/data/examples/MRI_Head/sub-2/ses-1/dwi/sub-2_ses-1_acq-1000b_dwi.bval b/data/examples/MRI_Head/sub-2/ses-1/dwi/sub-2_ses-1_acq-1000b_dwi.bval new file mode 100644 index 0000000..a72be1b --- /dev/null +++ b/data/examples/MRI_Head/sub-2/ses-1/dwi/sub-2_ses-1_acq-1000b_dwi.bval @@ -0,0 +1 @@ +1000 0 diff --git a/data/examples/MRI_Head/sub-2/ses-1/dwi/sub-2_ses-1_acq-1000b_dwi.bvec b/data/examples/MRI_Head/sub-2/ses-1/dwi/sub-2_ses-1_acq-1000b_dwi.bvec new file mode 100644 index 0000000..41c02d7 --- /dev/null +++ b/data/examples/MRI_Head/sub-2/ses-1/dwi/sub-2_ses-1_acq-1000b_dwi.bvec @@ -0,0 +1,3 @@ +0 0 +0 0 +0 0 diff --git a/data/examples/MRI_Head/sub-2/ses-1/dwi/sub-2_ses-1_acq-1000b_dwi.json b/data/examples/MRI_Head/sub-2/ses-1/dwi/sub-2_ses-1_acq-1000b_dwi.json new file mode 100644 index 0000000..192c3b3 --- /dev/null +++ b/data/examples/MRI_Head/sub-2/ses-1/dwi/sub-2_ses-1_acq-1000b_dwi.json @@ -0,0 +1 @@ +[{"tag1": "(0002,0001)", "vr": "OB", "value": "00\\01", "tag2": "", "desc": "File Meta Information Version"}, {"tag1": "(0002,0002)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "", "desc": "Media Storage SOP Class UID"}, {"tag1": "(0002,0003)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9529.1353572443.229", "tag2": "", "desc": "Media Storage SOP Instance UID"}, {"tag1": "(0002,0010)", "vr": "UI", "value": "1.2.840.10008.1.2.1", "tag2": "", "desc": "Transfer Syntax UID"}, {"tag1": "(0002,0012)", "vr": "UI", "value": "1.2.40.0.13.1.1", "tag2": "", "desc": "Implementation Class UID"}, {"tag1": "(0002,0013)", "vr": "SH", "value": "dcm4che-2.0", "tag2": "", "desc": "Implementation Version Name"}, {"tag1": "(0002,0016)", "vr": "AE", "value": "CTP", "tag2": "", "desc": "Source Application Entity Title"}, {"tag1": "(0008,0005)", "vr": "CS", "value": "ISO_IR 100", "tag2": "", "desc": "Specific Character Set"}, {"tag1": "(0008,0008)", "vr": "CS", "value": "ORIGINAL\\PRIMARY\\OTHER", "tag2": "", "desc": "Image Type"}, {"tag1": "(0008,0016)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "", "desc": "SOP Class UID"}, {"tag1": "(0008,0018)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9529.1353572443.229", "tag2": "", "desc": "SOP Instance UID"}, {"tag1": "(0008,0020)", "vr": "DA", "value": "20121122", "tag2": "", "desc": "Study Date"}, {"tag1": "(0008,0021)", "vr": "DA", "value": "20121122", "tag2": "", "desc": "Series Date"}, {"tag1": "(0008,0022)", "vr": "DA", "value": "20121122", "tag2": "", "desc": "Acquisition Date"}, {"tag1": "(0008,0023)", "vr": "DA", "value": "20121122", "tag2": "", "desc": "Content Date"}, {"tag1": "(0008,0030)", "vr": "TM", "value": "195032.000000", "tag2": "", "desc": "Study Time"}, {"tag1": "(0008,0031)", "vr": "TM", "value": "195445", "tag2": "", "desc": "Series Time"}, {"tag1": "(0008,0032)", "vr": "TM", "value": "195445", "tag2": "", "desc": "Acquisition Time"}, {"tag1": "(0008,0033)", "vr": "TM", "value": "195445", "tag2": "", "desc": "Content Time"}, {"tag1": "(0008,0050)", "vr": "SH", "value": "", "tag2": "", "desc": "Accession Number"}, {"tag1": "(0008,0060)", "vr": "CS", "value": "MR", "tag2": "", "desc": "Modality"}, {"tag1": "(0008,0070)", "vr": "LO", "value": "GE MEDICAL SYSTEMS", "tag2": "", "desc": "Manufacturer"}, {"tag1": "(0008,0090)", "vr": "PN", "value": "", "tag2": "", "desc": "Referring Physician’s Name"}, {"tag1": "(0008,1010)", "vr": "SH", "value": "I3-PIM02", "tag2": "", "desc": "Station Name"}, {"tag1": "(0008,1030)", "vr": "LO", "value": "MRI_Head", "tag2": "", "desc": "Study Description"}, {"tag1": "(0008,1032)", "vr": "SQ", "value": "", "tag2": "(0008,1032)", "desc": "Procedure Code Sequence"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "012071_30411", "tag2": "(0008,0100)", "desc": "Code Value"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "GEIIS", "tag2": "(0008,0102)", "desc": "Coding Scheme Designator"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "0", "tag2": "(0008,0103)", "desc": "Coding Scheme Version"}, {"tag1": "(0008,1032)", "vr": "LO", "value": "RM CRANEAL", "tag2": "(0008,0104)", "desc": "Code Meaning"}, {"tag1": "(0008,103E)", "vr": "LO", "value": "OAxDWI1000b", "tag2": "", "desc": "Series Description"}, {"tag1": "(0008,1090)", "vr": "LO", "value": "SIGNA EXCITE", "tag2": "", "desc": "Manufacturer’s Model Name"}, {"tag1": "(0008,1110)", "vr": "SQ", "value": "", "tag2": "(0008,1110)", "desc": "Referenced Study Sequence"}, {"tag1": "(0008,1110)", "vr": "UI", "value": "1.2.840.10008.3.1.2.3.1", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1110)", "vr": "UI", "value": "1.2.124.113532.80.22179.580.20121122.72334.20932853", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1111)", "vr": "SQ", "value": "", "tag2": "(0008,1111)", "desc": "Referenced Performed Procedure Step Sequence"}, {"tag1": "(0008,1111)", "vr": "UI", "value": "1.2.840.10008.3.1.2.3.3", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1111)", "vr": "UI", "value": "1.2.40.0.13.1.1.172.18.97.166.20121122070006446.32927", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9529.1353572442.912", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9529.1353572442.913", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0009,0010)", "vr": "LO", "value": "GEMS_IDEN_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0009,0011)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0010,0010)", "vr": "PN", "value": "206420261264115296606936483329680842341", "tag2": "", "desc": "Patient’s Name"}, {"tag1": "(0010,0020)", "vr": "LO", "value": "309742868506857266318767310985292225200", "tag2": "", "desc": "Patient ID"}, {"tag1": "(0010,0030)", "vr": "DA", "value": "19360612", "tag2": "", "desc": "Patient’s Birth Date"}, {"tag1": "(0010,0040)", "vr": "CS", "value": "M", "tag2": "", "desc": "Patient’s Sex"}, {"tag1": "(0010,1010)", "vr": "AS", "value": "076Y", "tag2": "", "desc": "Patient’s Age"}, {"tag1": "(0010,1030)", "vr": "DS", "value": "68", "tag2": "", "desc": "Patient’s Weight"}, {"tag1": "(0010,21B0)", "vr": "LT", "value": "", "tag2": "", "desc": "Additional Patient History"}, {"tag1": "(0011,0010)", "vr": "LO", "value": "GEMS_PATI_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0018,0020)", "vr": "CS", "value": "EP\\SE", "tag2": "", "desc": "Scanning Sequence"}, {"tag1": "(0018,0021)", "vr": "CS", "value": "NONE", "tag2": "", "desc": "Sequence Variant"}, {"tag1": "(0018,0022)", "vr": "CS", "value": "VB_GEMS\\EPI_GEMS\\FILTERED_GEMS\\PFF", "tag2": "", "desc": "Scan Options"}, {"tag1": "(0018,0023)", "vr": "CS", "value": "2D", "tag2": "", "desc": "MR Acquisition Type"}, {"tag1": "(0018,0025)", "vr": "CS", "value": "N", "tag2": "", "desc": "Angio Flag"}, {"tag1": "(0018,0050)", "vr": "DS", "value": "5", "tag2": "", "desc": "Slice Thickness"}, {"tag1": "(0018,0080)", "vr": "DS", "value": "10000", "tag2": "", "desc": "Repetition Time"}, {"tag1": "(0018,0081)", "vr": "DS", "value": "94.7", "tag2": "", "desc": "Echo Time"}, {"tag1": "(0018,0082)", "vr": "DS", "value": "0", "tag2": "", "desc": "Inversion Time"}, {"tag1": "(0018,0083)", "vr": "DS", "value": "1", "tag2": "", "desc": "Number of Averages"}, {"tag1": "(0018,0084)", "vr": "DS", "value": "63.858878", "tag2": "", "desc": "Imaging Frequency"}, {"tag1": "(0018,0085)", "vr": "SH", "value": "1H", "tag2": "", "desc": "Imaged Nucleus"}, {"tag1": "(0018,0086)", "vr": "IS", "value": "1", "tag2": "", "desc": "Echo Number(s)"}, {"tag1": "(0018,0087)", "vr": "DS", "value": "1.5", "tag2": "", "desc": "Magnetic Field Strength"}, {"tag1": "(0018,0088)", "vr": "DS", "value": "5.2", "tag2": "", "desc": "Spacing Between Slices"}, {"tag1": "(0018,0091)", "vr": "IS", "value": "1", "tag2": "", "desc": "Echo Train Length"}, {"tag1": "(0018,0093)", "vr": "DS", "value": "100", "tag2": "", "desc": "Percent Sampling"}, {"tag1": "(0018,0094)", "vr": "DS", "value": "100", "tag2": "", "desc": "Percent Phase Field of View"}, {"tag1": "(0018,0095)", "vr": "DS", "value": "1953.12", "tag2": "", "desc": "Pixel Bandwidth"}, {"tag1": "(0018,1000)", "vr": "LO", "value": "00000000NPV24000", "tag2": "", "desc": "Device Serial Number"}, {"tag1": "(0018,1020)", "vr": "LO", "value": "11\\LX\\MR Software release:11.1_M4_0818.a", "tag2": "", "desc": "Software Version(s)"}, {"tag1": "(0018,1030)", "vr": "LO", "value": "CEREBRLAPURE", "tag2": "", "desc": "Protocol Name"}, {"tag1": "(0018,1088)", "vr": "IS", "value": "0", "tag2": "", "desc": "Heart Rate"}, {"tag1": "(0018,1090)", "vr": "IS", "value": "0", "tag2": "", "desc": "Cardiac Number of Images"}, {"tag1": "(0018,1094)", "vr": "IS", "value": "0", "tag2": "", "desc": "Trigger Window"}, {"tag1": "(0018,1100)", "vr": "DS", "value": "280", "tag2": "", "desc": "Reconstruction Diameter"}, {"tag1": "(0018,1250)", "vr": "SH", "value": "8NVHEAD_A", "tag2": "", "desc": "Receive Coil Name"}, {"tag1": "(0018,1310)", "vr": "US", "value": "128\\0\\0\\128", "tag2": "", "desc": "Acquisition Matrix"}, {"tag1": "(0018,1312)", "vr": "CS", "value": "COL", "tag2": "", "desc": "In-plane Phase Encoding Direction"}, {"tag1": "(0018,1314)", "vr": "DS", "value": "90", "tag2": "", "desc": "Flip Angle"}, {"tag1": "(0018,1315)", "vr": "CS", "value": "N", "tag2": "", "desc": "Variable Flip Angle Flag"}, {"tag1": "(0018,1316)", "vr": "DS", "value": "0.145352", "tag2": "", "desc": "SAR"}, {"tag1": "(0018,5100)", "vr": "CS", "value": "HFS", "tag2": "", "desc": "Patient Position"}, {"tag1": "(0019,0010)", "vr": "LO", "value": "GEMS_ACQU_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0019,10BB)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10BC)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10BD)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10D9)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10DF)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10E0)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0020,000D)", "vr": "UI", "value": "1.2.124.113532.172.18.96.237.20121122.71447.1841208", "tag2": "", "desc": "Study Instance UID"}, {"tag1": "(0020,000E)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9529.1353572443.127", "tag2": "", "desc": "Series Instance UID"}, {"tag1": "(0020,0010)", "vr": "SH", "value": "", "tag2": "", "desc": "Study ID"}, {"tag1": "(0020,0011)", "vr": "IS", "value": "4", "tag2": "", "desc": "Series Number"}, {"tag1": "(0020,0012)", "vr": "IS", "value": "1", "tag2": "", "desc": "Acquisition Number"}, {"tag1": "(0020,0013)", "vr": "IS", "value": "37", "tag2": "", "desc": "Instance Number"}, {"tag1": "(0020,0032)", "vr": "DS", "value": "-139.095\\-147.621\\-7.93155", "tag2": "", "desc": "Image Position (Patient)"}, {"tag1": "(0020,0037)", "vr": "DS", "value": "0.999713\\-0\\0.0239567\\0.00146491\\0.998116\\-0.0613427", "tag2": "", "desc": "Image Orientation (Patient)"}, {"tag1": "(0020,0052)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9591.1353572129.48", "tag2": "", "desc": "Frame of Reference UID"}, {"tag1": "(0020,0060)", "vr": "CS", "value": "", "tag2": "", "desc": "Laterality"}, {"tag1": "(0020,0110)", "vr": "DS", "value": "0", "tag2": "", "desc": "Temporal Resolution"}, {"tag1": "(0020,1040)", "vr": "LO", "value": "", "tag2": "", "desc": "Position Reference Indicator"}, {"tag1": "(0020,1041)", "vr": "DS", "value": "-13.1450243", "tag2": "", "desc": "Slice Location"}, {"tag1": "(0021,0010)", "vr": "LO", "value": "GEMS_RELA_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0021,105A)", "vr": "UN", "value": "\\07\\00\\00\\00", "tag2": "", "desc": "?"}, {"tag1": "(0023,0010)", "vr": "LO", "value": "GEMS_STDY_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0025,0010)", "vr": "LO", "value": "GEMS_SERS_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0027,0010)", "vr": "LO", "value": "GEMS_IMAG_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0028,0002)", "vr": "US", "value": "1", "tag2": "", "desc": "Samples per Pixel"}, {"tag1": "(0028,0004)", "vr": "CS", "value": "MONOCHROME2", "tag2": "", "desc": "Photometric Interpretation"}, {"tag1": "(0028,0010)", "vr": "US", "value": "256", "tag2": "", "desc": "Rows"}, {"tag1": "(0028,0011)", "vr": "US", "value": "256", "tag2": "", "desc": "Columns"}, {"tag1": "(0028,0030)", "vr": "DS", "value": "1.09374\\1.09376", "tag2": "", "desc": "Pixel Spacing"}, {"tag1": "(0028,0100)", "vr": "US", "value": "16", "tag2": "", "desc": "Bits Allocated"}, {"tag1": "(0028,0101)", "vr": "US", "value": "16", "tag2": "", "desc": "Bits Stored"}, {"tag1": "(0028,0102)", "vr": "US", "value": "15", "tag2": "", "desc": "High Bit"}, {"tag1": "(0028,0103)", "vr": "US", "value": "1", "tag2": "", "desc": "Pixel Representation"}, {"tag1": "(0028,0120)", "vr": "SS", "value": "0", "tag2": "", "desc": "Pixel Padding Value"}, {"tag1": "(0028,0303)", "vr": "CS", "value": "", "tag2": "", "desc": "Longitudinal Temporal Information Modified"}, {"tag1": "(0028,1050)", "vr": "DS", "value": "4495", "tag2": "", "desc": "Window Center"}, {"tag1": "(0028,1051)", "vr": "DS", "value": "8990", "tag2": "", "desc": "Window Width"}, {"tag1": "(0029,0010)", "vr": "LO", "value": "GEMS_IMPS_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0032,000A)", "vr": "CS", "value": "READ", "tag2": "", "desc": "Study Status ID"}, {"tag1": "(0040,0241)", "vr": "AE", "value": "I3-PIM02", "tag2": "", "desc": "Performed Station AE Title"}, {"tag1": "(0040,0244)", "vr": "DA", "value": "20121122", "tag2": "", "desc": "Performed Procedure Step Start Date"}, {"tag1": "(0040,0245)", "vr": "TM", "value": "195032.000", "tag2": "", "desc": "Performed Procedure Step Start Time"}, {"tag1": "(0040,0254)", "vr": "LO", "value": "", "tag2": "", "desc": "Performed Procedure Step Description"}, {"tag1": "(0043,0010)", "vr": "LO", "value": "GEMS_PARM_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0043,1039)", "vr": "UN", "value": "0\\\\8\\\\0\\\\0 ", "tag2": "", "desc": "?"}, {"tag1": "(0903,0010)", "vr": "LO", "value": "GEIIS PACS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0905,0010)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(7FD1,0010)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}] \ No newline at end of file diff --git a/data/examples/MRI_Head/sub-2/ses-1/dwi/sub-2_ses-1_acq-1000b_dwi.nii.gz b/data/examples/MRI_Head/sub-2/ses-1/dwi/sub-2_ses-1_acq-1000b_dwi.nii.gz new file mode 100644 index 0000000..7e4f017 Binary files /dev/null and b/data/examples/MRI_Head/sub-2/ses-1/dwi/sub-2_ses-1_acq-1000b_dwi.nii.gz differ diff --git a/data/examples/MRI_Head/sub-2/ses-1/sub-2_ses-1_scans.tsv b/data/examples/MRI_Head/sub-2/ses-1/sub-2_ses-1_scans.tsv new file mode 100644 index 0000000..f93a78e --- /dev/null +++ b/data/examples/MRI_Head/sub-2/ses-1/sub-2_ses-1_scans.tsv @@ -0,0 +1,4 @@ +filename Manufacturer (0008,0070) Series Description (0008,103E) Manufacturer’s Model Name (0008,1090) Patient ID (0010,0020) Patient’s Sex (0010,0040) Patient’s Age (0010,1010) Patient’s Weight (0010,1030) Scanning Sequence (0018,0020) Sequence Variant (0018,0021) Scan Options (0018,0022) MR Acquisition Type (0018,0023) Slice Thickness (0018,0050) Repetition Time (0018,0080) Echo Time (0018,0081) Inversion Time (0018,0082) Imaging Frequency (0018,0084) Magnetic Field Strength (0018,0087) Manufacturer’s Model Name (0008,1090) Spacing Between Slices (0018,0088) Echo Train Length (0018,0091) Percent Sampling (0018,0093) Pixel Bandwidth (0018,0095) Flip Angle (0018,1314) Patient Position (0018,5100) Image Position (Patient) (0020,0032) Image Orientation (Patient) (0020,0037) Position Reference Indicator (0020,1040) Slice Location (0020,1041) Rows (0028,0010) Columns (0028,0011) Pixel Spacing (0028,0030) Bits Allocated (0028,0100) Number of Averages (0018,0083) Echo Number(s) (0018,0086) (0018,9461) +anat/sub-2_ses-1_run-2_T1w.nii.gz GE MEDICAL SYSTEMS CorT1FIR SIGNA EXCITE 309742868506857266318767310985292225200 M 076Y 68 IR n/a VB_GEMS\SEQ_GEMS\TRF_GEMS\FILTERED_GEMS 2D 5 2537.07 28.56 750 63.858867 1.5 SIGNA EXCITE 6.5 6 100 122.07 90 HFS -128.263\-55.68\115.683 0.997749\-0.0129399\0.0657984\0.0643033\-0.0941203\-0.993482 n/a 68.5019455 512 512 0.468744\0.468747 16 2 1 n/a +anat/sub-2_ses-1_run-1_T1w.nii.gz GE MEDICAL SYSTEMS 3plT2FGRES SIGNA EXCITE 309742868506857266318767310985292225200 M 076Y 68 RM OSP NPW\PFF 2D 4 39.5 1.8 0 63.858891 1.5 SIGNA EXCITE 5 1 100 244.141 30 HFS 5\-129.492\-20.5078 -0\1\0\-0\-0\-1 n/a -5 256 256 1.01562\1.01562 16 1 1 n/a +dwi/sub-2_ses-1_acq-1000b_dwi.nii.gz GE MEDICAL SYSTEMS OAxDWI1000b SIGNA EXCITE 309742868506857266318767310985292225200 M 076Y 68 EP\SE n/a VB_GEMS\EPI_GEMS\FILTERED_GEMS\PFF 2D 5 10000 94.7 0 63.858878 1.5 SIGNA EXCITE 5.2 1 100 1953.12 90 HFS -139.095\-147.621\-7.93155 0.999713\-0\0.0239567\0.00146491\0.998116\-0.0613427 n/a -13.1450243 256 256 1.09374\1.09376 16 1 1 n/a diff --git a/data/examples/MRI_Head/sub-2/ses-2/anat/sub-2_ses-2_run-1_T1w.json b/data/examples/MRI_Head/sub-2/ses-2/anat/sub-2_ses-2_run-1_T1w.json new file mode 100644 index 0000000..4395460 --- /dev/null +++ b/data/examples/MRI_Head/sub-2/ses-2/anat/sub-2_ses-2_run-1_T1w.json @@ -0,0 +1 @@ +[{"tag1": "(0002,0001)", "vr": "OB", "value": "00\\01", "tag2": "", "desc": "File Meta Information Version"}, {"tag1": "(0002,0002)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "", "desc": "Media Storage SOP Class UID"}, {"tag1": "(0002,0003)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9460.1354515255.267", "tag2": "", "desc": "Media Storage SOP Instance UID"}, {"tag1": "(0002,0010)", "vr": "UI", "value": "1.2.840.10008.1.2.1", "tag2": "", "desc": "Transfer Syntax UID"}, {"tag1": "(0002,0012)", "vr": "UI", "value": "1.2.40.0.13.1.1", "tag2": "", "desc": "Implementation Class UID"}, {"tag1": "(0002,0013)", "vr": "SH", "value": "dcm4che-2.0", "tag2": "", "desc": "Implementation Version Name"}, {"tag1": "(0002,0016)", "vr": "AE", "value": "CTP", "tag2": "", "desc": "Source Application Entity Title"}, {"tag1": "(0008,0005)", "vr": "CS", "value": "ISO_IR 100", "tag2": "", "desc": "Specific Character Set"}, {"tag1": "(0008,0008)", "vr": "CS", "value": "ORIGINAL\\PRIMARY\\OTHER", "tag2": "", "desc": "Image Type"}, {"tag1": "(0008,0016)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "", "desc": "SOP Class UID"}, {"tag1": "(0008,0018)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9460.1354515255.267", "tag2": "", "desc": "SOP Instance UID"}, {"tag1": "(0008,0020)", "vr": "DA", "value": "20121203", "tag2": "", "desc": "Study Date"}, {"tag1": "(0008,0021)", "vr": "DA", "value": "20121203", "tag2": "", "desc": "Series Date"}, {"tag1": "(0008,0022)", "vr": "DA", "value": "20121203", "tag2": "", "desc": "Acquisition Date"}, {"tag1": "(0008,0023)", "vr": "DA", "value": "20121203", "tag2": "", "desc": "Content Date"}, {"tag1": "(0008,0030)", "vr": "TM", "value": "124713.000000", "tag2": "", "desc": "Study Time"}, {"tag1": "(0008,0031)", "vr": "TM", "value": "124835", "tag2": "", "desc": "Series Time"}, {"tag1": "(0008,0032)", "vr": "TM", "value": "124835", "tag2": "", "desc": "Acquisition Time"}, {"tag1": "(0008,0033)", "vr": "TM", "value": "124835", "tag2": "", "desc": "Content Time"}, {"tag1": "(0008,0050)", "vr": "SH", "value": "", "tag2": "", "desc": "Accession Number"}, {"tag1": "(0008,0060)", "vr": "CS", "value": "MR", "tag2": "", "desc": "Modality"}, {"tag1": "(0008,0070)", "vr": "LO", "value": "GE MEDICAL SYSTEMS", "tag2": "", "desc": "Manufacturer"}, {"tag1": "(0008,0090)", "vr": "PN", "value": "", "tag2": "", "desc": "Referring Physician’s Name"}, {"tag1": "(0008,1010)", "vr": "SH", "value": "I3-PIM02", "tag2": "", "desc": "Station Name"}, {"tag1": "(0008,1030)", "vr": "LO", "value": "MRI_Head", "tag2": "", "desc": "Study Description"}, {"tag1": "(0008,1032)", "vr": "SQ", "value": "", "tag2": "(0008,1032)", "desc": "Procedure Code Sequence"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "012071_30411", "tag2": "(0008,0100)", "desc": "Code Value"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "GEIIS", "tag2": "(0008,0102)", "desc": "Coding Scheme Designator"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "0", "tag2": "(0008,0103)", "desc": "Coding Scheme Version"}, {"tag1": "(0008,1032)", "vr": "LO", "value": "RM CRANEAL", "tag2": "(0008,0104)", "desc": "Code Meaning"}, {"tag1": "(0008,103E)", "vr": "LO", "value": "AXT1SE", "tag2": "", "desc": "Series Description"}, {"tag1": "(0008,1090)", "vr": "LO", "value": "SIGNA EXCITE", "tag2": "", "desc": "Manufacturer’s Model Name"}, {"tag1": "(0008,1110)", "vr": "SQ", "value": "", "tag2": "(0008,1110)", "desc": "Referenced Study Sequence"}, {"tag1": "(0008,1110)", "vr": "UI", "value": "1.2.840.10008.3.1.2.3.1", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1110)", "vr": "UI", "value": "1.2.124.113532.80.22179.580.20121203.74630.24328626", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1111)", "vr": "SQ", "value": "", "tag2": "(0008,1111)", "desc": "Referenced Performed Procedure Step Sequence"}, {"tag1": "(0008,1111)", "vr": "UI", "value": "1.2.840.10008.3.1.2.3.3", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1111)", "vr": "UI", "value": "1.2.40.0.13.1.1.172.18.97.166.20121203070005189.32871", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9460.1354515255.49", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9460.1354515255.47", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0009,0010)", "vr": "LO", "value": "GEMS_IDEN_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0009,0011)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0010,0010)", "vr": "PN", "value": "206420261264115296606936483329680842341", "tag2": "", "desc": "Patient’s Name"}, {"tag1": "(0010,0020)", "vr": "LO", "value": "309742868506857266318767310985292225200", "tag2": "", "desc": "Patient ID"}, {"tag1": "(0010,0030)", "vr": "DA", "value": "19360612", "tag2": "", "desc": "Patient’s Birth Date"}, {"tag1": "(0010,0040)", "vr": "CS", "value": "M", "tag2": "", "desc": "Patient’s Sex"}, {"tag1": "(0010,1010)", "vr": "AS", "value": "076Y", "tag2": "", "desc": "Patient’s Age"}, {"tag1": "(0010,1030)", "vr": "DS", "value": "75", "tag2": "", "desc": "Patient’s Weight"}, {"tag1": "(0010,21B0)", "vr": "LT", "value": "", "tag2": "", "desc": "Additional Patient History"}, {"tag1": "(0011,0010)", "vr": "LO", "value": "GEMS_PATI_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0018,0020)", "vr": "CS", "value": "SE", "tag2": "", "desc": "Scanning Sequence"}, {"tag1": "(0018,0021)", "vr": "CS", "value": "NONE", "tag2": "", "desc": "Sequence Variant"}, {"tag1": "(0018,0022)", "vr": "CS", "value": "VB_GEMS\\FILTERED_GEMS", "tag2": "", "desc": "Scan Options"}, {"tag1": "(0018,0023)", "vr": "CS", "value": "2D", "tag2": "", "desc": "MR Acquisition Type"}, {"tag1": "(0018,0025)", "vr": "CS", "value": "N", "tag2": "", "desc": "Angio Flag"}, {"tag1": "(0018,0050)", "vr": "DS", "value": "4.5", "tag2": "", "desc": "Slice Thickness"}, {"tag1": "(0018,0080)", "vr": "DS", "value": "560", "tag2": "", "desc": "Repetition Time"}, {"tag1": "(0018,0081)", "vr": "DS", "value": "14", "tag2": "", "desc": "Echo Time"}, {"tag1": "(0018,0082)", "vr": "DS", "value": "0", "tag2": "", "desc": "Inversion Time"}, {"tag1": "(0018,0083)", "vr": "DS", "value": "1", "tag2": "", "desc": "Number of Averages"}, {"tag1": "(0018,0084)", "vr": "DS", "value": "63.858886", "tag2": "", "desc": "Imaging Frequency"}, {"tag1": "(0018,0085)", "vr": "SH", "value": "1H", "tag2": "", "desc": "Imaged Nucleus"}, {"tag1": "(0018,0086)", "vr": "IS", "value": "1", "tag2": "", "desc": "Echo Number(s)"}, {"tag1": "(0018,0087)", "vr": "DS", "value": "1.5", "tag2": "", "desc": "Magnetic Field Strength"}, {"tag1": "(0018,0088)", "vr": "DS", "value": "5.5", "tag2": "", "desc": "Spacing Between Slices"}, {"tag1": "(0018,0091)", "vr": "IS", "value": "1", "tag2": "", "desc": "Echo Train Length"}, {"tag1": "(0018,0093)", "vr": "DS", "value": "100", "tag2": "", "desc": "Percent Sampling"}, {"tag1": "(0018,0094)", "vr": "DS", "value": "100", "tag2": "", "desc": "Percent Phase Field of View"}, {"tag1": "(0018,0095)", "vr": "DS", "value": "75.1172", "tag2": "", "desc": "Pixel Bandwidth"}, {"tag1": "(0018,1000)", "vr": "LO", "value": "00000000NPV24000", "tag2": "", "desc": "Device Serial Number"}, {"tag1": "(0018,1020)", "vr": "LO", "value": "11\\LX\\MR Software release:11.1_M4_0818.a", "tag2": "", "desc": "Software Version(s)"}, {"tag1": "(0018,1030)", "vr": "LO", "value": "CEREBRLAPURE092011", "tag2": "", "desc": "Protocol Name"}, {"tag1": "(0018,1088)", "vr": "IS", "value": "0", "tag2": "", "desc": "Heart Rate"}, {"tag1": "(0018,1090)", "vr": "IS", "value": "0", "tag2": "", "desc": "Cardiac Number of Images"}, {"tag1": "(0018,1094)", "vr": "IS", "value": "0", "tag2": "", "desc": "Trigger Window"}, {"tag1": "(0018,1100)", "vr": "DS", "value": "240", "tag2": "", "desc": "Reconstruction Diameter"}, {"tag1": "(0018,1250)", "vr": "SH", "value": "8HRBRAIN", "tag2": "", "desc": "Receive Coil Name"}, {"tag1": "(0018,1310)", "vr": "US", "value": "0\\320\\224\\0", "tag2": "", "desc": "Acquisition Matrix"}, {"tag1": "(0018,1312)", "vr": "CS", "value": "ROW", "tag2": "", "desc": "In-plane Phase Encoding Direction"}, {"tag1": "(0018,1314)", "vr": "DS", "value": "90", "tag2": "", "desc": "Flip Angle"}, {"tag1": "(0018,1315)", "vr": "CS", "value": "N", "tag2": "", "desc": "Variable Flip Angle Flag"}, {"tag1": "(0018,1316)", "vr": "DS", "value": "1.336960", "tag2": "", "desc": "SAR"}, {"tag1": "(0018,5100)", "vr": "CS", "value": "HFS", "tag2": "", "desc": "Patient Position"}, {"tag1": "(0019,0010)", "vr": "LO", "value": "GEMS_ACQU_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0019,10BB)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10BC)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10BD)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10D9)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10DF)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10E0)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0020,000D)", "vr": "UI", "value": "1.2.124.113532.172.18.96.237.20121203.71750.1850124", "tag2": "", "desc": "Study Instance UID"}, {"tag1": "(0020,000E)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9460.1354515255.185", "tag2": "", "desc": "Series Instance UID"}, {"tag1": "(0020,0010)", "vr": "SH", "value": "", "tag2": "", "desc": "Study ID"}, {"tag1": "(0020,0011)", "vr": "IS", "value": "3", "tag2": "", "desc": "Series Number"}, {"tag1": "(0020,0012)", "vr": "IS", "value": "1", "tag2": "", "desc": "Acquisition Number"}, {"tag1": "(0020,0013)", "vr": "IS", "value": "17", "tag2": "", "desc": "Instance Number"}, {"tag1": "(0020,0032)", "vr": "DS", "value": "-121.627\\-140.585\\45.2051", "tag2": "", "desc": "Image Position (Patient)"}, {"tag1": "(0020,0037)", "vr": "DS", "value": "0.999934\\-0.0113528\\-0.00152594\\0.0112615\\0.9983\\-0.0571922", "tag2": "", "desc": "Image Orientation (Patient)"}, {"tag1": "(0020,0052)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9529.1354515231.885", "tag2": "", "desc": "Frame of Reference UID"}, {"tag1": "(0020,0060)", "vr": "CS", "value": "", "tag2": "", "desc": "Laterality"}, {"tag1": "(0020,0110)", "vr": "DS", "value": "0", "tag2": "", "desc": "Temporal Resolution"}, {"tag1": "(0020,1040)", "vr": "LO", "value": "", "tag2": "", "desc": "Position Reference Indicator"}, {"tag1": "(0020,1041)", "vr": "DS", "value": "38.1727562", "tag2": "", "desc": "Slice Location"}, {"tag1": "(0021,0010)", "vr": "LO", "value": "GEMS_RELA_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0021,105A)", "vr": "UN", "value": "\\00\\00\\00\\00", "tag2": "", "desc": "?"}, {"tag1": "(0023,0010)", "vr": "LO", "value": "GEMS_STDY_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0025,0010)", "vr": "LO", "value": "GEMS_SERS_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0027,0010)", "vr": "LO", "value": "GEMS_IMAG_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0028,0002)", "vr": "US", "value": "1", "tag2": "", "desc": "Samples per Pixel"}, {"tag1": "(0028,0004)", "vr": "CS", "value": "MONOCHROME2", "tag2": "", "desc": "Photometric Interpretation"}, {"tag1": "(0028,0010)", "vr": "US", "value": "512", "tag2": "", "desc": "Rows"}, {"tag1": "(0028,0011)", "vr": "US", "value": "512", "tag2": "", "desc": "Columns"}, {"tag1": "(0028,0030)", "vr": "DS", "value": "0.468746\\0.468752", "tag2": "", "desc": "Pixel Spacing"}, {"tag1": "(0028,0100)", "vr": "US", "value": "16", "tag2": "", "desc": "Bits Allocated"}, {"tag1": "(0028,0101)", "vr": "US", "value": "16", "tag2": "", "desc": "Bits Stored"}, {"tag1": "(0028,0102)", "vr": "US", "value": "15", "tag2": "", "desc": "High Bit"}, {"tag1": "(0028,0103)", "vr": "US", "value": "1", "tag2": "", "desc": "Pixel Representation"}, {"tag1": "(0028,0120)", "vr": "SS", "value": "0", "tag2": "", "desc": "Pixel Padding Value"}, {"tag1": "(0028,0303)", "vr": "CS", "value": "", "tag2": "", "desc": "Longitudinal Temporal Information Modified"}, {"tag1": "(0028,1050)", "vr": "DS", "value": "1070", "tag2": "", "desc": "Window Center"}, {"tag1": "(0028,1051)", "vr": "DS", "value": "2140", "tag2": "", "desc": "Window Width"}, {"tag1": "(0029,0010)", "vr": "LO", "value": "GEMS_IMPS_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0032,000A)", "vr": "CS", "value": "READ", "tag2": "", "desc": "Study Status ID"}, {"tag1": "(0040,0241)", "vr": "AE", "value": "I3-PIM02", "tag2": "", "desc": "Performed Station AE Title"}, {"tag1": "(0040,0244)", "vr": "DA", "value": "20121203", "tag2": "", "desc": "Performed Procedure Step Start Date"}, {"tag1": "(0040,0245)", "vr": "TM", "value": "124713.000", "tag2": "", "desc": "Performed Procedure Step Start Time"}, {"tag1": "(0040,0254)", "vr": "LO", "value": "", "tag2": "", "desc": "Performed Procedure Step Description"}, {"tag1": "(0043,0010)", "vr": "LO", "value": "GEMS_PARM_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0043,1039)", "vr": "UN", "value": "0\\\\0\\\\0\\\\0 ", "tag2": "", "desc": "?"}, {"tag1": "(0903,0010)", "vr": "LO", "value": "GEIIS PACS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0905,0010)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(7FD1,0010)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}] \ No newline at end of file diff --git a/data/examples/MRI_Head/sub-2/ses-2/anat/sub-2_ses-2_run-1_T1w.nii.gz b/data/examples/MRI_Head/sub-2/ses-2/anat/sub-2_ses-2_run-1_T1w.nii.gz new file mode 100644 index 0000000..3d82c7f Binary files /dev/null and b/data/examples/MRI_Head/sub-2/ses-2/anat/sub-2_ses-2_run-1_T1w.nii.gz differ diff --git a/data/examples/MRI_Head/sub-2/ses-2/anat/sub-2_ses-2_run-2_T1w.json b/data/examples/MRI_Head/sub-2/ses-2/anat/sub-2_ses-2_run-2_T1w.json new file mode 100644 index 0000000..d7d9e9b --- /dev/null +++ b/data/examples/MRI_Head/sub-2/ses-2/anat/sub-2_ses-2_run-2_T1w.json @@ -0,0 +1 @@ +[{"tag1": "(0002,0001)", "vr": "OB", "value": "00\\01", "tag2": "", "desc": "File Meta Information Version"}, {"tag1": "(0002,0002)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "", "desc": "Media Storage SOP Class UID"}, {"tag1": "(0002,0003)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9460.1354515255.465", "tag2": "", "desc": "Media Storage SOP Instance UID"}, {"tag1": "(0002,0010)", "vr": "UI", "value": "1.2.840.10008.1.2.1", "tag2": "", "desc": "Transfer Syntax UID"}, {"tag1": "(0002,0012)", "vr": "UI", "value": "1.2.40.0.13.1.1", "tag2": "", "desc": "Implementation Class UID"}, {"tag1": "(0002,0013)", "vr": "SH", "value": "dcm4che-2.0", "tag2": "", "desc": "Implementation Version Name"}, {"tag1": "(0002,0016)", "vr": "AE", "value": "CTP", "tag2": "", "desc": "Source Application Entity Title"}, {"tag1": "(0008,0005)", "vr": "CS", "value": "ISO_IR 100", "tag2": "", "desc": "Specific Character Set"}, {"tag1": "(0008,0008)", "vr": "CS", "value": "ORIGINAL\\PRIMARY\\OTHER", "tag2": "", "desc": "Image Type"}, {"tag1": "(0008,0016)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "", "desc": "SOP Class UID"}, {"tag1": "(0008,0018)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9460.1354515255.465", "tag2": "", "desc": "SOP Instance UID"}, {"tag1": "(0008,0020)", "vr": "DA", "value": "20121203", "tag2": "", "desc": "Study Date"}, {"tag1": "(0008,0021)", "vr": "DA", "value": "20121203", "tag2": "", "desc": "Series Date"}, {"tag1": "(0008,0022)", "vr": "DA", "value": "20121203", "tag2": "", "desc": "Acquisition Date"}, {"tag1": "(0008,0023)", "vr": "DA", "value": "20121203", "tag2": "", "desc": "Content Date"}, {"tag1": "(0008,0030)", "vr": "TM", "value": "124713.000000", "tag2": "", "desc": "Study Time"}, {"tag1": "(0008,0031)", "vr": "TM", "value": "130050", "tag2": "", "desc": "Series Time"}, {"tag1": "(0008,0032)", "vr": "TM", "value": "130050", "tag2": "", "desc": "Acquisition Time"}, {"tag1": "(0008,0033)", "vr": "TM", "value": "130050", "tag2": "", "desc": "Content Time"}, {"tag1": "(0008,0050)", "vr": "SH", "value": "", "tag2": "", "desc": "Accession Number"}, {"tag1": "(0008,0060)", "vr": "CS", "value": "MR", "tag2": "", "desc": "Modality"}, {"tag1": "(0008,0070)", "vr": "LO", "value": "GE MEDICAL SYSTEMS", "tag2": "", "desc": "Manufacturer"}, {"tag1": "(0008,0090)", "vr": "PN", "value": "", "tag2": "", "desc": "Referring Physician’s Name"}, {"tag1": "(0008,1010)", "vr": "SH", "value": "I3-PIM02", "tag2": "", "desc": "Station Name"}, {"tag1": "(0008,1030)", "vr": "LO", "value": "RMI_Cabeza", "tag2": "", "desc": "Study Description"}, {"tag1": "(0008,1032)", "vr": "SQ", "value": "", "tag2": "(0008,1032)", "desc": "Procedure Code Sequence"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "012071_30411", "tag2": "(0008,0100)", "desc": "Code Value"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "GEIIS", "tag2": "(0008,0102)", "desc": "Coding Scheme Designator"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "0", "tag2": "(0008,0103)", "desc": "Coding Scheme Version"}, {"tag1": "(0008,1032)", "vr": "LO", "value": "RM CRANEAL", "tag2": "(0008,0104)", "desc": "Code Meaning"}, {"tag1": "(0008,103E)", "vr": "LO", "value": "AXT1SE", "tag2": "", "desc": "Series Description"}, {"tag1": "(0008,1090)", "vr": "LO", "value": "SIGNA EXCITE", "tag2": "", "desc": "Manufacturer’s Model Name"}, {"tag1": "(0008,1110)", "vr": "SQ", "value": "", "tag2": "(0008,1110)", "desc": "Referenced Study Sequence"}, {"tag1": "(0008,1110)", "vr": "UI", "value": "1.2.840.10008.3.1.2.3.1", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1110)", "vr": "UI", "value": "1.2.124.113532.80.22179.580.20121203.74630.24328626", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1111)", "vr": "SQ", "value": "", "tag2": "(0008,1111)", "desc": "Referenced Performed Procedure Step Sequence"}, {"tag1": "(0008,1111)", "vr": "UI", "value": "1.2.840.10008.3.1.2.3.3", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1111)", "vr": "UI", "value": "1.2.40.0.13.1.1.172.18.97.166.20121203070005189.32871", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9460.1354515255.49", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9460.1354515255.47", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0009,0010)", "vr": "LO", "value": "GEMS_IDEN_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0009,0011)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0010,0010)", "vr": "PN", "value": "206420261264115296606936483329680842341", "tag2": "", "desc": "Patient’s Name"}, {"tag1": "(0010,0020)", "vr": "LO", "value": "309742868506857266318767310985292225200", "tag2": "", "desc": "Patient ID"}, {"tag1": "(0010,0030)", "vr": "DA", "value": "19360612", "tag2": "", "desc": "Patient’s Birth Date"}, {"tag1": "(0010,0040)", "vr": "CS", "value": "M", "tag2": "", "desc": "Patient’s Sex"}, {"tag1": "(0010,1010)", "vr": "AS", "value": "076Y", "tag2": "", "desc": "Patient’s Age"}, {"tag1": "(0010,1030)", "vr": "DS", "value": "75", "tag2": "", "desc": "Patient’s Weight"}, {"tag1": "(0010,21B0)", "vr": "LT", "value": "", "tag2": "", "desc": "Additional Patient History"}, {"tag1": "(0011,0010)", "vr": "LO", "value": "GEMS_PATI_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0018,0020)", "vr": "CS", "value": "SE", "tag2": "", "desc": "Scanning Sequence"}, {"tag1": "(0018,0021)", "vr": "CS", "value": "NONE", "tag2": "", "desc": "Sequence Variant"}, {"tag1": "(0018,0022)", "vr": "CS", "value": "VB_GEMS\\FILTERED_GEMS", "tag2": "", "desc": "Scan Options"}, {"tag1": "(0018,0023)", "vr": "CS", "value": "2D", "tag2": "", "desc": "MR Acquisition Type"}, {"tag1": "(0018,0025)", "vr": "CS", "value": "N", "tag2": "", "desc": "Angio Flag"}, {"tag1": "(0018,0050)", "vr": "DS", "value": "4.5", "tag2": "", "desc": "Slice Thickness"}, {"tag1": "(0018,0080)", "vr": "DS", "value": "560", "tag2": "", "desc": "Repetition Time"}, {"tag1": "(0018,0081)", "vr": "DS", "value": "14", "tag2": "", "desc": "Echo Time"}, {"tag1": "(0018,0082)", "vr": "DS", "value": "0", "tag2": "", "desc": "Inversion Time"}, {"tag1": "(0018,0083)", "vr": "DS", "value": "1", "tag2": "", "desc": "Number of Averages"}, {"tag1": "(0018,0084)", "vr": "DS", "value": "63.858881", "tag2": "", "desc": "Imaging Frequency"}, {"tag1": "(0018,0085)", "vr": "SH", "value": "1H", "tag2": "", "desc": "Imaged Nucleus"}, {"tag1": "(0018,0086)", "vr": "IS", "value": "1", "tag2": "", "desc": "Echo Number(s)"}, {"tag1": "(0018,0087)", "vr": "DS", "value": "1.5", "tag2": "", "desc": "Magnetic Field Strength"}, {"tag1": "(0018,0088)", "vr": "DS", "value": "5.5", "tag2": "", "desc": "Spacing Between Slices"}, {"tag1": "(0018,0091)", "vr": "IS", "value": "1", "tag2": "", "desc": "Echo Train Length"}, {"tag1": "(0018,0093)", "vr": "DS", "value": "100", "tag2": "", "desc": "Percent Sampling"}, {"tag1": "(0018,0094)", "vr": "DS", "value": "100", "tag2": "", "desc": "Percent Phase Field of View"}, {"tag1": "(0018,0095)", "vr": "DS", "value": "75.1172", "tag2": "", "desc": "Pixel Bandwidth"}, {"tag1": "(0018,1000)", "vr": "LO", "value": "00000000NPV24000", "tag2": "", "desc": "Device Serial Number"}, {"tag1": "(0018,1020)", "vr": "LO", "value": "11\\LX\\MR Software release:11.1_M4_0818.a", "tag2": "", "desc": "Software Version(s)"}, {"tag1": "(0018,1030)", "vr": "LO", "value": "CEREBRLAPURE092011", "tag2": "", "desc": "Protocol Name"}, {"tag1": "(0018,1088)", "vr": "IS", "value": "0", "tag2": "", "desc": "Heart Rate"}, {"tag1": "(0018,1090)", "vr": "IS", "value": "0", "tag2": "", "desc": "Cardiac Number of Images"}, {"tag1": "(0018,1094)", "vr": "IS", "value": "0", "tag2": "", "desc": "Trigger Window"}, {"tag1": "(0018,1100)", "vr": "DS", "value": "240", "tag2": "", "desc": "Reconstruction Diameter"}, {"tag1": "(0018,1250)", "vr": "SH", "value": "8HRBRAIN", "tag2": "", "desc": "Receive Coil Name"}, {"tag1": "(0018,1310)", "vr": "US", "value": "0\\320\\224\\0", "tag2": "", "desc": "Acquisition Matrix"}, {"tag1": "(0018,1312)", "vr": "CS", "value": "ROW", "tag2": "", "desc": "In-plane Phase Encoding Direction"}, {"tag1": "(0018,1314)", "vr": "DS", "value": "90", "tag2": "", "desc": "Flip Angle"}, {"tag1": "(0018,1315)", "vr": "CS", "value": "N", "tag2": "", "desc": "Variable Flip Angle Flag"}, {"tag1": "(0018,1316)", "vr": "DS", "value": "1.336960", "tag2": "", "desc": "SAR"}, {"tag1": "(0018,5100)", "vr": "CS", "value": "HFS", "tag2": "", "desc": "Patient Position"}, {"tag1": "(0019,0010)", "vr": "LO", "value": "GEMS_ACQU_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0019,10BB)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10BC)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10BD)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10D9)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10DF)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10E0)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0020,000D)", "vr": "UI", "value": "1.2.124.113532.172.18.96.237.20121203.71750.1850124", "tag2": "", "desc": "Study Instance UID"}, {"tag1": "(0020,000E)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9460.1354515255.397", "tag2": "", "desc": "Series Instance UID"}, {"tag1": "(0020,0010)", "vr": "SH", "value": "", "tag2": "", "desc": "Study ID"}, {"tag1": "(0020,0011)", "vr": "IS", "value": "5", "tag2": "", "desc": "Series Number"}, {"tag1": "(0020,0012)", "vr": "IS", "value": "1", "tag2": "", "desc": "Acquisition Number"}, {"tag1": "(0020,0013)", "vr": "IS", "value": "3", "tag2": "", "desc": "Instance Number"}, {"tag1": "(0020,0032)", "vr": "DS", "value": "-121.793\\-144.987\\-31.6688", "tag2": "", "desc": "Image Position (Patient)"}, {"tag1": "(0020,0037)", "vr": "DS", "value": "0.999934\\-0.0113528\\-0.00152591\\0.0112615\\0.9983\\-0.0571922", "tag2": "", "desc": "Image Orientation (Patient)"}, {"tag1": "(0020,0052)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9529.1354515231.885", "tag2": "", "desc": "Frame of Reference UID"}, {"tag1": "(0020,0060)", "vr": "CS", "value": "", "tag2": "", "desc": "Laterality"}, {"tag1": "(0020,0110)", "vr": "DS", "value": "0", "tag2": "", "desc": "Temporal Resolution"}, {"tag1": "(0020,1040)", "vr": "LO", "value": "", "tag2": "", "desc": "Position Reference Indicator"}, {"tag1": "(0020,1041)", "vr": "DS", "value": "-38.70117188", "tag2": "", "desc": "Slice Location"}, {"tag1": "(0021,0010)", "vr": "LO", "value": "GEMS_RELA_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0021,105A)", "vr": "UN", "value": "\\00\\00\\00\\00", "tag2": "", "desc": "?"}, {"tag1": "(0023,0010)", "vr": "LO", "value": "GEMS_STDY_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0025,0010)", "vr": "LO", "value": "GEMS_SERS_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0027,0010)", "vr": "LO", "value": "GEMS_IMAG_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0028,0002)", "vr": "US", "value": "1", "tag2": "", "desc": "Samples per Pixel"}, {"tag1": "(0028,0004)", "vr": "CS", "value": "MONOCHROME2", "tag2": "", "desc": "Photometric Interpretation"}, {"tag1": "(0028,0010)", "vr": "US", "value": "512", "tag2": "", "desc": "Rows"}, {"tag1": "(0028,0011)", "vr": "US", "value": "512", "tag2": "", "desc": "Columns"}, {"tag1": "(0028,0030)", "vr": "DS", "value": "0.468746\\0.468752", "tag2": "", "desc": "Pixel Spacing"}, {"tag1": "(0028,0100)", "vr": "US", "value": "16", "tag2": "", "desc": "Bits Allocated"}, {"tag1": "(0028,0101)", "vr": "US", "value": "16", "tag2": "", "desc": "Bits Stored"}, {"tag1": "(0028,0102)", "vr": "US", "value": "15", "tag2": "", "desc": "High Bit"}, {"tag1": "(0028,0103)", "vr": "US", "value": "1", "tag2": "", "desc": "Pixel Representation"}, {"tag1": "(0028,0120)", "vr": "SS", "value": "0", "tag2": "", "desc": "Pixel Padding Value"}, {"tag1": "(0028,0303)", "vr": "CS", "value": "", "tag2": "", "desc": "Longitudinal Temporal Information Modified"}, {"tag1": "(0028,1050)", "vr": "DS", "value": "1563", "tag2": "", "desc": "Window Center"}, {"tag1": "(0028,1051)", "vr": "DS", "value": "3126", "tag2": "", "desc": "Window Width"}, {"tag1": "(0029,0010)", "vr": "LO", "value": "GEMS_IMPS_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0032,000A)", "vr": "CS", "value": "READ", "tag2": "", "desc": "Study Status ID"}, {"tag1": "(0040,0241)", "vr": "AE", "value": "I3-PIM02", "tag2": "", "desc": "Performed Station AE Title"}, {"tag1": "(0040,0244)", "vr": "DA", "value": "20121203", "tag2": "", "desc": "Performed Procedure Step Start Date"}, {"tag1": "(0040,0245)", "vr": "TM", "value": "124713.000", "tag2": "", "desc": "Performed Procedure Step Start Time"}, {"tag1": "(0040,0254)", "vr": "LO", "value": "", "tag2": "", "desc": "Performed Procedure Step Description"}, {"tag1": "(0043,0010)", "vr": "LO", "value": "GEMS_PARM_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0043,1039)", "vr": "UN", "value": "0\\\\0\\\\0\\\\0 ", "tag2": "", "desc": "?"}, {"tag1": "(0903,0010)", "vr": "LO", "value": "GEIIS PACS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0905,0010)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(7FD1,0010)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}] \ No newline at end of file diff --git a/data/examples/MRI_Head/sub-2/ses-2/anat/sub-2_ses-2_run-2_T1w.nii.gz b/data/examples/MRI_Head/sub-2/ses-2/anat/sub-2_ses-2_run-2_T1w.nii.gz new file mode 100644 index 0000000..0875b69 Binary files /dev/null and b/data/examples/MRI_Head/sub-2/ses-2/anat/sub-2_ses-2_run-2_T1w.nii.gz differ diff --git a/data/examples/MRI_Head/sub-2/ses-2/anat/sub-2_ses-2_run-3_T1w.json b/data/examples/MRI_Head/sub-2/ses-2/anat/sub-2_ses-2_run-3_T1w.json new file mode 100644 index 0000000..9f5d66c --- /dev/null +++ b/data/examples/MRI_Head/sub-2/ses-2/anat/sub-2_ses-2_run-3_T1w.json @@ -0,0 +1 @@ +[{"tag1": "(0002,0001)", "vr": "OB", "value": "00\\01", "tag2": "", "desc": "File Meta Information Version"}, {"tag1": "(0002,0002)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "", "desc": "Media Storage SOP Class UID"}, {"tag1": "(0002,0003)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9460.1354515255.378", "tag2": "", "desc": "Media Storage SOP Instance UID"}, {"tag1": "(0002,0010)", "vr": "UI", "value": "1.2.840.10008.1.2.1", "tag2": "", "desc": "Transfer Syntax UID"}, {"tag1": "(0002,0012)", "vr": "UI", "value": "1.2.40.0.13.1.1", "tag2": "", "desc": "Implementation Class UID"}, {"tag1": "(0002,0013)", "vr": "SH", "value": "dcm4che-2.0", "tag2": "", "desc": "Implementation Version Name"}, {"tag1": "(0002,0016)", "vr": "AE", "value": "CTP", "tag2": "", "desc": "Source Application Entity Title"}, {"tag1": "(0008,0005)", "vr": "CS", "value": "ISO_IR 100", "tag2": "", "desc": "Specific Character Set"}, {"tag1": "(0008,0008)", "vr": "CS", "value": "ORIGINAL\\PRIMARY\\OTHER", "tag2": "", "desc": "Image Type"}, {"tag1": "(0008,0016)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "", "desc": "SOP Class UID"}, {"tag1": "(0008,0018)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9460.1354515255.378", "tag2": "", "desc": "SOP Instance UID"}, {"tag1": "(0008,0020)", "vr": "DA", "value": "20121203", "tag2": "", "desc": "Study Date"}, {"tag1": "(0008,0021)", "vr": "DA", "value": "20121203", "tag2": "", "desc": "Series Date"}, {"tag1": "(0008,0022)", "vr": "DA", "value": "20121203", "tag2": "", "desc": "Acquisition Date"}, {"tag1": "(0008,0023)", "vr": "DA", "value": "20121203", "tag2": "", "desc": "Content Date"}, {"tag1": "(0008,0030)", "vr": "TM", "value": "124713.000000", "tag2": "", "desc": "Study Time"}, {"tag1": "(0008,0031)", "vr": "TM", "value": "125113", "tag2": "", "desc": "Series Time"}, {"tag1": "(0008,0032)", "vr": "TM", "value": "125754", "tag2": "", "desc": "Acquisition Time"}, {"tag1": "(0008,0033)", "vr": "TM", "value": "125754", "tag2": "", "desc": "Content Time"}, {"tag1": "(0008,0050)", "vr": "SH", "value": "", "tag2": "", "desc": "Accession Number"}, {"tag1": "(0008,0060)", "vr": "CS", "value": "MR", "tag2": "", "desc": "Modality"}, {"tag1": "(0008,0070)", "vr": "LO", "value": "GE MEDICAL SYSTEMS", "tag2": "", "desc": "Manufacturer"}, {"tag1": "(0008,0090)", "vr": "PN", "value": "", "tag2": "", "desc": "Referring Physician’s Name"}, {"tag1": "(0008,1010)", "vr": "SH", "value": "I3-PIM02", "tag2": "", "desc": "Station Name"}, {"tag1": "(0008,1030)", "vr": "LO", "value": "RMI_Cabeza", "tag2": "", "desc": "Study Description"}, {"tag1": "(0008,1032)", "vr": "SQ", "value": "", "tag2": "(0008,1032)", "desc": "Procedure Code Sequence"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "012071_30411", "tag2": "(0008,0100)", "desc": "Code Value"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "GEIIS", "tag2": "(0008,0102)", "desc": "Coding Scheme Designator"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "0", "tag2": "(0008,0103)", "desc": "Coding Scheme Version"}, {"tag1": "(0008,1032)", "vr": "LO", "value": "RM CRANEAL", "tag2": "(0008,0104)", "desc": "Code Meaning"}, {"tag1": "(0008,103E)", "vr": "LO", "value": "CORT1SE", "tag2": "", "desc": "Series Description"}, {"tag1": "(0008,1090)", "vr": "LO", "value": "SIGNA EXCITE", "tag2": "", "desc": "Manufacturer’s Model Name"}, {"tag1": "(0008,1110)", "vr": "SQ", "value": "", "tag2": "(0008,1110)", "desc": "Referenced Study Sequence"}, {"tag1": "(0008,1110)", "vr": "UI", "value": "1.2.840.10008.3.1.2.3.1", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1110)", "vr": "UI", "value": "1.2.124.113532.80.22179.580.20121203.74630.24328626", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1111)", "vr": "SQ", "value": "", "tag2": "(0008,1111)", "desc": "Referenced Performed Procedure Step Sequence"}, {"tag1": "(0008,1111)", "vr": "UI", "value": "1.2.840.10008.3.1.2.3.3", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1111)", "vr": "UI", "value": "1.2.40.0.13.1.1.172.18.97.166.20121203070005189.32871", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9460.1354515255.49", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9460.1354515255.45", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0009,0010)", "vr": "LO", "value": "GEMS_IDEN_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0009,0011)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0010,0010)", "vr": "PN", "value": "206420261264115296606936483329680842341", "tag2": "", "desc": "Patient’s Name"}, {"tag1": "(0010,0020)", "vr": "LO", "value": "309742868506857266318767310985292225200", "tag2": "", "desc": "Patient ID"}, {"tag1": "(0010,0030)", "vr": "DA", "value": "19360612", "tag2": "", "desc": "Patient’s Birth Date"}, {"tag1": "(0010,0040)", "vr": "CS", "value": "M", "tag2": "", "desc": "Patient’s Sex"}, {"tag1": "(0010,1010)", "vr": "AS", "value": "076Y", "tag2": "", "desc": "Patient’s Age"}, {"tag1": "(0010,1030)", "vr": "DS", "value": "75", "tag2": "", "desc": "Patient’s Weight"}, {"tag1": "(0010,21B0)", "vr": "LT", "value": "", "tag2": "", "desc": "Additional Patient History"}, {"tag1": "(0011,0010)", "vr": "LO", "value": "GEMS_PATI_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0018,0020)", "vr": "CS", "value": "SE", "tag2": "", "desc": "Scanning Sequence"}, {"tag1": "(0018,0021)", "vr": "CS", "value": "NONE", "tag2": "", "desc": "Sequence Variant"}, {"tag1": "(0018,0022)", "vr": "CS", "value": "VB_GEMS\\FILTERED_GEMS", "tag2": "", "desc": "Scan Options"}, {"tag1": "(0018,0023)", "vr": "CS", "value": "2D", "tag2": "", "desc": "MR Acquisition Type"}, {"tag1": "(0018,0025)", "vr": "CS", "value": "N", "tag2": "", "desc": "Angio Flag"}, {"tag1": "(0018,0050)", "vr": "DS", "value": "5", "tag2": "", "desc": "Slice Thickness"}, {"tag1": "(0018,0080)", "vr": "DS", "value": "360", "tag2": "", "desc": "Repetition Time"}, {"tag1": "(0018,0081)", "vr": "DS", "value": "16", "tag2": "", "desc": "Echo Time"}, {"tag1": "(0018,0082)", "vr": "DS", "value": "0", "tag2": "", "desc": "Inversion Time"}, {"tag1": "(0018,0083)", "vr": "DS", "value": "1", "tag2": "", "desc": "Number of Averages"}, {"tag1": "(0018,0084)", "vr": "DS", "value": "63.858874", "tag2": "", "desc": "Imaging Frequency"}, {"tag1": "(0018,0085)", "vr": "SH", "value": "1H", "tag2": "", "desc": "Imaged Nucleus"}, {"tag1": "(0018,0086)", "vr": "IS", "value": "1", "tag2": "", "desc": "Echo Number(s)"}, {"tag1": "(0018,0087)", "vr": "DS", "value": "1.5", "tag2": "", "desc": "Magnetic Field Strength"}, {"tag1": "(0018,0088)", "vr": "DS", "value": "6", "tag2": "", "desc": "Spacing Between Slices"}, {"tag1": "(0018,0091)", "vr": "IS", "value": "1", "tag2": "", "desc": "Echo Train Length"}, {"tag1": "(0018,0093)", "vr": "DS", "value": "100", "tag2": "", "desc": "Percent Sampling"}, {"tag1": "(0018,0094)", "vr": "DS", "value": "100", "tag2": "", "desc": "Percent Phase Field of View"}, {"tag1": "(0018,0095)", "vr": "DS", "value": "61.0547", "tag2": "", "desc": "Pixel Bandwidth"}, {"tag1": "(0018,1000)", "vr": "LO", "value": "00000000NPV24000", "tag2": "", "desc": "Device Serial Number"}, {"tag1": "(0018,1020)", "vr": "LO", "value": "11\\LX\\MR Software release:11.1_M4_0818.a", "tag2": "", "desc": "Software Version(s)"}, {"tag1": "(0018,1030)", "vr": "LO", "value": "CEREBRLAPURE0920113", "tag2": "", "desc": "Protocol Name"}, {"tag1": "(0018,1088)", "vr": "IS", "value": "0", "tag2": "", "desc": "Heart Rate"}, {"tag1": "(0018,1090)", "vr": "IS", "value": "0", "tag2": "", "desc": "Cardiac Number of Images"}, {"tag1": "(0018,1094)", "vr": "IS", "value": "0", "tag2": "", "desc": "Trigger Window"}, {"tag1": "(0018,1100)", "vr": "DS", "value": "240", "tag2": "", "desc": "Reconstruction Diameter"}, {"tag1": "(0018,1250)", "vr": "SH", "value": "8HRBRAIN", "tag2": "", "desc": "Receive Coil Name"}, {"tag1": "(0018,1310)", "vr": "US", "value": "0\\320\\224\\0", "tag2": "", "desc": "Acquisition Matrix"}, {"tag1": "(0018,1312)", "vr": "CS", "value": "ROW", "tag2": "", "desc": "In-plane Phase Encoding Direction"}, {"tag1": "(0018,1314)", "vr": "DS", "value": "90", "tag2": "", "desc": "Flip Angle"}, {"tag1": "(0018,1315)", "vr": "CS", "value": "N", "tag2": "", "desc": "Variable Flip Angle Flag"}, {"tag1": "(0018,1316)", "vr": "DS", "value": "1.215609", "tag2": "", "desc": "SAR"}, {"tag1": "(0018,5100)", "vr": "CS", "value": "HFS", "tag2": "", "desc": "Patient Position"}, {"tag1": "(0019,0010)", "vr": "LO", "value": "GEMS_ACQU_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0019,10BB)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10BC)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10BD)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10D9)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10DF)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10E0)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0020,000D)", "vr": "UI", "value": "1.2.124.113532.172.18.96.237.20121203.71750.1850124", "tag2": "", "desc": "Study Instance UID"}, {"tag1": "(0020,000E)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9460.1354515255.275", "tag2": "", "desc": "Series Instance UID"}, {"tag1": "(0020,0010)", "vr": "SH", "value": "", "tag2": "", "desc": "Study ID"}, {"tag1": "(0020,0011)", "vr": "IS", "value": "4", "tag2": "", "desc": "Series Number"}, {"tag1": "(0020,0012)", "vr": "IS", "value": "2", "tag2": "", "desc": "Acquisition Number"}, {"tag1": "(0020,0013)", "vr": "IS", "value": "47", "tag2": "", "desc": "Instance Number"}, {"tag1": "(0020,0032)", "vr": "DS", "value": "-118.432\\-24.5346\\117.8", "tag2": "", "desc": "Image Position (Patient)"}, {"tag1": "(0020,0037)", "vr": "DS", "value": "0.998115\\-0.0590232\\-0.0168158\\-0.0234989\\-0.114473\\-0.993148", "tag2": "", "desc": "Image Orientation (Patient)"}, {"tag1": "(0020,0052)", "vr": "UI", "value": "1.2.840.113619.2.222.2025.1750492.9529.1354515231.885", "tag2": "", "desc": "Frame of Reference UID"}, {"tag1": "(0020,0060)", "vr": "CS", "value": "", "tag2": "", "desc": "Laterality"}, {"tag1": "(0020,0110)", "vr": "DS", "value": "0", "tag2": "", "desc": "Temporal Resolution"}, {"tag1": "(0020,1040)", "vr": "LO", "value": "", "tag2": "", "desc": "Position Reference Indicator"}, {"tag1": "(0020,1041)", "vr": "DS", "value": "45.31367493", "tag2": "", "desc": "Slice Location"}, {"tag1": "(0021,0010)", "vr": "LO", "value": "GEMS_RELA_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0021,105A)", "vr": "UN", "value": "\\00\\00\\00\\00", "tag2": "", "desc": "?"}, {"tag1": "(0023,0010)", "vr": "LO", "value": "GEMS_STDY_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0025,0010)", "vr": "LO", "value": "GEMS_SERS_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0027,0010)", "vr": "LO", "value": "GEMS_IMAG_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0028,0002)", "vr": "US", "value": "1", "tag2": "", "desc": "Samples per Pixel"}, {"tag1": "(0028,0004)", "vr": "CS", "value": "MONOCHROME2", "tag2": "", "desc": "Photometric Interpretation"}, {"tag1": "(0028,0010)", "vr": "US", "value": "512", "tag2": "", "desc": "Rows"}, {"tag1": "(0028,0011)", "vr": "US", "value": "512", "tag2": "", "desc": "Columns"}, {"tag1": "(0028,0030)", "vr": "DS", "value": "0.468757\\0.468747", "tag2": "", "desc": "Pixel Spacing"}, {"tag1": "(0028,0100)", "vr": "US", "value": "16", "tag2": "", "desc": "Bits Allocated"}, {"tag1": "(0028,0101)", "vr": "US", "value": "16", "tag2": "", "desc": "Bits Stored"}, {"tag1": "(0028,0102)", "vr": "US", "value": "15", "tag2": "", "desc": "High Bit"}, {"tag1": "(0028,0103)", "vr": "US", "value": "1", "tag2": "", "desc": "Pixel Representation"}, {"tag1": "(0028,0120)", "vr": "SS", "value": "0", "tag2": "", "desc": "Pixel Padding Value"}, {"tag1": "(0028,0303)", "vr": "CS", "value": "", "tag2": "", "desc": "Longitudinal Temporal Information Modified"}, {"tag1": "(0028,1050)", "vr": "DS", "value": "1565", "tag2": "", "desc": "Window Center"}, {"tag1": "(0028,1051)", "vr": "DS", "value": "3131", "tag2": "", "desc": "Window Width"}, {"tag1": "(0029,0010)", "vr": "LO", "value": "GEMS_IMPS_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0032,000A)", "vr": "CS", "value": "READ", "tag2": "", "desc": "Study Status ID"}, {"tag1": "(0040,0241)", "vr": "AE", "value": "I3-PIM02", "tag2": "", "desc": "Performed Station AE Title"}, {"tag1": "(0040,0244)", "vr": "DA", "value": "20121203", "tag2": "", "desc": "Performed Procedure Step Start Date"}, {"tag1": "(0040,0245)", "vr": "TM", "value": "124713.000", "tag2": "", "desc": "Performed Procedure Step Start Time"}, {"tag1": "(0040,0254)", "vr": "LO", "value": "", "tag2": "", "desc": "Performed Procedure Step Description"}, {"tag1": "(0043,0010)", "vr": "LO", "value": "GEMS_PARM_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0043,1039)", "vr": "UN", "value": "0\\\\0\\\\0\\\\0 ", "tag2": "", "desc": "?"}, {"tag1": "(0903,0010)", "vr": "LO", "value": "GEIIS PACS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0905,0010)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(7FD1,0010)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}] \ No newline at end of file diff --git a/data/examples/MRI_Head/sub-2/ses-2/anat/sub-2_ses-2_run-3_T1w.nii.gz b/data/examples/MRI_Head/sub-2/ses-2/anat/sub-2_ses-2_run-3_T1w.nii.gz new file mode 100644 index 0000000..d1bbae0 Binary files /dev/null and b/data/examples/MRI_Head/sub-2/ses-2/anat/sub-2_ses-2_run-3_T1w.nii.gz differ diff --git a/data/examples/MRI_Head/sub-2/ses-2/sub-2_ses-2_scans.tsv b/data/examples/MRI_Head/sub-2/ses-2/sub-2_ses-2_scans.tsv new file mode 100644 index 0000000..18922ab --- /dev/null +++ b/data/examples/MRI_Head/sub-2/ses-2/sub-2_ses-2_scans.tsv @@ -0,0 +1,4 @@ +filename Manufacturer (0008,0070) Series Description (0008,103E) Manufacturer’s Model Name (0008,1090) Patient ID (0010,0020) Patient’s Sex (0010,0040) Patient’s Age (0010,1010) Patient’s Weight (0010,1030) Scanning Sequence (0018,0020) Sequence Variant (0018,0021) Scan Options (0018,0022) MR Acquisition Type (0018,0023) Slice Thickness (0018,0050) Repetition Time (0018,0080) Echo Time (0018,0081) Inversion Time (0018,0082) Imaging Frequency (0018,0084) Magnetic Field Strength (0018,0087) Manufacturer’s Model Name (0008,1090) Spacing Between Slices (0018,0088) Echo Train Length (0018,0091) Percent Sampling (0018,0093) Pixel Bandwidth (0018,0095) Flip Angle (0018,1314) Patient Position (0018,5100) Image Position (Patient) (0020,0032) Image Orientation (Patient) (0020,0037) Position Reference Indicator (0020,1040) Slice Location (0020,1041) Rows (0028,0010) Columns (0028,0011) Pixel Spacing (0028,0030) Bits Allocated (0028,0100) Number of Averages (0018,0083) Echo Number(s) (0018,0086) (0018,9461) +anat/sub-2_ses-2_run-1_bp-head_vp-ax_T1w.nii.gz,anat/sub-2_ses-2_run-2_bp-head_vp-ax_T1w.nii.gz,anat/sub-2_ses-2_bp-head_vp-cor_T1w.nii.gz GE MEDICAL SYSTEMS CORT1SE SIGNA EXCITE 309742868506857266318767310985292225200 M 076Y 75 SE n/a VB_GEMS\FILTERED_GEMS 2D 5 360 16 0 63.858874 1.5 SIGNA EXCITE 6 1 100 61.0547 90 HFS -118.432\-24.5346\117.8 0.998115\-0.0590232\-0.0168158\-0.0234989\-0.114473\-0.993148 n/a 45.31367493 512 512 0.468757\0.468747 16 1 1 n/a +anat/sub-2_ses-2_run-1_bp-head_vp-ax_T1w.nii.gz GE MEDICAL SYSTEMS AXT1SE SIGNA EXCITE 309742868506857266318767310985292225200 M 076Y 75 SE n/a VB_GEMS\FILTERED_GEMS 2D 4.5 560 14 0 63.858886 1.5 SIGNA EXCITE 5.5 1 100 75.1172 90 HFS -121.627\-140.585\45.2051 0.999934\-0.0113528\-0.00152594\0.0112615\0.9983\-0.0571922 n/a 38.1727562 512 512 0.468746\0.468752 16 1 1 n/a +anat/sub-2_ses-2_run-2_bp-head_vp-ax_T1w.nii.gz GE MEDICAL SYSTEMS AXT1SE SIGNA EXCITE 309742868506857266318767310985292225200 M 076Y 75 SE n/a VB_GEMS\FILTERED_GEMS 2D 4.5 560 14 0 63.858881 1.5 SIGNA EXCITE 5.5 1 100 75.1172 90 HFS -121.793\-144.987\-31.6688 0.999934\-0.0113528\-0.00152591\0.0112615\0.9983\-0.0571922 n/a -38.70117188 512 512 0.468746\0.468752 16 1 1 n/a diff --git a/data/examples/MRI_Head/sub-3/ses-1/anat/sub-3_ses-1_T1w.json b/data/examples/MRI_Head/sub-3/ses-1/anat/sub-3_ses-1_T1w.json new file mode 100644 index 0000000..48d33d8 --- /dev/null +++ b/data/examples/MRI_Head/sub-3/ses-1/anat/sub-3_ses-1_T1w.json @@ -0,0 +1 @@ +[{"tag1": "(0002,0001)", "vr": "OB", "value": "00\\01", "tag2": "", "desc": "File Meta Information Version"}, {"tag1": "(0002,0002)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "", "desc": "Media Storage SOP Class UID"}, {"tag1": "(0002,0003)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.11490.1409292834.142", "tag2": "", "desc": "Media Storage SOP Instance UID"}, {"tag1": "(0002,0010)", "vr": "UI", "value": "1.2.840.10008.1.2.1", "tag2": "", "desc": "Transfer Syntax UID"}, {"tag1": "(0002,0012)", "vr": "UI", "value": "1.2.40.0.13.1.1", "tag2": "", "desc": "Implementation Class UID"}, {"tag1": "(0002,0013)", "vr": "SH", "value": "dcm4che-2.0", "tag2": "", "desc": "Implementation Version Name"}, {"tag1": "(0002,0016)", "vr": "AE", "value": "CTP", "tag2": "", "desc": "Source Application Entity Title"}, {"tag1": "(0008,0005)", "vr": "CS", "value": "ISO_IR 100", "tag2": "", "desc": "Specific Character Set"}, {"tag1": "(0008,0008)", "vr": "CS", "value": "ORIGINAL\\PRIMARY\\OTHER", "tag2": "", "desc": "Image Type"}, {"tag1": "(0008,0016)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "", "desc": "SOP Class UID"}, {"tag1": "(0008,0018)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.11490.1409292834.142", "tag2": "", "desc": "SOP Instance UID"}, {"tag1": "(0008,0020)", "vr": "DA", "value": "20140829", "tag2": "", "desc": "Study Date"}, {"tag1": "(0008,0021)", "vr": "DA", "value": "20140829", "tag2": "", "desc": "Series Date"}, {"tag1": "(0008,0022)", "vr": "DA", "value": "20140829", "tag2": "", "desc": "Acquisition Date"}, {"tag1": "(0008,0023)", "vr": "DA", "value": "20140829", "tag2": "", "desc": "Content Date"}, {"tag1": "(0008,0030)", "vr": "TM", "value": "115822.000000", "tag2": "", "desc": "Study Time"}, {"tag1": "(0008,0031)", "vr": "TM", "value": "122347", "tag2": "", "desc": "Series Time"}, {"tag1": "(0008,0032)", "vr": "TM", "value": "122347", "tag2": "", "desc": "Acquisition Time"}, {"tag1": "(0008,0033)", "vr": "TM", "value": "122347", "tag2": "", "desc": "Content Time"}, {"tag1": "(0008,0050)", "vr": "SH", "value": "", "tag2": "", "desc": "Accession Number"}, {"tag1": "(0008,0060)", "vr": "CS", "value": "MR", "tag2": "", "desc": "Modality"}, {"tag1": "(0008,0070)", "vr": "LO", "value": "GE MEDICAL SYSTEMS", "tag2": "", "desc": "Manufacturer"}, {"tag1": "(0008,0090)", "vr": "PN", "value": "", "tag2": "", "desc": "Referring Physician’s Name"}, {"tag1": "(0008,1010)", "vr": "SH", "value": "NHFEMR07", "tag2": "", "desc": "Station Name"}, {"tag1": "(0008,1030)", "vr": "LO", "value": "MRI_Head", "tag2": "", "desc": "Study Description"}, {"tag1": "(0008,1032)", "vr": "SQ", "value": "", "tag2": "(0008,1032)", "desc": "Procedure Code Sequence"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "904001_RM111", "tag2": "(0008,0100)", "desc": "Code Value"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "GEIIS", "tag2": "(0008,0102)", "desc": "Coding Scheme Designator"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "0", "tag2": "(0008,0103)", "desc": "Coding Scheme Version"}, {"tag1": "(0008,1032)", "vr": "LO", "value": "RM111 - RM CEREBRAL", "tag2": "(0008,0104)", "desc": "Code Meaning"}, {"tag1": "(0008,103E)", "vr": "LO", "value": "SagT1MEMP", "tag2": "", "desc": "Series Description"}, {"tag1": "(0008,1090)", "vr": "LO", "value": "Signa HDxt", "tag2": "", "desc": "Manufacturer’s Model Name"}, {"tag1": "(0008,1110)", "vr": "SQ", "value": "", "tag2": "(0008,1110)", "desc": "Referenced Study Sequence"}, {"tag1": "(0008,1110)", "vr": "UI", "value": "1.2.840.10008.3.1.2.3.1", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1110)", "vr": "UI", "value": "1.2.124.113532.12.10529.61843.20140828.125803.45246674", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1111)", "vr": "SQ", "value": "", "tag2": "(0008,1111)", "desc": "Referenced Performed Procedure Step Sequence"}, {"tag1": "(0008,1111)", "vr": "UI", "value": "1.2.840.10008.3.1.2.3.3", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1111)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.12137.1409292383.190", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.11490.1409292833.502", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.11490.1409292833.178", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0009,0010)", "vr": "LO", "value": "GEMS_IDEN_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0009,0011)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0010,0010)", "vr": "PN", "value": "228068469937235231595795351598802870893", "tag2": "", "desc": "Patient’s Name"}, {"tag1": "(0010,0020)", "vr": "LO", "value": "280497372964350258462589225688693110743", "tag2": "", "desc": "Patient ID"}, {"tag1": "(0010,0030)", "vr": "DA", "value": "20060103", "tag2": "", "desc": "Patient’s Birth Date"}, {"tag1": "(0010,0040)", "vr": "CS", "value": "M", "tag2": "", "desc": "Patient’s Sex"}, {"tag1": "(0010,1010)", "vr": "AS", "value": "008Y", "tag2": "", "desc": "Patient’s Age"}, {"tag1": "(0010,1030)", "vr": "DS", "value": "42", "tag2": "", "desc": "Patient’s Weight"}, {"tag1": "(0010,21B0)", "vr": "LT", "value": "", "tag2": "", "desc": "Additional Patient History"}, {"tag1": "(0018,0010)", "vr": "LO", "value": "", "tag2": "", "desc": "Contrast/Bolus Agent"}, {"tag1": "(0018,0020)", "vr": "CS", "value": "RM", "tag2": "", "desc": "Scanning Sequence"}, {"tag1": "(0018,0021)", "vr": "CS", "value": "NONE", "tag2": "", "desc": "Sequence Variant"}, {"tag1": "(0018,0022)", "vr": "CS", "value": "FILTERED_GEMS", "tag2": "", "desc": "Scan Options"}, {"tag1": "(0018,0023)", "vr": "CS", "value": "2D", "tag2": "", "desc": "MR Acquisition Type"}, {"tag1": "(0018,0025)", "vr": "CS", "value": "N", "tag2": "", "desc": "Angio Flag"}, {"tag1": "(0018,0050)", "vr": "DS", "value": "5", "tag2": "", "desc": "Slice Thickness"}, {"tag1": "(0018,0080)", "vr": "DS", "value": "520", "tag2": "", "desc": "Repetition Time"}, {"tag1": "(0018,0081)", "vr": "DS", "value": "16", "tag2": "", "desc": "Echo Time"}, {"tag1": "(0018,0082)", "vr": "DS", "value": "0", "tag2": "", "desc": "Inversion Time"}, {"tag1": "(0018,0083)", "vr": "DS", "value": "1", "tag2": "", "desc": "Number of Averages"}, {"tag1": "(0018,0084)", "vr": "DS", "value": "63.832258", "tag2": "", "desc": "Imaging Frequency"}, {"tag1": "(0018,0085)", "vr": "SH", "value": "1H", "tag2": "", "desc": "Imaged Nucleus"}, {"tag1": "(0018,0086)", "vr": "IS", "value": "1", "tag2": "", "desc": "Echo Number(s)"}, {"tag1": "(0018,0087)", "vr": "DS", "value": "1.5", "tag2": "", "desc": "Magnetic Field Strength"}, {"tag1": "(0018,0088)", "vr": "DS", "value": "6.5", "tag2": "", "desc": "Spacing Between Slices"}, {"tag1": "(0018,0091)", "vr": "IS", "value": "1", "tag2": "", "desc": "Echo Train Length"}, {"tag1": "(0018,0093)", "vr": "DS", "value": "100", "tag2": "", "desc": "Percent Sampling"}, {"tag1": "(0018,0094)", "vr": "DS", "value": "100", "tag2": "", "desc": "Percent Phase Field of View"}, {"tag1": "(0018,0095)", "vr": "DS", "value": "57.4609", "tag2": "", "desc": "Pixel Bandwidth"}, {"tag1": "(0018,1000)", "vr": "LO", "value": "00000000NPV84504", "tag2": "", "desc": "Device Serial Number"}, {"tag1": "(0018,1020)", "vr": "LO", "value": "15\\LX\\MR Software release:15.0_M4B_1034.a", "tag2": "", "desc": "Software Version(s)"}, {"tag1": "(0018,1030)", "vr": "LO", "value": "ECEREBRALGD8HRBRAIN", "tag2": "", "desc": "Protocol Name"}, {"tag1": "(0018,1040)", "vr": "LO", "value": "IV", "tag2": "", "desc": "Contrast/Bolus Route"}, {"tag1": "(0018,1088)", "vr": "IS", "value": "0", "tag2": "", "desc": "Heart Rate"}, {"tag1": "(0018,1090)", "vr": "IS", "value": "0", "tag2": "", "desc": "Cardiac Number of Images"}, {"tag1": "(0018,1094)", "vr": "IS", "value": "0", "tag2": "", "desc": "Trigger Window"}, {"tag1": "(0018,1100)", "vr": "DS", "value": "240", "tag2": "", "desc": "Reconstruction Diameter"}, {"tag1": "(0018,1250)", "vr": "SH", "value": "8HRBRAIN", "tag2": "", "desc": "Receive Coil Name"}, {"tag1": "(0018,1310)", "vr": "US", "value": "0\\320\\256\\0", "tag2": "", "desc": "Acquisition Matrix"}, {"tag1": "(0018,1312)", "vr": "CS", "value": "ROW", "tag2": "", "desc": "In-plane Phase Encoding Direction"}, {"tag1": "(0018,1314)", "vr": "DS", "value": "70", "tag2": "", "desc": "Flip Angle"}, {"tag1": "(0018,1315)", "vr": "CS", "value": "N", "tag2": "", "desc": "Variable Flip Angle Flag"}, {"tag1": "(0018,1316)", "vr": "DS", "value": "0.863881", "tag2": "", "desc": "SAR"}, {"tag1": "(0018,5100)", "vr": "CS", "value": "HFS", "tag2": "", "desc": "Patient Position"}, {"tag1": "(0019,0010)", "vr": "LO", "value": "GEMS_ACQU_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0019,10BB)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10BC)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10BD)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10D9)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10DF)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10E0)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0020,000D)", "vr": "UI", "value": "1.2.124.113532.12.10529.61843.20140828.125803.45246674", "tag2": "", "desc": "Study Instance UID"}, {"tag1": "(0020,000E)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.12137.1409292383.200", "tag2": "", "desc": "Series Instance UID"}, {"tag1": "(0020,0010)", "vr": "SH", "value": "", "tag2": "", "desc": "Study ID"}, {"tag1": "(0020,0011)", "vr": "IS", "value": "9", "tag2": "", "desc": "Series Number"}, {"tag1": "(0020,0012)", "vr": "IS", "value": "1", "tag2": "", "desc": "Acquisition Number"}, {"tag1": "(0020,0013)", "vr": "IS", "value": "12", "tag2": "", "desc": "Instance Number"}, {"tag1": "(0020,0032)", "vr": "DS", "value": "21.2763\\-144.929\\158.012", "tag2": "", "desc": "Image Position (Patient)"}, {"tag1": "(0020,0037)", "vr": "DS", "value": "-0.0827058\\0.996193\\0.0275584\\-0.0270703\\0.0253917\\-0.999311", "tag2": "", "desc": "Image Orientation (Patient)"}, {"tag1": "(0020,0052)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.12137.1409292383.192", "tag2": "", "desc": "Frame of Reference UID"}, {"tag1": "(0020,0060)", "vr": "CS", "value": "", "tag2": "", "desc": "Laterality"}, {"tag1": "(0020,1002)", "vr": "IS", "value": "20", "tag2": "", "desc": "Images in Acquisition"}, {"tag1": "(0020,1040)", "vr": "LO", "value": "", "tag2": "", "desc": "Position Reference Indicator"}, {"tag1": "(0020,1041)", "vr": "DS", "value": "-8.129069328", "tag2": "", "desc": "Slice Location"}, {"tag1": "(0020,9056)", "vr": "SH", "value": "1", "tag2": "", "desc": "Stack ID"}, {"tag1": "(0020,9057)", "vr": "UL", "value": "12", "tag2": "", "desc": "In-Stack Position Number"}, {"tag1": "(0021,0010)", "vr": "LO", "value": "GEMS_RELA_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0021,105A)", "vr": "UN", "value": "\\00\\00\\00\\00", "tag2": "", "desc": "?"}, {"tag1": "(0023,0010)", "vr": "LO", "value": "GEMS_STDY_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0025,0010)", "vr": "LO", "value": "GEMS_SERS_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0027,0010)", "vr": "LO", "value": "GEMS_IMAG_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0028,0002)", "vr": "US", "value": "1", "tag2": "", "desc": "Samples per Pixel"}, {"tag1": "(0028,0004)", "vr": "CS", "value": "MONOCHROME2", "tag2": "", "desc": "Photometric Interpretation"}, {"tag1": "(0028,0010)", "vr": "US", "value": "512", "tag2": "", "desc": "Rows"}, {"tag1": "(0028,0011)", "vr": "US", "value": "512", "tag2": "", "desc": "Columns"}, {"tag1": "(0028,0030)", "vr": "DS", "value": "0.4688\\0.4688", "tag2": "", "desc": "Pixel Spacing"}, {"tag1": "(0028,0100)", "vr": "US", "value": "16", "tag2": "", "desc": "Bits Allocated"}, {"tag1": "(0028,0101)", "vr": "US", "value": "16", "tag2": "", "desc": "Bits Stored"}, {"tag1": "(0028,0102)", "vr": "US", "value": "15", "tag2": "", "desc": "High Bit"}, {"tag1": "(0028,0103)", "vr": "US", "value": "1", "tag2": "", "desc": "Pixel Representation"}, {"tag1": "(0028,0106)", "vr": "US", "value": "0", "tag2": "", "desc": "Smallest Image Pixel Value"}, {"tag1": "(0028,0107)", "vr": "US", "value": "1138", "tag2": "", "desc": "Largest Image Pixel Value"}, {"tag1": "(0028,0303)", "vr": "CS", "value": "", "tag2": "", "desc": "Longitudinal Temporal Information Modified"}, {"tag1": "(0028,1050)", "vr": "DS", "value": "569", "tag2": "", "desc": "Window Center"}, {"tag1": "(0028,1051)", "vr": "DS", "value": "1138", "tag2": "", "desc": "Window Width"}, {"tag1": "(0029,0010)", "vr": "LO", "value": "GEMS_IMPS_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0031,0010)", "vr": "LO", "value": "MITRA LINKED ATTRIBUTES 1.0", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0031,0011)", "vr": "LO", "value": "AGFA PACS Archive Mirroring 1.0", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0032,000A)", "vr": "CS", "value": "READ", "tag2": "", "desc": "Study Status ID"}, {"tag1": "(0033,0010)", "vr": "LO", "value": "MITRA OBJECT UTF8 ATTRIBUTES 1.0", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0040,0244)", "vr": "DA", "value": "20140829", "tag2": "", "desc": "Performed Procedure Step Start Date"}, {"tag1": "(0040,0245)", "vr": "TM", "value": "115822.000000", "tag2": "", "desc": "Performed Procedure Step Start Time"}, {"tag1": "(0040,0254)", "vr": "LO", "value": "", "tag2": "", "desc": "Performed Procedure Step Description"}, {"tag1": "(0043,0010)", "vr": "LO", "value": "GEMS_PARM_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0043,1039)", "vr": "UN", "value": "0\\\\32\\\\0\\\\0", "tag2": "", "desc": "?"}, {"tag1": "(0903,0010)", "vr": "LO", "value": "GEIIS PACS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0905,0010)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(7FD1,0010)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}] \ No newline at end of file diff --git a/data/examples/MRI_Head/sub-3/ses-1/anat/sub-3_ses-1_T1w.nii.gz b/data/examples/MRI_Head/sub-3/ses-1/anat/sub-3_ses-1_T1w.nii.gz new file mode 100644 index 0000000..5400f7e Binary files /dev/null and b/data/examples/MRI_Head/sub-3/ses-1/anat/sub-3_ses-1_T1w.nii.gz differ diff --git a/data/examples/MRI_Head/sub-3/ses-1/anat/sub-3_ses-1_acq-highres_T1w.json b/data/examples/MRI_Head/sub-3/ses-1/anat/sub-3_ses-1_acq-highres_T1w.json new file mode 100644 index 0000000..8741f18 --- /dev/null +++ b/data/examples/MRI_Head/sub-3/ses-1/anat/sub-3_ses-1_acq-highres_T1w.json @@ -0,0 +1 @@ +[{"tag1": "(0002,0001)", "vr": "OB", "value": "00\\01", "tag2": "", "desc": "File Meta Information Version"}, {"tag1": "(0002,0002)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "", "desc": "Media Storage SOP Class UID"}, {"tag1": "(0002,0003)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.11490.1409292833.2", "tag2": "", "desc": "Media Storage SOP Instance UID"}, {"tag1": "(0002,0010)", "vr": "UI", "value": "1.2.840.10008.1.2.1", "tag2": "", "desc": "Transfer Syntax UID"}, {"tag1": "(0002,0012)", "vr": "UI", "value": "1.2.40.0.13.1.1", "tag2": "", "desc": "Implementation Class UID"}, {"tag1": "(0002,0013)", "vr": "SH", "value": "dcm4che-2.0", "tag2": "", "desc": "Implementation Version Name"}, {"tag1": "(0002,0016)", "vr": "AE", "value": "CTP", "tag2": "", "desc": "Source Application Entity Title"}, {"tag1": "(0008,0005)", "vr": "CS", "value": "ISO_IR 100", "tag2": "", "desc": "Specific Character Set"}, {"tag1": "(0008,0008)", "vr": "CS", "value": "ORIGINAL\\PRIMARY\\OTHER", "tag2": "", "desc": "Image Type"}, {"tag1": "(0008,0016)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "", "desc": "SOP Class UID"}, {"tag1": "(0008,0018)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.11490.1409292833.2", "tag2": "", "desc": "SOP Instance UID"}, {"tag1": "(0008,0020)", "vr": "DA", "value": "20140829", "tag2": "", "desc": "Study Date"}, {"tag1": "(0008,0021)", "vr": "DA", "value": "20140829", "tag2": "", "desc": "Series Date"}, {"tag1": "(0008,0022)", "vr": "DA", "value": "20140829", "tag2": "", "desc": "Acquisition Date"}, {"tag1": "(0008,0023)", "vr": "DA", "value": "20140829", "tag2": "", "desc": "Content Date"}, {"tag1": "(0008,0030)", "vr": "TM", "value": "115822.000000", "tag2": "", "desc": "Study Time"}, {"tag1": "(0008,0031)", "vr": "TM", "value": "115954", "tag2": "", "desc": "Series Time"}, {"tag1": "(0008,0032)", "vr": "TM", "value": "115954", "tag2": "", "desc": "Acquisition Time"}, {"tag1": "(0008,0033)", "vr": "TM", "value": "115954", "tag2": "", "desc": "Content Time"}, {"tag1": "(0008,0050)", "vr": "SH", "value": "", "tag2": "", "desc": "Accession Number"}, {"tag1": "(0008,0060)", "vr": "CS", "value": "MR", "tag2": "", "desc": "Modality"}, {"tag1": "(0008,0070)", "vr": "LO", "value": "GE MEDICAL SYSTEMS", "tag2": "", "desc": "Manufacturer"}, {"tag1": "(0008,0090)", "vr": "PN", "value": "", "tag2": "", "desc": "Referring Physician’s Name"}, {"tag1": "(0008,1010)", "vr": "SH", "value": "NHFEMR07", "tag2": "", "desc": "Station Name"}, {"tag1": "(0008,1030)", "vr": "LO", "value": "MRI_Head", "tag2": "", "desc": "Study Description"}, {"tag1": "(0008,1032)", "vr": "SQ", "value": "", "tag2": "(0008,1032)", "desc": "Procedure Code Sequence"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "904001_RM111", "tag2": "(0008,0100)", "desc": "Code Value"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "GEIIS", "tag2": "(0008,0102)", "desc": "Coding Scheme Designator"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "0", "tag2": "(0008,0103)", "desc": "Coding Scheme Version"}, {"tag1": "(0008,1032)", "vr": "LO", "value": "RM111 - RM CEREBRAL", "tag2": "(0008,0104)", "desc": "Code Meaning"}, {"tag1": "(0008,103E)", "vr": "LO", "value": "sag3dt1", "tag2": "", "desc": "Series Description"}, {"tag1": "(0008,1090)", "vr": "LO", "value": "Signa HDxt", "tag2": "", "desc": "Manufacturer’s Model Name"}, {"tag1": "(0008,1110)", "vr": "SQ", "value": "", "tag2": "(0008,1110)", "desc": "Referenced Study Sequence"}, {"tag1": "(0008,1110)", "vr": "UI", "value": "1.2.840.10008.3.1.2.3.1", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1110)", "vr": "UI", "value": "1.2.124.113532.12.10529.61843.20140828.125803.45246674", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1111)", "vr": "SQ", "value": "", "tag2": "(0008,1111)", "desc": "Referenced Performed Procedure Step Sequence"}, {"tag1": "(0008,1111)", "vr": "UI", "value": "1.2.840.10008.3.1.2.3.3", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1111)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.12137.1409292383.190", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.11490.1409292832.391", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.11490.1409292832.388", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.11490.1409292832.384", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0009,0010)", "vr": "LO", "value": "GEMS_IDEN_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0009,0011)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0010,0010)", "vr": "PN", "value": "228068469937235231595795351598802870893", "tag2": "", "desc": "Patient’s Name"}, {"tag1": "(0010,0020)", "vr": "LO", "value": "280497372964350258462589225688693110743", "tag2": "", "desc": "Patient ID"}, {"tag1": "(0010,0030)", "vr": "DA", "value": "20060103", "tag2": "", "desc": "Patient’s Birth Date"}, {"tag1": "(0010,0040)", "vr": "CS", "value": "M", "tag2": "", "desc": "Patient’s Sex"}, {"tag1": "(0010,1010)", "vr": "AS", "value": "008Y", "tag2": "", "desc": "Patient’s Age"}, {"tag1": "(0010,1030)", "vr": "DS", "value": "42", "tag2": "", "desc": "Patient’s Weight"}, {"tag1": "(0010,21B0)", "vr": "LT", "value": "", "tag2": "", "desc": "Additional Patient History"}, {"tag1": "(0018,0020)", "vr": "CS", "value": "GR", "tag2": "", "desc": "Scanning Sequence"}, {"tag1": "(0018,0021)", "vr": "CS", "value": "SS\\SK", "tag2": "", "desc": "Sequence Variant"}, {"tag1": "(0018,0022)", "vr": "CS", "value": "FAST_GEMS\\EDR_GEMS\\FILTERED_GEMS\\ACC_GEMS", "tag2": "", "desc": "Scan Options"}, {"tag1": "(0018,0023)", "vr": "CS", "value": "3D", "tag2": "", "desc": "MR Acquisition Type"}, {"tag1": "(0018,0025)", "vr": "CS", "value": "N", "tag2": "", "desc": "Angio Flag"}, {"tag1": "(0018,0050)", "vr": "DS", "value": "1.2", "tag2": "", "desc": "Slice Thickness"}, {"tag1": "(0018,0080)", "vr": "DS", "value": "8.216", "tag2": "", "desc": "Repetition Time"}, {"tag1": "(0018,0081)", "vr": "DS", "value": "3.136", "tag2": "", "desc": "Echo Time"}, {"tag1": "(0018,0082)", "vr": "DS", "value": "450", "tag2": "", "desc": "Inversion Time"}, {"tag1": "(0018,0083)", "vr": "DS", "value": "1", "tag2": "", "desc": "Number of Averages"}, {"tag1": "(0018,0084)", "vr": "DS", "value": "63.832227", "tag2": "", "desc": "Imaging Frequency"}, {"tag1": "(0018,0085)", "vr": "SH", "value": "1H", "tag2": "", "desc": "Imaged Nucleus"}, {"tag1": "(0018,0086)", "vr": "IS", "value": "1", "tag2": "", "desc": "Echo Number(s)"}, {"tag1": "(0018,0087)", "vr": "DS", "value": "1.5", "tag2": "", "desc": "Magnetic Field Strength"}, {"tag1": "(0018,0088)", "vr": "DS", "value": "0.600002", "tag2": "", "desc": "Spacing Between Slices"}, {"tag1": "(0018,0091)", "vr": "IS", "value": "1", "tag2": "", "desc": "Echo Train Length"}, {"tag1": "(0018,0093)", "vr": "DS", "value": "100", "tag2": "", "desc": "Percent Sampling"}, {"tag1": "(0018,0094)", "vr": "DS", "value": "90", "tag2": "", "desc": "Percent Phase Field of View"}, {"tag1": "(0018,0095)", "vr": "DS", "value": "122.07", "tag2": "", "desc": "Pixel Bandwidth"}, {"tag1": "(0018,1000)", "vr": "LO", "value": "00000000NPV84504", "tag2": "", "desc": "Device Serial Number"}, {"tag1": "(0018,1020)", "vr": "LO", "value": "15\\LX\\MR Software release:15.0_M4B_1034.a", "tag2": "", "desc": "Software Version(s)"}, {"tag1": "(0018,1030)", "vr": "LO", "value": "NFCEREBRAL20123", "tag2": "", "desc": "Protocol Name"}, {"tag1": "(0018,1088)", "vr": "IS", "value": "0", "tag2": "", "desc": "Heart Rate"}, {"tag1": "(0018,1090)", "vr": "IS", "value": "0", "tag2": "", "desc": "Cardiac Number of Images"}, {"tag1": "(0018,1094)", "vr": "IS", "value": "0", "tag2": "", "desc": "Trigger Window"}, {"tag1": "(0018,1100)", "vr": "DS", "value": "260", "tag2": "", "desc": "Reconstruction Diameter"}, {"tag1": "(0018,1250)", "vr": "SH", "value": "8HRBRAIN", "tag2": "", "desc": "Receive Coil Name"}, {"tag1": "(0018,1310)", "vr": "US", "value": "0\\256\\256\\0", "tag2": "", "desc": "Acquisition Matrix"}, {"tag1": "(0018,1312)", "vr": "CS", "value": "ROW", "tag2": "", "desc": "In-plane Phase Encoding Direction"}, {"tag1": "(0018,1314)", "vr": "DS", "value": "13", "tag2": "", "desc": "Flip Angle"}, {"tag1": "(0018,1315)", "vr": "CS", "value": "N", "tag2": "", "desc": "Variable Flip Angle Flag"}, {"tag1": "(0018,1316)", "vr": "DS", "value": "0.0815411", "tag2": "", "desc": "SAR"}, {"tag1": "(0018,5100)", "vr": "CS", "value": "HFS", "tag2": "", "desc": "Patient Position"}, {"tag1": "(0019,0010)", "vr": "LO", "value": "GEMS_ACQU_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0019,10BB)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10BC)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10BD)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10D9)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10DF)", "vr": "UN", "value": "100.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10E0)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0020,000D)", "vr": "UI", "value": "1.2.124.113532.12.10529.61843.20140828.125803.45246674", "tag2": "", "desc": "Study Instance UID"}, {"tag1": "(0020,000E)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.12137.1409292383.194", "tag2": "", "desc": "Series Instance UID"}, {"tag1": "(0020,0010)", "vr": "SH", "value": "", "tag2": "", "desc": "Study ID"}, {"tag1": "(0020,0011)", "vr": "IS", "value": "3", "tag2": "", "desc": "Series Number"}, {"tag1": "(0020,0012)", "vr": "IS", "value": "1", "tag2": "", "desc": "Acquisition Number"}, {"tag1": "(0020,0013)", "vr": "IS", "value": "224", "tag2": "", "desc": "Instance Number"}, {"tag1": "(0020,0032)", "vr": "DS", "value": "-60.0033\\-154.088\\162.919", "tag2": "", "desc": "Image Position (Patient)"}, {"tag1": "(0020,0037)", "vr": "DS", "value": "-0\\1\\0\\-0\\-0\\-1", "tag2": "", "desc": "Image Orientation (Patient)"}, {"tag1": "(0020,0052)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.12137.1409292383.192", "tag2": "", "desc": "Frame of Reference UID"}, {"tag1": "(0020,0060)", "vr": "CS", "value": "", "tag2": "", "desc": "Laterality"}, {"tag1": "(0020,1002)", "vr": "IS", "value": "248", "tag2": "", "desc": "Images in Acquisition"}, {"tag1": "(0020,1040)", "vr": "LO", "value": "", "tag2": "", "desc": "Position Reference Indicator"}, {"tag1": "(0020,1041)", "vr": "DS", "value": "60.0032692", "tag2": "", "desc": "Slice Location"}, {"tag1": "(0020,9056)", "vr": "SH", "value": "1", "tag2": "", "desc": "Stack ID"}, {"tag1": "(0020,9057)", "vr": "UL", "value": "114", "tag2": "", "desc": "In-Stack Position Number"}, {"tag1": "(0021,0010)", "vr": "LO", "value": "GEMS_RELA_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0021,105A)", "vr": "UN", "value": "\\00\\00\\00\\00", "tag2": "", "desc": "?"}, {"tag1": "(0023,0010)", "vr": "LO", "value": "GEMS_STDY_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0025,0010)", "vr": "LO", "value": "GEMS_SERS_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0027,0010)", "vr": "LO", "value": "GEMS_IMAG_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0028,0002)", "vr": "US", "value": "1", "tag2": "", "desc": "Samples per Pixel"}, {"tag1": "(0028,0004)", "vr": "CS", "value": "MONOCHROME2", "tag2": "", "desc": "Photometric Interpretation"}, {"tag1": "(0028,0010)", "vr": "US", "value": "512", "tag2": "", "desc": "Rows"}, {"tag1": "(0028,0011)", "vr": "US", "value": "512", "tag2": "", "desc": "Columns"}, {"tag1": "(0028,0030)", "vr": "DS", "value": "0.5078\\0.5078", "tag2": "", "desc": "Pixel Spacing"}, {"tag1": "(0028,0100)", "vr": "US", "value": "16", "tag2": "", "desc": "Bits Allocated"}, {"tag1": "(0028,0101)", "vr": "US", "value": "16", "tag2": "", "desc": "Bits Stored"}, {"tag1": "(0028,0102)", "vr": "US", "value": "15", "tag2": "", "desc": "High Bit"}, {"tag1": "(0028,0103)", "vr": "US", "value": "1", "tag2": "", "desc": "Pixel Representation"}, {"tag1": "(0028,0106)", "vr": "US", "value": "0", "tag2": "", "desc": "Smallest Image Pixel Value"}, {"tag1": "(0028,0107)", "vr": "US", "value": "4807", "tag2": "", "desc": "Largest Image Pixel Value"}, {"tag1": "(0028,0303)", "vr": "CS", "value": "", "tag2": "", "desc": "Longitudinal Temporal Information Modified"}, {"tag1": "(0028,1050)", "vr": "DS", "value": "2403", "tag2": "", "desc": "Window Center"}, {"tag1": "(0028,1051)", "vr": "DS", "value": "4807", "tag2": "", "desc": "Window Width"}, {"tag1": "(0029,0010)", "vr": "LO", "value": "GEMS_IMPS_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0031,0010)", "vr": "LO", "value": "MITRA LINKED ATTRIBUTES 1.0", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0031,0011)", "vr": "LO", "value": "AGFA PACS Archive Mirroring 1.0", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0032,000A)", "vr": "CS", "value": "READ", "tag2": "", "desc": "Study Status ID"}, {"tag1": "(0033,0010)", "vr": "LO", "value": "MITRA OBJECT UTF8 ATTRIBUTES 1.0", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0040,0244)", "vr": "DA", "value": "20140829", "tag2": "", "desc": "Performed Procedure Step Start Date"}, {"tag1": "(0040,0245)", "vr": "TM", "value": "115822.000000", "tag2": "", "desc": "Performed Procedure Step Start Time"}, {"tag1": "(0040,0254)", "vr": "LO", "value": "", "tag2": "", "desc": "Performed Procedure Step Description"}, {"tag1": "(0043,0010)", "vr": "LO", "value": "GEMS_PARM_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0043,1039)", "vr": "UN", "value": "0\\\\96\\\\0\\\\0", "tag2": "", "desc": "?"}, {"tag1": "(0903,0010)", "vr": "LO", "value": "GEIIS PACS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0905,0010)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(7FD1,0010)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}] \ No newline at end of file diff --git a/data/examples/MRI_Head/sub-3/ses-1/anat/sub-3_ses-1_acq-highres_T1w.nii.gz b/data/examples/MRI_Head/sub-3/ses-1/anat/sub-3_ses-1_acq-highres_T1w.nii.gz new file mode 100644 index 0000000..d73cf9b Binary files /dev/null and b/data/examples/MRI_Head/sub-3/ses-1/anat/sub-3_ses-1_acq-highres_T1w.nii.gz differ diff --git a/data/examples/MRI_Head/sub-3/ses-1/anat/sub-3_ses-1_acq-highres_ce-GADOLINIUM_T1w.json b/data/examples/MRI_Head/sub-3/ses-1/anat/sub-3_ses-1_acq-highres_ce-GADOLINIUM_T1w.json new file mode 100644 index 0000000..4371003 --- /dev/null +++ b/data/examples/MRI_Head/sub-3/ses-1/anat/sub-3_ses-1_acq-highres_ce-GADOLINIUM_T1w.json @@ -0,0 +1 @@ +[{"tag1": "(0002,0001)", "vr": "OB", "value": "00\\01", "tag2": "", "desc": "File Meta Information Version"}, {"tag1": "(0002,0002)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "", "desc": "Media Storage SOP Class UID"}, {"tag1": "(0002,0003)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.11490.1409292833.896", "tag2": "", "desc": "Media Storage SOP Instance UID"}, {"tag1": "(0002,0010)", "vr": "UI", "value": "1.2.840.10008.1.2.1", "tag2": "", "desc": "Transfer Syntax UID"}, {"tag1": "(0002,0012)", "vr": "UI", "value": "1.2.40.0.13.1.1", "tag2": "", "desc": "Implementation Class UID"}, {"tag1": "(0002,0013)", "vr": "SH", "value": "dcm4che-2.0", "tag2": "", "desc": "Implementation Version Name"}, {"tag1": "(0002,0016)", "vr": "AE", "value": "CTP", "tag2": "", "desc": "Source Application Entity Title"}, {"tag1": "(0008,0005)", "vr": "CS", "value": "ISO_IR 100", "tag2": "", "desc": "Specific Character Set"}, {"tag1": "(0008,0008)", "vr": "CS", "value": "ORIGINAL\\PRIMARY\\OTHER", "tag2": "", "desc": "Image Type"}, {"tag1": "(0008,0016)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "", "desc": "SOP Class UID"}, {"tag1": "(0008,0018)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.11490.1409292833.896", "tag2": "", "desc": "SOP Instance UID"}, {"tag1": "(0008,0020)", "vr": "DA", "value": "20140829", "tag2": "", "desc": "Study Date"}, {"tag1": "(0008,0021)", "vr": "DA", "value": "20140829", "tag2": "", "desc": "Series Date"}, {"tag1": "(0008,0022)", "vr": "DA", "value": "20140829", "tag2": "", "desc": "Acquisition Date"}, {"tag1": "(0008,0023)", "vr": "DA", "value": "20140829", "tag2": "", "desc": "Content Date"}, {"tag1": "(0008,0030)", "vr": "TM", "value": "115822.000000", "tag2": "", "desc": "Study Time"}, {"tag1": "(0008,0031)", "vr": "TM", "value": "121544", "tag2": "", "desc": "Series Time"}, {"tag1": "(0008,0032)", "vr": "TM", "value": "121544", "tag2": "", "desc": "Acquisition Time"}, {"tag1": "(0008,0033)", "vr": "TM", "value": "121544", "tag2": "", "desc": "Content Time"}, {"tag1": "(0008,0050)", "vr": "SH", "value": "", "tag2": "", "desc": "Accession Number"}, {"tag1": "(0008,0060)", "vr": "CS", "value": "MR", "tag2": "", "desc": "Modality"}, {"tag1": "(0008,0070)", "vr": "LO", "value": "GE MEDICAL SYSTEMS", "tag2": "", "desc": "Manufacturer"}, {"tag1": "(0008,0090)", "vr": "PN", "value": "", "tag2": "", "desc": "Referring Physician’s Name"}, {"tag1": "(0008,1010)", "vr": "SH", "value": "NHFEMR07", "tag2": "", "desc": "Station Name"}, {"tag1": "(0008,1030)", "vr": "LO", "value": "MRI_Head", "tag2": "", "desc": "Study Description"}, {"tag1": "(0008,1032)", "vr": "SQ", "value": "", "tag2": "(0008,1032)", "desc": "Procedure Code Sequence"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "904001_RM111", "tag2": "(0008,0100)", "desc": "Code Value"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "GEIIS", "tag2": "(0008,0102)", "desc": "Coding Scheme Designator"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "0", "tag2": "(0008,0103)", "desc": "Coding Scheme Version"}, {"tag1": "(0008,1032)", "vr": "LO", "value": "RM111 - RM CEREBRAL", "tag2": "(0008,0104)", "desc": "Code Meaning"}, {"tag1": "(0008,103E)", "vr": "LO", "value": "AXIAL3DBRAVONAVEGADORCTE", "tag2": "", "desc": "Series Description"}, {"tag1": "(0008,1090)", "vr": "LO", "value": "Signa HDxt", "tag2": "", "desc": "Manufacturer’s Model Name"}, {"tag1": "(0008,1110)", "vr": "SQ", "value": "", "tag2": "(0008,1110)", "desc": "Referenced Study Sequence"}, {"tag1": "(0008,1110)", "vr": "UI", "value": "1.2.840.10008.3.1.2.3.1", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1110)", "vr": "UI", "value": "1.2.124.113532.12.10529.61843.20140828.125803.45246674", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1111)", "vr": "SQ", "value": "", "tag2": "(0008,1111)", "desc": "Referenced Performed Procedure Step Sequence"}, {"tag1": "(0008,1111)", "vr": "UI", "value": "1.2.840.10008.3.1.2.3.3", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1111)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.12137.1409292383.190", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.11490.1409292832.902", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.11490.1409292833.490", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.11490.1409292833.173", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0009,0010)", "vr": "LO", "value": "GEMS_IDEN_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0009,0011)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0010,0010)", "vr": "PN", "value": "228068469937235231595795351598802870893", "tag2": "", "desc": "Patient’s Name"}, {"tag1": "(0010,0020)", "vr": "LO", "value": "280497372964350258462589225688693110743", "tag2": "", "desc": "Patient ID"}, {"tag1": "(0010,0030)", "vr": "DA", "value": "20060103", "tag2": "", "desc": "Patient’s Birth Date"}, {"tag1": "(0010,0040)", "vr": "CS", "value": "M", "tag2": "", "desc": "Patient’s Sex"}, {"tag1": "(0010,1010)", "vr": "AS", "value": "008Y", "tag2": "", "desc": "Patient’s Age"}, {"tag1": "(0010,1030)", "vr": "DS", "value": "42", "tag2": "", "desc": "Patient’s Weight"}, {"tag1": "(0010,21B0)", "vr": "LT", "value": "", "tag2": "", "desc": "Additional Patient History"}, {"tag1": "(0018,0010)", "vr": "LO", "value": "", "tag2": "", "desc": "Contrast/Bolus Agent"}, {"tag1": "(0018,0020)", "vr": "CS", "value": "GR", "tag2": "", "desc": "Scanning Sequence"}, {"tag1": "(0018,0021)", "vr": "CS", "value": "SS\\SK", "tag2": "", "desc": "Sequence Variant"}, {"tag1": "(0018,0022)", "vr": "CS", "value": "FAST_GEMS\\EDR_GEMS\\FILTERED_GEMS\\ACC_GEMS", "tag2": "", "desc": "Scan Options"}, {"tag1": "(0018,0023)", "vr": "CS", "value": "3D", "tag2": "", "desc": "MR Acquisition Type"}, {"tag1": "(0018,0025)", "vr": "CS", "value": "N", "tag2": "", "desc": "Angio Flag"}, {"tag1": "(0018,0050)", "vr": "DS", "value": "1", "tag2": "", "desc": "Slice Thickness"}, {"tag1": "(0018,0080)", "vr": "DS", "value": "10.852", "tag2": "", "desc": "Repetition Time"}, {"tag1": "(0018,0081)", "vr": "DS", "value": "4.428", "tag2": "", "desc": "Echo Time"}, {"tag1": "(0018,0082)", "vr": "DS", "value": "450", "tag2": "", "desc": "Inversion Time"}, {"tag1": "(0018,0083)", "vr": "DS", "value": "1", "tag2": "", "desc": "Number of Averages"}, {"tag1": "(0018,0084)", "vr": "DS", "value": "63.832258", "tag2": "", "desc": "Imaging Frequency"}, {"tag1": "(0018,0085)", "vr": "SH", "value": "1H", "tag2": "", "desc": "Imaged Nucleus"}, {"tag1": "(0018,0086)", "vr": "IS", "value": "1", "tag2": "", "desc": "Echo Number(s)"}, {"tag1": "(0018,0087)", "vr": "DS", "value": "1.5", "tag2": "", "desc": "Magnetic Field Strength"}, {"tag1": "(0018,0088)", "vr": "DS", "value": "1", "tag2": "", "desc": "Spacing Between Slices"}, {"tag1": "(0018,0091)", "vr": "IS", "value": "1", "tag2": "", "desc": "Echo Train Length"}, {"tag1": "(0018,0093)", "vr": "DS", "value": "100", "tag2": "", "desc": "Percent Sampling"}, {"tag1": "(0018,0094)", "vr": "DS", "value": "80", "tag2": "", "desc": "Percent Phase Field of View"}, {"tag1": "(0018,0095)", "vr": "DS", "value": "97.6562", "tag2": "", "desc": "Pixel Bandwidth"}, {"tag1": "(0018,1000)", "vr": "LO", "value": "00000000NPV84504", "tag2": "", "desc": "Device Serial Number"}, {"tag1": "(0018,1020)", "vr": "LO", "value": "15\\LX\\MR Software release:15.0_M4B_1034.a", "tag2": "", "desc": "Software Version(s)"}, {"tag1": "(0018,1030)", "vr": "LO", "value": "NFCEREBRAL20128", "tag2": "", "desc": "Protocol Name"}, {"tag1": "(0018,1040)", "vr": "LO", "value": "IV", "tag2": "", "desc": "Contrast/Bolus Route"}, {"tag1": "(0018,1088)", "vr": "IS", "value": "0", "tag2": "", "desc": "Heart Rate"}, {"tag1": "(0018,1090)", "vr": "IS", "value": "0", "tag2": "", "desc": "Cardiac Number of Images"}, {"tag1": "(0018,1094)", "vr": "IS", "value": "0", "tag2": "", "desc": "Trigger Window"}, {"tag1": "(0018,1100)", "vr": "DS", "value": "240", "tag2": "", "desc": "Reconstruction Diameter"}, {"tag1": "(0018,1250)", "vr": "SH", "value": "8HRBRAIN", "tag2": "", "desc": "Receive Coil Name"}, {"tag1": "(0018,1310)", "vr": "US", "value": "0\\320\\320\\0", "tag2": "", "desc": "Acquisition Matrix"}, {"tag1": "(0018,1312)", "vr": "CS", "value": "ROW", "tag2": "", "desc": "In-plane Phase Encoding Direction"}, {"tag1": "(0018,1314)", "vr": "DS", "value": "13", "tag2": "", "desc": "Flip Angle"}, {"tag1": "(0018,1315)", "vr": "CS", "value": "N", "tag2": "", "desc": "Variable Flip Angle Flag"}, {"tag1": "(0018,1316)", "vr": "DS", "value": "0.063638", "tag2": "", "desc": "SAR"}, {"tag1": "(0018,5100)", "vr": "CS", "value": "HFS", "tag2": "", "desc": "Patient Position"}, {"tag1": "(0019,0010)", "vr": "LO", "value": "GEMS_ACQU_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0019,10BB)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10BC)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10BD)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10D9)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10DF)", "vr": "UN", "value": "100.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10E0)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0020,000D)", "vr": "UI", "value": "1.2.124.113532.12.10529.61843.20140828.125803.45246674", "tag2": "", "desc": "Study Instance UID"}, {"tag1": "(0020,000E)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.12137.1409292383.199", "tag2": "", "desc": "Series Instance UID"}, {"tag1": "(0020,0010)", "vr": "SH", "value": "", "tag2": "", "desc": "Study ID"}, {"tag1": "(0020,0011)", "vr": "IS", "value": "8", "tag2": "", "desc": "Series Number"}, {"tag1": "(0020,0012)", "vr": "IS", "value": "1", "tag2": "", "desc": "Acquisition Number"}, {"tag1": "(0020,0013)", "vr": "IS", "value": "80", "tag2": "", "desc": "Instance Number"}, {"tag1": "(0020,0032)", "vr": "DS", "value": "-116.435\\-149.15\\26.2069", "tag2": "", "desc": "Image Position (Patient)"}, {"tag1": "(0020,0037)", "vr": "DS", "value": "0.99847\\0.0455029\\-0.0314339\\-0.038759\\0.981123\\0.189462", "tag2": "", "desc": "Image Orientation (Patient)"}, {"tag1": "(0020,0052)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.12137.1409292383.192", "tag2": "", "desc": "Frame of Reference UID"}, {"tag1": "(0020,0060)", "vr": "CS", "value": "", "tag2": "", "desc": "Laterality"}, {"tag1": "(0020,1002)", "vr": "IS", "value": "184", "tag2": "", "desc": "Images in Acquisition"}, {"tag1": "(0020,1040)", "vr": "LO", "value": "", "tag2": "", "desc": "Position Reference Indicator"}, {"tag1": "(0020,1041)", "vr": "DS", "value": "45.13284302", "tag2": "", "desc": "Slice Location"}, {"tag1": "(0020,9056)", "vr": "SH", "value": "1", "tag2": "", "desc": "Stack ID"}, {"tag1": "(0020,9057)", "vr": "UL", "value": "82", "tag2": "", "desc": "In-Stack Position Number"}, {"tag1": "(0021,0010)", "vr": "LO", "value": "GEMS_RELA_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0021,105A)", "vr": "UN", "value": "\\00\\00\\00\\00", "tag2": "", "desc": "?"}, {"tag1": "(0023,0010)", "vr": "LO", "value": "GEMS_STDY_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0025,0010)", "vr": "LO", "value": "GEMS_SERS_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0027,0010)", "vr": "LO", "value": "GEMS_IMAG_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0028,0002)", "vr": "US", "value": "1", "tag2": "", "desc": "Samples per Pixel"}, {"tag1": "(0028,0004)", "vr": "CS", "value": "MONOCHROME2", "tag2": "", "desc": "Photometric Interpretation"}, {"tag1": "(0028,0010)", "vr": "US", "value": "512", "tag2": "", "desc": "Rows"}, {"tag1": "(0028,0011)", "vr": "US", "value": "512", "tag2": "", "desc": "Columns"}, {"tag1": "(0028,0030)", "vr": "DS", "value": "0.4688\\0.4688", "tag2": "", "desc": "Pixel Spacing"}, {"tag1": "(0028,0100)", "vr": "US", "value": "16", "tag2": "", "desc": "Bits Allocated"}, {"tag1": "(0028,0101)", "vr": "US", "value": "16", "tag2": "", "desc": "Bits Stored"}, {"tag1": "(0028,0102)", "vr": "US", "value": "15", "tag2": "", "desc": "High Bit"}, {"tag1": "(0028,0103)", "vr": "US", "value": "1", "tag2": "", "desc": "Pixel Representation"}, {"tag1": "(0028,0106)", "vr": "US", "value": "0", "tag2": "", "desc": "Smallest Image Pixel Value"}, {"tag1": "(0028,0107)", "vr": "US", "value": "7083", "tag2": "", "desc": "Largest Image Pixel Value"}, {"tag1": "(0028,0303)", "vr": "CS", "value": "", "tag2": "", "desc": "Longitudinal Temporal Information Modified"}, {"tag1": "(0028,1050)", "vr": "DS", "value": "3541", "tag2": "", "desc": "Window Center"}, {"tag1": "(0028,1051)", "vr": "DS", "value": "7083", "tag2": "", "desc": "Window Width"}, {"tag1": "(0029,0010)", "vr": "LO", "value": "GEMS_IMPS_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0031,0010)", "vr": "LO", "value": "MITRA LINKED ATTRIBUTES 1.0", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0031,0011)", "vr": "LO", "value": "AGFA PACS Archive Mirroring 1.0", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0032,000A)", "vr": "CS", "value": "READ", "tag2": "", "desc": "Study Status ID"}, {"tag1": "(0033,0010)", "vr": "LO", "value": "MITRA OBJECT UTF8 ATTRIBUTES 1.0", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0040,0244)", "vr": "DA", "value": "20140829", "tag2": "", "desc": "Performed Procedure Step Start Date"}, {"tag1": "(0040,0245)", "vr": "TM", "value": "115822.000000", "tag2": "", "desc": "Performed Procedure Step Start Time"}, {"tag1": "(0040,0254)", "vr": "LO", "value": "", "tag2": "", "desc": "Performed Procedure Step Description"}, {"tag1": "(0043,0010)", "vr": "LO", "value": "GEMS_PARM_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0043,1039)", "vr": "UN", "value": "0\\\\32\\\\0\\\\0", "tag2": "", "desc": "?"}, {"tag1": "(0903,0010)", "vr": "LO", "value": "GEIIS PACS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0905,0010)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(7FD1,0010)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}] \ No newline at end of file diff --git a/data/examples/MRI_Head/sub-3/ses-1/anat/sub-3_ses-1_acq-highres_ce-GADOLINIUM_T1w.nii.gz b/data/examples/MRI_Head/sub-3/ses-1/anat/sub-3_ses-1_acq-highres_ce-GADOLINIUM_T1w.nii.gz new file mode 100644 index 0000000..ee46ca1 Binary files /dev/null and b/data/examples/MRI_Head/sub-3/ses-1/anat/sub-3_ses-1_acq-highres_ce-GADOLINIUM_T1w.nii.gz differ diff --git a/data/examples/MRI_Head/sub-3/ses-1/dwi/sub-3_ses-1_acq-b1000_dwi.bval b/data/examples/MRI_Head/sub-3/ses-1/dwi/sub-3_ses-1_acq-b1000_dwi.bval new file mode 100644 index 0000000..a72be1b --- /dev/null +++ b/data/examples/MRI_Head/sub-3/ses-1/dwi/sub-3_ses-1_acq-b1000_dwi.bval @@ -0,0 +1 @@ +1000 0 diff --git a/data/examples/MRI_Head/sub-3/ses-1/dwi/sub-3_ses-1_acq-b1000_dwi.bvec b/data/examples/MRI_Head/sub-3/ses-1/dwi/sub-3_ses-1_acq-b1000_dwi.bvec new file mode 100644 index 0000000..41c02d7 --- /dev/null +++ b/data/examples/MRI_Head/sub-3/ses-1/dwi/sub-3_ses-1_acq-b1000_dwi.bvec @@ -0,0 +1,3 @@ +0 0 +0 0 +0 0 diff --git a/data/examples/MRI_Head/sub-3/ses-1/dwi/sub-3_ses-1_acq-b1000_dwi.json b/data/examples/MRI_Head/sub-3/ses-1/dwi/sub-3_ses-1_acq-b1000_dwi.json new file mode 100644 index 0000000..5ffaf0f --- /dev/null +++ b/data/examples/MRI_Head/sub-3/ses-1/dwi/sub-3_ses-1_acq-b1000_dwi.json @@ -0,0 +1 @@ +[{"tag1": "(0002,0001)", "vr": "OB", "value": "00\\01", "tag2": "", "desc": "File Meta Information Version"}, {"tag1": "(0002,0002)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "", "desc": "Media Storage SOP Class UID"}, {"tag1": "(0002,0003)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.11490.1409292833.681", "tag2": "", "desc": "Media Storage SOP Instance UID"}, {"tag1": "(0002,0010)", "vr": "UI", "value": "1.2.840.10008.1.2.1", "tag2": "", "desc": "Transfer Syntax UID"}, {"tag1": "(0002,0012)", "vr": "UI", "value": "1.2.40.0.13.1.1", "tag2": "", "desc": "Implementation Class UID"}, {"tag1": "(0002,0013)", "vr": "SH", "value": "dcm4che-2.0", "tag2": "", "desc": "Implementation Version Name"}, {"tag1": "(0002,0016)", "vr": "AE", "value": "CTP", "tag2": "", "desc": "Source Application Entity Title"}, {"tag1": "(0008,0005)", "vr": "CS", "value": "ISO_IR 100", "tag2": "", "desc": "Specific Character Set"}, {"tag1": "(0008,0008)", "vr": "CS", "value": "ORIGINAL\\PRIMARY\\OTHER", "tag2": "", "desc": "Image Type"}, {"tag1": "(0008,0016)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "", "desc": "SOP Class UID"}, {"tag1": "(0008,0018)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.11490.1409292833.681", "tag2": "", "desc": "SOP Instance UID"}, {"tag1": "(0008,0020)", "vr": "DA", "value": "20140829", "tag2": "", "desc": "Study Date"}, {"tag1": "(0008,0021)", "vr": "DA", "value": "20140829", "tag2": "", "desc": "Series Date"}, {"tag1": "(0008,0022)", "vr": "DA", "value": "20140829", "tag2": "", "desc": "Acquisition Date"}, {"tag1": "(0008,0023)", "vr": "DA", "value": "20140829", "tag2": "", "desc": "Content Date"}, {"tag1": "(0008,0030)", "vr": "TM", "value": "115822.000000", "tag2": "", "desc": "Study Time"}, {"tag1": "(0008,0031)", "vr": "TM", "value": "121110", "tag2": "", "desc": "Series Time"}, {"tag1": "(0008,0032)", "vr": "TM", "value": "121110", "tag2": "", "desc": "Acquisition Time"}, {"tag1": "(0008,0033)", "vr": "TM", "value": "121110", "tag2": "", "desc": "Content Time"}, {"tag1": "(0008,0050)", "vr": "SH", "value": "", "tag2": "", "desc": "Accession Number"}, {"tag1": "(0008,0060)", "vr": "CS", "value": "MR", "tag2": "", "desc": "Modality"}, {"tag1": "(0008,0070)", "vr": "LO", "value": "GE MEDICAL SYSTEMS", "tag2": "", "desc": "Manufacturer"}, {"tag1": "(0008,0090)", "vr": "PN", "value": "", "tag2": "", "desc": "Referring Physician’s Name"}, {"tag1": "(0008,1010)", "vr": "SH", "value": "NHFEMR07", "tag2": "", "desc": "Station Name"}, {"tag1": "(0008,1030)", "vr": "LO", "value": "MRI_Head", "tag2": "", "desc": "Study Description"}, {"tag1": "(0008,1032)", "vr": "SQ", "value": "", "tag2": "(0008,1032)", "desc": "Procedure Code Sequence"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "904001_RM111", "tag2": "(0008,0100)", "desc": "Code Value"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "GEIIS", "tag2": "(0008,0102)", "desc": "Coding Scheme Designator"}, {"tag1": "(0008,1032)", "vr": "SH", "value": "0", "tag2": "(0008,0103)", "desc": "Coding Scheme Version"}, {"tag1": "(0008,1032)", "vr": "LO", "value": "RM111 - RM CEREBRAL", "tag2": "(0008,0104)", "desc": "Code Meaning"}, {"tag1": "(0008,103E)", "vr": "LO", "value": "OAxDWI1000b", "tag2": "", "desc": "Series Description"}, {"tag1": "(0008,1090)", "vr": "LO", "value": "Signa HDxt", "tag2": "", "desc": "Manufacturer’s Model Name"}, {"tag1": "(0008,1110)", "vr": "SQ", "value": "", "tag2": "(0008,1110)", "desc": "Referenced Study Sequence"}, {"tag1": "(0008,1110)", "vr": "UI", "value": "1.2.840.10008.3.1.2.3.1", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1110)", "vr": "UI", "value": "1.2.124.113532.12.10529.61843.20140828.125803.45246674", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1111)", "vr": "SQ", "value": "", "tag2": "(0008,1111)", "desc": "Referenced Performed Procedure Step Sequence"}, {"tag1": "(0008,1111)", "vr": "UI", "value": "1.2.840.10008.3.1.2.3.3", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1111)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.12137.1409292383.190", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.11490.1409292832.902", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0008,1140)", "vr": "SQ", "value": "", "tag2": "(0008,1140)", "desc": "Referenced Image Sequence"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.10008.5.1.4.1.1.4", "tag2": "(0008,1150)", "desc": "Referenced SOP Class UID"}, {"tag1": "(0008,1140)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.11490.1409292832.390", "tag2": "(0008,1155)", "desc": "Referenced SOP Instance UID"}, {"tag1": "(0009,0010)", "vr": "LO", "value": "GEMS_IDEN_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0009,0011)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0010,0010)", "vr": "PN", "value": "228068469937235231595795351598802870893", "tag2": "", "desc": "Patient’s Name"}, {"tag1": "(0010,0020)", "vr": "LO", "value": "280497372964350258462589225688693110743", "tag2": "", "desc": "Patient ID"}, {"tag1": "(0010,0030)", "vr": "DA", "value": "20060103", "tag2": "", "desc": "Patient’s Birth Date"}, {"tag1": "(0010,0040)", "vr": "CS", "value": "M", "tag2": "", "desc": "Patient’s Sex"}, {"tag1": "(0010,1010)", "vr": "AS", "value": "008Y", "tag2": "", "desc": "Patient’s Age"}, {"tag1": "(0010,1030)", "vr": "DS", "value": "42", "tag2": "", "desc": "Patient’s Weight"}, {"tag1": "(0010,21B0)", "vr": "LT", "value": "", "tag2": "", "desc": "Additional Patient History"}, {"tag1": "(0018,0020)", "vr": "CS", "value": "EP\\SE", "tag2": "", "desc": "Scanning Sequence"}, {"tag1": "(0018,0021)", "vr": "CS", "value": "NONE", "tag2": "", "desc": "Sequence Variant"}, {"tag1": "(0018,0022)", "vr": "CS", "value": "EPI_GEMS\\ACC_GEMS\\PFF", "tag2": "", "desc": "Scan Options"}, {"tag1": "(0018,0023)", "vr": "CS", "value": "2D", "tag2": "", "desc": "MR Acquisition Type"}, {"tag1": "(0018,0025)", "vr": "CS", "value": "N", "tag2": "", "desc": "Angio Flag"}, {"tag1": "(0018,0050)", "vr": "DS", "value": "6", "tag2": "", "desc": "Slice Thickness"}, {"tag1": "(0018,0080)", "vr": "DS", "value": "8000", "tag2": "", "desc": "Repetition Time"}, {"tag1": "(0018,0081)", "vr": "DS", "value": "99.8", "tag2": "", "desc": "Echo Time"}, {"tag1": "(0018,0082)", "vr": "DS", "value": "0", "tag2": "", "desc": "Inversion Time"}, {"tag1": "(0018,0083)", "vr": "DS", "value": "2", "tag2": "", "desc": "Number of Averages"}, {"tag1": "(0018,0084)", "vr": "DS", "value": "63.832258", "tag2": "", "desc": "Imaging Frequency"}, {"tag1": "(0018,0085)", "vr": "SH", "value": "1H", "tag2": "", "desc": "Imaged Nucleus"}, {"tag1": "(0018,0086)", "vr": "IS", "value": "1", "tag2": "", "desc": "Echo Number(s)"}, {"tag1": "(0018,0087)", "vr": "DS", "value": "1.5", "tag2": "", "desc": "Magnetic Field Strength"}, {"tag1": "(0018,0088)", "vr": "DS", "value": "7", "tag2": "", "desc": "Spacing Between Slices"}, {"tag1": "(0018,0091)", "vr": "IS", "value": "1", "tag2": "", "desc": "Echo Train Length"}, {"tag1": "(0018,0093)", "vr": "DS", "value": "100", "tag2": "", "desc": "Percent Sampling"}, {"tag1": "(0018,0094)", "vr": "DS", "value": "100", "tag2": "", "desc": "Percent Phase Field of View"}, {"tag1": "(0018,0095)", "vr": "DS", "value": "1953.12", "tag2": "", "desc": "Pixel Bandwidth"}, {"tag1": "(0018,1000)", "vr": "LO", "value": "00000000NPV84504", "tag2": "", "desc": "Device Serial Number"}, {"tag1": "(0018,1020)", "vr": "LO", "value": "15\\LX\\MR Software release:15.0_M4B_1034.a", "tag2": "", "desc": "Software Version(s)"}, {"tag1": "(0018,1030)", "vr": "LO", "value": "NFCEREBRAL20127", "tag2": "", "desc": "Protocol Name"}, {"tag1": "(0018,1088)", "vr": "IS", "value": "0", "tag2": "", "desc": "Heart Rate"}, {"tag1": "(0018,1090)", "vr": "IS", "value": "0", "tag2": "", "desc": "Cardiac Number of Images"}, {"tag1": "(0018,1094)", "vr": "IS", "value": "0", "tag2": "", "desc": "Trigger Window"}, {"tag1": "(0018,1100)", "vr": "DS", "value": "220", "tag2": "", "desc": "Reconstruction Diameter"}, {"tag1": "(0018,1250)", "vr": "SH", "value": "8HRBRAIN", "tag2": "", "desc": "Receive Coil Name"}, {"tag1": "(0018,1310)", "vr": "US", "value": "128\\0\\0\\128", "tag2": "", "desc": "Acquisition Matrix"}, {"tag1": "(0018,1312)", "vr": "CS", "value": "COL", "tag2": "", "desc": "In-plane Phase Encoding Direction"}, {"tag1": "(0018,1314)", "vr": "DS", "value": "90", "tag2": "", "desc": "Flip Angle"}, {"tag1": "(0018,1315)", "vr": "CS", "value": "N", "tag2": "", "desc": "Variable Flip Angle Flag"}, {"tag1": "(0018,1316)", "vr": "DS", "value": "0.128155", "tag2": "", "desc": "SAR"}, {"tag1": "(0018,5100)", "vr": "CS", "value": "HFS", "tag2": "", "desc": "Patient Position"}, {"tag1": "(0019,0010)", "vr": "LO", "value": "GEMS_ACQU_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0019,10BB)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10BC)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10BD)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10D9)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10DF)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0019,10E0)", "vr": "UN", "value": "0.000000", "tag2": "", "desc": "?"}, {"tag1": "(0020,000D)", "vr": "UI", "value": "1.2.124.113532.12.10529.61843.20140828.125803.45246674", "tag2": "", "desc": "Study Instance UID"}, {"tag1": "(0020,000E)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.12137.1409292383.198", "tag2": "", "desc": "Series Instance UID"}, {"tag1": "(0020,0010)", "vr": "SH", "value": "", "tag2": "", "desc": "Study ID"}, {"tag1": "(0020,0011)", "vr": "IS", "value": "7", "tag2": "", "desc": "Series Number"}, {"tag1": "(0020,0012)", "vr": "IS", "value": "1", "tag2": "", "desc": "Acquisition Number"}, {"tag1": "(0020,0013)", "vr": "IS", "value": "43", "tag2": "", "desc": "Instance Number"}, {"tag1": "(0020,0032)", "vr": "DS", "value": "-103.027\\-151.042\\72.4013", "tag2": "", "desc": "Image Position (Patient)"}, {"tag1": "(0020,0037)", "vr": "DS", "value": "0.998419\\0.0417801\\-0.037599\\-0.0308847\\0.966613\\0.254372", "tag2": "", "desc": "Image Orientation (Patient)"}, {"tag1": "(0020,0052)", "vr": "UI", "value": "1.2.840.113619.2.244.4120.7587258.12137.1409292383.192", "tag2": "", "desc": "Frame of Reference UID"}, {"tag1": "(0020,0060)", "vr": "CS", "value": "", "tag2": "", "desc": "Laterality"}, {"tag1": "(0020,1002)", "vr": "IS", "value": "48", "tag2": "", "desc": "Images in Acquisition"}, {"tag1": "(0020,1040)", "vr": "LO", "value": "", "tag2": "", "desc": "Position Reference Indicator"}, {"tag1": "(0020,1041)", "vr": "DS", "value": "96.15316772", "tag2": "", "desc": "Slice Location"}, {"tag1": "(0020,9056)", "vr": "SH", "value": "1", "tag2": "", "desc": "Stack ID"}, {"tag1": "(0020,9057)", "vr": "UL", "value": "19", "tag2": "", "desc": "In-Stack Position Number"}, {"tag1": "(0021,0010)", "vr": "LO", "value": "GEMS_RELA_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0021,105A)", "vr": "UN", "value": "\\07\\00\\00\\00", "tag2": "", "desc": "?"}, {"tag1": "(0023,0010)", "vr": "LO", "value": "GEMS_STDY_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0025,0010)", "vr": "LO", "value": "GEMS_SERS_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0027,0010)", "vr": "LO", "value": "GEMS_IMAG_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0028,0002)", "vr": "US", "value": "1", "tag2": "", "desc": "Samples per Pixel"}, {"tag1": "(0028,0004)", "vr": "CS", "value": "MONOCHROME2", "tag2": "", "desc": "Photometric Interpretation"}, {"tag1": "(0028,0010)", "vr": "US", "value": "256", "tag2": "", "desc": "Rows"}, {"tag1": "(0028,0011)", "vr": "US", "value": "256", "tag2": "", "desc": "Columns"}, {"tag1": "(0028,0030)", "vr": "DS", "value": "0.8594\\0.8594", "tag2": "", "desc": "Pixel Spacing"}, {"tag1": "(0028,0100)", "vr": "US", "value": "16", "tag2": "", "desc": "Bits Allocated"}, {"tag1": "(0028,0101)", "vr": "US", "value": "16", "tag2": "", "desc": "Bits Stored"}, {"tag1": "(0028,0102)", "vr": "US", "value": "15", "tag2": "", "desc": "High Bit"}, {"tag1": "(0028,0103)", "vr": "US", "value": "1", "tag2": "", "desc": "Pixel Representation"}, {"tag1": "(0028,0106)", "vr": "US", "value": "0", "tag2": "", "desc": "Smallest Image Pixel Value"}, {"tag1": "(0028,0107)", "vr": "US", "value": "2215", "tag2": "", "desc": "Largest Image Pixel Value"}, {"tag1": "(0028,0303)", "vr": "CS", "value": "", "tag2": "", "desc": "Longitudinal Temporal Information Modified"}, {"tag1": "(0028,1050)", "vr": "DS", "value": "1107", "tag2": "", "desc": "Window Center"}, {"tag1": "(0028,1051)", "vr": "DS", "value": "2215", "tag2": "", "desc": "Window Width"}, {"tag1": "(0029,0010)", "vr": "LO", "value": "GEMS_IMPS_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0031,0010)", "vr": "LO", "value": "MITRA LINKED ATTRIBUTES 1.0", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0031,0011)", "vr": "LO", "value": "AGFA PACS Archive Mirroring 1.0", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0032,000A)", "vr": "CS", "value": "READ", "tag2": "", "desc": "Study Status ID"}, {"tag1": "(0033,0010)", "vr": "LO", "value": "MITRA OBJECT UTF8 ATTRIBUTES 1.0", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0040,0244)", "vr": "DA", "value": "20140829", "tag2": "", "desc": "Performed Procedure Step Start Date"}, {"tag1": "(0040,0245)", "vr": "TM", "value": "115822.000000", "tag2": "", "desc": "Performed Procedure Step Start Time"}, {"tag1": "(0040,0254)", "vr": "LO", "value": "", "tag2": "", "desc": "Performed Procedure Step Description"}, {"tag1": "(0043,0010)", "vr": "LO", "value": "GEMS_PARM_01", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0043,1039)", "vr": "UN", "value": "0\\\\8\\\\0\\\\0 ", "tag2": "", "desc": "?"}, {"tag1": "(0903,0010)", "vr": "LO", "value": "GEIIS PACS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(0905,0010)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}, {"tag1": "(7FD1,0010)", "vr": "LO", "value": "GEIIS", "tag2": "", "desc": "Private Creator Data Element"}] \ No newline at end of file diff --git a/data/examples/MRI_Head/sub-3/ses-1/dwi/sub-3_ses-1_acq-b1000_dwi.nii.gz b/data/examples/MRI_Head/sub-3/ses-1/dwi/sub-3_ses-1_acq-b1000_dwi.nii.gz new file mode 100644 index 0000000..c18f38f Binary files /dev/null and b/data/examples/MRI_Head/sub-3/ses-1/dwi/sub-3_ses-1_acq-b1000_dwi.nii.gz differ diff --git a/data/examples/MRI_Head/sub-3/ses-1/sub-3_ses-1_scans.tsv b/data/examples/MRI_Head/sub-3/ses-1/sub-3_ses-1_scans.tsv new file mode 100644 index 0000000..ee874c5 --- /dev/null +++ b/data/examples/MRI_Head/sub-3/ses-1/sub-3_ses-1_scans.tsv @@ -0,0 +1,5 @@ +filename Manufacturer (0008,0070) Series Description (0008,103E) Manufacturer’s Model Name (0008,1090) Patient ID (0010,0020) Patient’s Sex (0010,0040) Patient’s Age (0010,1010) Patient’s Weight (0010,1030) Scanning Sequence (0018,0020) Sequence Variant (0018,0021) Scan Options (0018,0022) MR Acquisition Type (0018,0023) Slice Thickness (0018,0050) Repetition Time (0018,0080) Echo Time (0018,0081) Inversion Time (0018,0082) Imaging Frequency (0018,0084) Magnetic Field Strength (0018,0087) Manufacturer’s Model Name (0008,1090) Spacing Between Slices (0018,0088) Echo Train Length (0018,0091) Percent Sampling (0018,0093) Pixel Bandwidth (0018,0095) Flip Angle (0018,1314) Patient Position (0018,5100) Image Position (Patient) (0020,0032) Image Orientation (Patient) (0020,0037) Position Reference Indicator (0020,1040) Slice Location (0020,1041) Rows (0028,0010) Columns (0028,0011) Pixel Spacing (0028,0030) Bits Allocated (0028,0100) Number of Averages (0018,0083) Echo Number(s) (0018,0086) (0018,9461) +anat/sub-3_ses-1_T1w.nii.gz GE MEDICAL SYSTEMS sag3dt1 Signa HDxt 280497372964350258462589225688693110743 M 008Y 42 GR SS\SK FAST_GEMS\EDR_GEMS\FILTERED_GEMS\ACC_GEMS 3D 1.2 8.216 3.136 450 63.832227 1.5 Signa HDxt 0.600002 1 100 122.07 13 HFS -60.0033\-154.088\162.919 -0\1\0\-0\-0\-1 n/a 60.0032692 512 512 0.5078\0.5078 16 1 1 n/a +anat/sub-3_ses-1_acq-highres_ce-GADOLINIUM_T1w.nii.gz GE MEDICAL SYSTEMS AXIAL3DBRAVONAVEGADORCTE Signa HDxt 280497372964350258462589225688693110743 M 008Y 42 GR SS\SK FAST_GEMS\EDR_GEMS\FILTERED_GEMS\ACC_GEMS 3D 1 10.852 4.428 450 63.832258 1.5 Signa HDxt 1 1 100 97.6562 13 HFS -116.435\-149.15\26.2069 0.99847\0.0455029\-0.0314339\-0.038759\0.981123\0.189462 n/a 45.13284302 512 512 0.4688\0.4688 16 1 1 n/a +anat/sub-3_ses-1_acq-highres_T1w.nii.gz GE MEDICAL SYSTEMS SagT1MEMP Signa HDxt 280497372964350258462589225688693110743 M 008Y 42 RM n/a FILTERED_GEMS 2D 5 520 16 0 63.832258 1.5 Signa HDxt 6.5 1 100 57.4609 70 HFS 21.2763\-144.929\158.012 -0.0827058\0.996193\0.0275584\-0.0270703\0.0253917\-0.999311 n/a -8.129069328 512 512 0.4688\0.4688 16 1 1 n/a +dwi/sub-3_ses-1_acq-b1000_bp-head_vp-ax_dwi.nii.gz GE MEDICAL SYSTEMS OAxDWI1000b Signa HDxt 280497372964350258462589225688693110743 M 008Y 42 EP\SE n/a EPI_GEMS\ACC_GEMS\PFF 2D 6 8000 99.8 0 63.832258 1.5 Signa HDxt 7 1 100 1953.12 90 HFS -103.027\-151.042\72.4013 0.998419\0.0417801\-0.037599\-0.0308847\0.966613\0.254372 n/a 96.15316772 256 256 0.8594\0.8594 16 2 1 n/a diff --git a/data/examples/MRI_Lumbar/CHANGES.txt b/data/examples/MRI_Lumbar/CHANGES.txt new file mode 100644 index 0000000..b49c10f --- /dev/null +++ b/data/examples/MRI_Lumbar/CHANGES.txt @@ -0,0 +1,12 @@ +1.0.1 2018-05-03 + - Derivatives of the disk degradation characteristics are included. +1.0.1 2017-08-27 + - DICOM information. +1.0.0 2016-05-26 + - Initial release. + +AUTHOR + - Jhon Jairo Sáenz Gamboa + +COPYRIGHT AND LICENSE + diff --git a/data/examples/MRI_Lumbar/README.txt b/data/examples/MRI_Lumbar/README.txt new file mode 100644 index 0000000..e69de29 diff --git a/data/examples/MRI_Lumbar/dataset_description.json b/data/examples/MRI_Lumbar/dataset_description.json new file mode 100644 index 0000000..060f0f0 --- /dev/null +++ b/data/examples/MRI_Lumbar/dataset_description.json @@ -0,0 +1,12 @@ +{ + "Name": "MRI_Lumbar", + "BIDSVersion": "1.1.0", + "MIDSVersion": "0.10.23", + "License": "CC BI 4.0", + "Authors": ["Jhon Saenz","CEIB-CSUSP"], + "Acknowledgements": "A special thanks to Jose Saborit for the help to format this data set in MIDS, to Joaquim Montell for the management of the XNAT platform, to María de la Iglesia Vayá, head of Lab. for her support; Thanks to the CEIB-CSUSP team of scientists, who developed the download, anonymization and scientific knowledge processes necessary to carry out this data set, and to the Public Health Department of Valencia for providing the data.", + "HowToAcknowledge": "Please cite this paper: ", + "Funding": ["Centre of Excellence and Technological Innovation in Bioimaging, Health Regional Ministry of Valencia and Public Health(CEIB-CSUSP), http://ceib.san.gva.es/ceib-cs", "Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), http://fisabio.san.gva.es/","Conselleria de Sanitat Universal i Salut Pública, http://www.san.gva.es"], + "ReferencesAndLinks": ["http://bimcv.cipf.es/2_projects/mids/", "http://bimcv.cipf.es/es/proyectos/midas-2/"], + "DatasetDOI": "" +} diff --git a/data/examples/MRI_Lumbar/derivatives/README.txt b/data/examples/MRI_Lumbar/derivatives/README.txt new file mode 100644 index 0000000..e69de29 diff --git a/data/examples/MRI_Lumbar/derivatives/feacturesDegradationDiscs/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-3_vp-sag_T2w.csv b/data/examples/MRI_Lumbar/derivatives/feacturesDegradationDiscs/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-3_vp-sag_T2w.csv new file mode 100644 index 0000000..1c11504 --- /dev/null +++ b/data/examples/MRI_Lumbar/derivatives/feacturesDegradationDiscs/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-3_vp-sag_T2w.csv @@ -0,0 +1,16 @@ +user disc pfirrman Disc Narrowing Spondylolisthesis Stenosis Endplate Defects Disc Prolapse Modic Types Information +researcher01 L1-L2 2 1 0 0 0 0 0 TEST +researcher01 L2-L3 3 1 0 0 0 0 0 +researcher01 L3-L4 1 1 0 0 0 0 0 +researcher01 L4-L5 1 3 0 0 1 1 2 +researcher01 L5-S1 1 1 1 1 0 0 0 +researcher02 L1-L2 2 2 1 1 1 1 2 +researcher02 L2-L3 3 3 1 1 1 2 2 +researcher02 L3-L4 4 3 1 1 1 2 3 +researcher02 L4-L5 3 4 1 1 1 2 2 +researcher02 L5-S1 4 3 1 1 1 2 2 +researcher03 L1-L2 3 3 1 1 1 0 0 +researcher03 L2-L3 4 3 0 0 0 0 0 +researcher03 L3-L4 3 3 1 0 0 0 0 +researcher03 L4-L5 3 2 0 0 0 0 0 +researcher03 L5-S1 3 4 1 1 1 2 2 diff --git a/data/examples/MRI_Lumbar/derivatives/feacturesDegradationDiscs/sub-2/ses-1/anat/sub-2_ses-1_bp-lsspine_acq-1_run-3_vp-sag_T2w.csv b/data/examples/MRI_Lumbar/derivatives/feacturesDegradationDiscs/sub-2/ses-1/anat/sub-2_ses-1_bp-lsspine_acq-1_run-3_vp-sag_T2w.csv new file mode 100644 index 0000000..4a0b003 --- /dev/null +++ b/data/examples/MRI_Lumbar/derivatives/feacturesDegradationDiscs/sub-2/ses-1/anat/sub-2_ses-1_bp-lsspine_acq-1_run-3_vp-sag_T2w.csv @@ -0,0 +1,16 @@ +user disc pfirrman Disc Narrowing Spondylolisthesis Stenosis Endplate Defects Disc Prolapse Modic Types Information +researcher01 L1-L2 1 1 0 0 0 0 0 +researcher01 L2-L3 1 1 0 0 0 0 0 +researcher01 L3-L4 1 1 0 0 0 0 0 +researcher01 L4-L5 1 1 0 0 0 0 0 +researcher01 L5-S1 1 1 0 0 0 0 0 +researcher02 L1-L2 3 1 0 0 0 0 0 +researcher02 L2-L3 1 3 0 0 0 2 2 test 1 +researcher02 L3-L4 5 1 0 0 0 0 0 +researcher02 L4-L5 5 3 0 0 0 0 0 test 1 +researcher02 L5-S1 1 3 1 1 1 0 3 +researcher03 L1-L2 1 1 0 1 0 0 0 test 1 +researcher03 L2-L3 5 1 0 0 0 0 3 +researcher03 L3-L4 3 4 1 0 0 2 3 test 1 +researcher03 L4-L5 1 1 0 0 1 2 0 +researcher03 L5-S1 4 3 0 0 0 0 0 test 1 diff --git a/data/examples/MRI_Lumbar/participants.tsv b/data/examples/MRI_Lumbar/participants.tsv new file mode 100644 index 0000000..9341844 --- /dev/null +++ b/data/examples/MRI_Lumbar/participants.tsv @@ -0,0 +1,3 @@ +participant_id age gender control +sub-1 46 F 1 +sub-2 19 F 1 \ No newline at end of file diff --git a/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-1_vp-sag_T1w.json b/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-1_vp-sag_T1w.json new file mode 100644 index 0000000..8f67a2f --- /dev/null +++ b/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-1_vp-sag_T1w.json @@ -0,0 +1,881 @@ +{ + "ResultSet": { + "Result": [ + { + "desc": "File Meta Information Version", + "tag1": "(0002,0001)", + "tag2": "", + "value": "00\\01", + "vr": "OB" + }, + { + "desc": "Media Storage SOP Class UID", + "tag1": "(0002,0002)", + "tag2": "", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Media Storage SOP Instance UID", + "tag1": "(0002,0003)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.9125.1458715748.175", + "vr": "UI" + }, + { + "desc": "Transfer Syntax UID", + "tag1": "(0002,0010)", + "tag2": "", + "value": "1.2.840.10008.1.2.1", + "vr": "UI" + }, + { + "desc": "Implementation Class UID", + "tag1": "(0002,0012)", + "tag2": "", + "value": "1.2.40.0.13.1.1", + "vr": "UI" + }, + { + "desc": "Implementation Version Name", + "tag1": "(0002,0013)", + "tag2": "", + "value": "dcm4che-2.0", + "vr": "SH" + }, + { + "desc": "Source Application Entity Title", + "tag1": "(0002,0016)", + "tag2": "", + "value": "CTP", + "vr": "AE" + }, + { + "desc": "Specific Character Set", + "tag1": "(0008,0005)", + "tag2": "", + "value": "ISO_IR 100", + "vr": "CS" + }, + { + "desc": "Image Type", + "tag1": "(0008,0008)", + "tag2": "", + "value": "ORIGINAL\\PRIMARY\\OTHER", + "vr": "CS" + }, + { + "desc": "SOP Class UID", + "tag1": "(0008,0016)", + "tag2": "", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "SOP Instance UID", + "tag1": "(0008,0018)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.9125.1458715748.175", + "vr": "UI" + }, + { + "desc": "Study Date", + "tag1": "(0008,0020)", + "tag2": "", + "value": "20160323", + "vr": "DA" + }, + { + "desc": "Series Date", + "tag1": "(0008,0021)", + "tag2": "", + "value": "20160323", + "vr": "DA" + }, + { + "desc": "Acquisition Date", + "tag1": "(0008,0022)", + "tag2": "", + "value": "20160323", + "vr": "DA" + }, + { + "desc": "Content Date", + "tag1": "(0008,0023)", + "tag2": "", + "value": "20160323", + "vr": "DA" + }, + { + "desc": "Study Time", + "tag1": "(0008,0030)", + "tag2": "", + "value": "074907", + "vr": "TM" + }, + { + "desc": "Series Time", + "tag1": "(0008,0031)", + "tag2": "", + "value": "075322", + "vr": "TM" + }, + { + "desc": "Acquisition Time", + "tag1": "(0008,0032)", + "tag2": "", + "value": "075322", + "vr": "TM" + }, + { + "desc": "Content Time", + "tag1": "(0008,0033)", + "tag2": "", + "value": "075322", + "vr": "TM" + }, + { + "desc": "Accession Number", + "tag1": "(0008,0050)", + "tag2": "", + "value": "ceibcs_E19219", + "vr": "SH" + }, + { + "desc": "Modality", + "tag1": "(0008,0060)", + "tag2": "", + "value": "MR", + "vr": "CS" + }, + { + "desc": "Manufacturer", + "tag1": "(0008,0070)", + "tag2": "", + "value": "GE MEDICAL SYSTEMS", + "vr": "LO" + }, + { + "desc": "Referring Physician's Name", + "tag1": "(0008,0090)", + "tag2": "", + "value": "", + "vr": "PN" + }, + { + "desc": "Station Name", + "tag1": "(0008,1010)", + "tag2": "", + "value": "CASTMRI", + "vr": "SH" + }, + { + "desc": "Study Description", + "tag1": "(0008,1030)", + "tag2": "", + "value": "MRI_Lumbar", + "vr": "LO" + }, + { + "desc": "Procedure Code Sequence", + "tag1": "(0008,1032)", + "tag2": "(0008,1032)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Code Value", + "tag1": "(0008,1032)", + "tag2": "(0008,0100)", + "value": "015001_RM502", + "vr": "SH" + }, + { + "desc": "Coding Scheme Designator", + "tag1": "(0008,1032)", + "tag2": "(0008,0102)", + "value": "GEIIS", + "vr": "SH" + }, + { + "desc": "Coding Scheme Version", + "tag1": "(0008,1032)", + "tag2": "(0008,0103)", + "value": "0", + "vr": "SH" + }, + { + "desc": "Code Meaning", + "tag1": "(0008,1032)", + "tag2": "(0008,0104)", + "value": "RM COLUMNA LUMBAR", + "vr": "LO" + }, + { + "desc": "Series Description", + "tag1": "(0008,103E)", + "tag2": "", + "value": "SAGT1LUMBAR", + "vr": "LO" + }, + { + "desc": "Manufacturer's Model Name", + "tag1": "(0008,1090)", + "tag2": "", + "value": "SIGNA EXCITE", + "vr": "LO" + }, + { + "desc": "Referenced Image Sequence", + "tag1": "(0008,1140)", + "tag2": "(0008,1140)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Referenced SOP Class UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1150)", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Referenced SOP Instance UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1155)", + "value": "1.2.840.113619.2.222.2025.1616754.9125.1458715748.26", + "vr": "UI" + }, + { + "desc": "Referenced Image Sequence", + "tag1": "(0008,1140)", + "tag2": "(0008,1140)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Referenced SOP Class UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1150)", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Referenced SOP Instance UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1155)", + "value": "1.2.840.113619.2.222.2025.1616754.9125.1458715748.19", + "vr": "UI" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0009,0010)", + "tag2": "", + "value": "GEMS_IDEN_01", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0009,0011)", + "tag2": "", + "value": "GEIIS", + "vr": "LO" + }, + { + "desc": "Patient's Name", + "tag1": "(0010,0010)", + "tag2": "", + "value": "213117108914127596262799978540518347712", + "vr": "PN" + }, + { + "desc": "Patient ID", + "tag1": "(0010,0020)", + "tag2": "", + "value": "171834704726005099248999303401096937503", + "vr": "LO" + }, + { + "desc": "Patient's Birth Date", + "tag1": "(0010,0030)", + "tag2": "", + "value": "19690513", + "vr": "DA" + }, + { + "desc": "Patient's Sex", + "tag1": "(0010,0040)", + "tag2": "", + "value": "F", + "vr": "CS" + }, + { + "desc": "Patient's Age", + "tag1": "(0010,1010)", + "tag2": "", + "value": "046Y", + "vr": "AS" + }, + { + "desc": "Patient's Weight", + "tag1": "(0010,1030)", + "tag2": "", + "value": "72", + "vr": "DS" + }, + { + "desc": "Additional Patient History", + "tag1": "(0010,21B0)", + "tag2": "", + "value": "", + "vr": "LT" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0011,0010)", + "tag2": "", + "value": "GEMS_PATI_01", + "vr": "LO" + }, + { + "desc": "Scanning Sequence", + "tag1": "(0018,0020)", + "tag2": "", + "value": "RM", + "vr": "CS" + }, + { + "desc": "Sequence Variant", + "tag1": "(0018,0021)", + "tag2": "", + "value": "NONE", + "vr": "CS" + }, + { + "desc": "Scan Options", + "tag1": "(0018,0022)", + "tag2": "", + "value": "FC_FREQ_AX_GEMS\\FC\\SAT_GEMS\\VB_GEMS\\TRF_GEMS\\FILTERED_GEMS\\SP", + "vr": "CS" + }, + { + "desc": "MR Acquisition Type", + "tag1": "(0018,0023)", + "tag2": "", + "value": "2D", + "vr": "CS" + }, + { + "desc": "Angio Flag", + "tag1": "(0018,0025)", + "tag2": "", + "value": "N", + "vr": "CS" + }, + { + "desc": "Slice Thickness", + "tag1": "(0018,0050)", + "tag2": "", + "value": "4.5", + "vr": "DS" + }, + { + "desc": "Repetition Time", + "tag1": "(0018,0080)", + "tag2": "", + "value": "400", + "vr": "DS" + }, + { + "desc": "Echo Time", + "tag1": "(0018,0081)", + "tag2": "", + "value": "15.072", + "vr": "DS" + }, + { + "desc": "Inversion Time", + "tag1": "(0018,0082)", + "tag2": "", + "value": "0", + "vr": "DS" + }, + { + "desc": "Number of Averages", + "tag1": "(0018,0083)", + "tag2": "", + "value": "3", + "vr": "DS" + }, + { + "desc": "Imaging Frequency", + "tag1": "(0018,0084)", + "tag2": "", + "value": "63.869763", + "vr": "DS" + }, + { + "desc": "Imaged Nucleus", + "tag1": "(0018,0085)", + "tag2": "", + "value": "1H", + "vr": "SH" + }, + { + "desc": "Echo Number(s)", + "tag1": "(0018,0086)", + "tag2": "", + "value": "1", + "vr": "IS" + }, + { + "desc": "Magnetic Field Strength", + "tag1": "(0018,0087)", + "tag2": "", + "value": "1.5", + "vr": "DS" + }, + { + "desc": "Spacing Between Slices", + "tag1": "(0018,0088)", + "tag2": "", + "value": "5.5", + "vr": "DS" + }, + { + "desc": "Echo Train Length", + "tag1": "(0018,0091)", + "tag2": "", + "value": "4", + "vr": "IS" + }, + { + "desc": "Percent Sampling", + "tag1": "(0018,0093)", + "tag2": "", + "value": "100", + "vr": "DS" + }, + { + "desc": "Percent Phase Field of View", + "tag1": "(0018,0094)", + "tag2": "", + "value": "90", + "vr": "DS" + }, + { + "desc": "Pixel Bandwidth", + "tag1": "(0018,0095)", + "tag2": "", + "value": "139.492", + "vr": "DS" + }, + { + "desc": "Device Serial Number", + "tag1": "(0018,1000)", + "tag2": "", + "value": "00000000NPV24200", + "vr": "LO" + }, + { + "desc": "Software Version(s)", + "tag1": "(0018,1020)", + "tag2": "", + "value": "11\\LX\\MR Software release:11.1_M4_0818.a", + "vr": "LO" + }, + { + "desc": "Protocol Name", + "tag1": "(0018,1030)", + "tag2": "", + "value": "", + "vr": "LO" + }, + { + "desc": "Heart Rate", + "tag1": "(0018,1088)", + "tag2": "", + "value": "0", + "vr": "IS" + }, + { + "desc": "Cardiac Number of Images", + "tag1": "(0018,1090)", + "tag2": "", + "value": "0", + "vr": "IS" + }, + { + "desc": "Trigger Window", + "tag1": "(0018,1094)", + "tag2": "", + "value": "0", + "vr": "IS" + }, + { + "desc": "Reconstruction Diameter", + "tag1": "(0018,1100)", + "tag2": "", + "value": "300", + "vr": "DS" + }, + { + "desc": "Receive Coil Name", + "tag1": "(0018,1250)", + "tag2": "", + "value": "USCTLBOT", + "vr": "SH" + }, + { + "desc": "Acquisition Matrix", + "tag1": "(0018,1310)", + "tag2": "", + "value": "0\\320\\224\\0", + "vr": "US" + }, + { + "desc": "In-plane Phase Encoding Direction", + "tag1": "(0018,1312)", + "tag2": "", + "value": "ROW", + "vr": "CS" + }, + { + "desc": "Flip Angle", + "tag1": "(0018,1314)", + "tag2": "", + "value": "90", + "vr": "DS" + }, + { + "desc": "Variable Flip Angle Flag", + "tag1": "(0018,1315)", + "tag2": "", + "value": "N", + "vr": "CS" + }, + { + "desc": "SAR", + "tag1": "(0018,1316)", + "tag2": "", + "value": "0.985200", + "vr": "DS" + }, + { + "desc": "Patient Position", + "tag1": "(0018,5100)", + "tag2": "", + "value": "HFS", + "vr": "CS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0019,0010)", + "tag2": "", + "value": "GEMS_ACQU_01", + "vr": "LO" + }, + { + "desc": "?", + "tag1": "(0019,10BB)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10BC)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10BD)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10D9)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10DF)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10E0)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "Study Instance UID", + "tag1": "(0020,000D)", + "tag2": "", + "value": "1.2.840.113619.2.182.10808617210140.1458670669.96565", + "vr": "UI" + }, + { + "desc": "Series Instance UID", + "tag1": "(0020,000E)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.9125.1458715748.105", + "vr": "UI" + }, + { + "desc": "Study ID", + "tag1": "(0020,0010)", + "tag2": "", + "value": "", + "vr": "SH" + }, + { + "desc": "Series Number", + "tag1": "(0020,0011)", + "tag2": "", + "value": "3", + "vr": "IS" + }, + { + "desc": "Acquisition Number", + "tag1": "(0020,0012)", + "tag2": "", + "value": "1", + "vr": "IS" + }, + { + "desc": "Instance Number", + "tag1": "(0020,0013)", + "tag2": "", + "value": "9", + "vr": "IS" + }, + { + "desc": "Image Position (Patient)", + "tag1": "(0020,0032)", + "tag2": "", + "value": "3.99976\\-169.707\\222.878", + "vr": "DS" + }, + { + "desc": "Image Orientation (Patient)", + "tag1": "(0020,0037)", + "tag2": "", + "value": "-0\\1\\0\\-0\\-0\\-1", + "vr": "DS" + }, + { + "desc": "Frame of Reference UID", + "tag1": "(0020,0052)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.9229.1458715506.517", + "vr": "UI" + }, + { + "desc": "Laterality", + "tag1": "(0020,0060)", + "tag2": "", + "value": "", + "vr": "CS" + }, + { + "desc": "Temporal Resolution", + "tag1": "(0020,0110)", + "tag2": "", + "value": "0", + "vr": "DS" + }, + { + "desc": "Position Reference Indicator", + "tag1": "(0020,1040)", + "tag2": "", + "value": "", + "vr": "LO" + }, + { + "desc": "Slice Location", + "tag1": "(0020,1041)", + "tag2": "", + "value": "-3.999755859", + "vr": "DS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0021,0010)", + "tag2": "", + "value": "GEMS_RELA_01", + "vr": "LO" + }, + { + "desc": "?", + "tag1": "(0021,105A)", + "tag2": "", + "value": "0", + "vr": "SL" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0023,0010)", + "tag2": "", + "value": "GEMS_STDY_01", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0025,0010)", + "tag2": "", + "value": "GEMS_SERS_01", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0027,0010)", + "tag2": "", + "value": "GEMS_IMAG_01", + "vr": "LO" + }, + { + "desc": "Samples per Pixel", + "tag1": "(0028,0002)", + "tag2": "", + "value": "1", + "vr": "US" + }, + { + "desc": "Photometric Interpretation", + "tag1": "(0028,0004)", + "tag2": "", + "value": "MONOCHROME2", + "vr": "CS" + }, + { + "desc": "Rows", + "tag1": "(0028,0010)", + "tag2": "", + "value": "512", + "vr": "US" + }, + { + "desc": "Columns", + "tag1": "(0028,0011)", + "tag2": "", + "value": "512", + "vr": "US" + }, + { + "desc": "Pixel Spacing", + "tag1": "(0028,0030)", + "tag2": "", + "value": "0.585938\\0.585938", + "vr": "DS" + }, + { + "desc": "Bits Allocated", + "tag1": "(0028,0100)", + "tag2": "", + "value": "16", + "vr": "US" + }, + { + "desc": "Bits Stored", + "tag1": "(0028,0101)", + "tag2": "", + "value": "16", + "vr": "US" + }, + { + "desc": "High Bit", + "tag1": "(0028,0102)", + "tag2": "", + "value": "15", + "vr": "US" + }, + { + "desc": "Pixel Representation", + "tag1": "(0028,0103)", + "tag2": "", + "value": "1", + "vr": "US" + }, + { + "desc": "?", + "tag1": "(0028,0303)", + "tag2": "", + "value": "", + "vr": "CS" + }, + { + "desc": "Window Center", + "tag1": "(0028,1050)", + "tag2": "", + "value": "784", + "vr": "DS" + }, + { + "desc": "Window Width", + "tag1": "(0028,1051)", + "tag2": "", + "value": "1569", + "vr": "DS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0029,0010)", + "tag2": "", + "value": "GEMS_IMPS_01", + "vr": "LO" + }, + { + "desc": "Performed Procedure Step Description", + "tag1": "(0040,0254)", + "tag2": "", + "value": "", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0043,0010)", + "tag2": "", + "value": "GEMS_PARM_01", + "vr": "LO" + }, + { + "desc": "?", + "tag1": "(0043,1039)", + "tag2": "", + "value": "0\\0\\0\\0", + "vr": "IS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0903,0010)", + "tag2": "", + "value": "GEIIS PACS", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0905,0010)", + "tag2": "", + "value": "GEIIS", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(7FD1,0010)", + "tag2": "", + "value": "GEIIS", + "vr": "LO" + } + ] + } +} \ No newline at end of file diff --git a/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-1_vp-sag_T1w.nii.gz b/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-1_vp-sag_T1w.nii.gz new file mode 100644 index 0000000..2fc70e8 Binary files /dev/null and b/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-1_vp-sag_T1w.nii.gz differ diff --git a/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-2_vp-sag_Stir.json b/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-2_vp-sag_Stir.json new file mode 100644 index 0000000..d5add92 --- /dev/null +++ b/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-2_vp-sag_Stir.json @@ -0,0 +1,881 @@ +{ + "ResultSet": { + "Result": [ + { + "desc": "File Meta Information Version", + "tag1": "(0002,0001)", + "tag2": "", + "value": "00\\01", + "vr": "OB" + }, + { + "desc": "Media Storage SOP Class UID", + "tag1": "(0002,0002)", + "tag2": "", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Media Storage SOP Instance UID", + "tag1": "(0002,0003)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.9125.1458715748.254", + "vr": "UI" + }, + { + "desc": "Transfer Syntax UID", + "tag1": "(0002,0010)", + "tag2": "", + "value": "1.2.840.10008.1.2.1", + "vr": "UI" + }, + { + "desc": "Implementation Class UID", + "tag1": "(0002,0012)", + "tag2": "", + "value": "1.2.40.0.13.1.1", + "vr": "UI" + }, + { + "desc": "Implementation Version Name", + "tag1": "(0002,0013)", + "tag2": "", + "value": "dcm4che-2.0", + "vr": "SH" + }, + { + "desc": "Source Application Entity Title", + "tag1": "(0002,0016)", + "tag2": "", + "value": "CTP", + "vr": "AE" + }, + { + "desc": "Specific Character Set", + "tag1": "(0008,0005)", + "tag2": "", + "value": "ISO_IR 100", + "vr": "CS" + }, + { + "desc": "Image Type", + "tag1": "(0008,0008)", + "tag2": "", + "value": "ORIGINAL\\PRIMARY\\OTHER", + "vr": "CS" + }, + { + "desc": "SOP Class UID", + "tag1": "(0008,0016)", + "tag2": "", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "SOP Instance UID", + "tag1": "(0008,0018)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.9125.1458715748.254", + "vr": "UI" + }, + { + "desc": "Study Date", + "tag1": "(0008,0020)", + "tag2": "", + "value": "20160323", + "vr": "DA" + }, + { + "desc": "Series Date", + "tag1": "(0008,0021)", + "tag2": "", + "value": "20160323", + "vr": "DA" + }, + { + "desc": "Acquisition Date", + "tag1": "(0008,0022)", + "tag2": "", + "value": "20160323", + "vr": "DA" + }, + { + "desc": "Content Date", + "tag1": "(0008,0023)", + "tag2": "", + "value": "20160323", + "vr": "DA" + }, + { + "desc": "Study Time", + "tag1": "(0008,0030)", + "tag2": "", + "value": "074907", + "vr": "TM" + }, + { + "desc": "Series Time", + "tag1": "(0008,0031)", + "tag2": "", + "value": "075541", + "vr": "TM" + }, + { + "desc": "Acquisition Time", + "tag1": "(0008,0032)", + "tag2": "", + "value": "075541", + "vr": "TM" + }, + { + "desc": "Content Time", + "tag1": "(0008,0033)", + "tag2": "", + "value": "075541", + "vr": "TM" + }, + { + "desc": "Accession Number", + "tag1": "(0008,0050)", + "tag2": "", + "value": "ceibcs_E19219", + "vr": "SH" + }, + { + "desc": "Modality", + "tag1": "(0008,0060)", + "tag2": "", + "value": "MR", + "vr": "CS" + }, + { + "desc": "Manufacturer", + "tag1": "(0008,0070)", + "tag2": "", + "value": "GE MEDICAL SYSTEMS", + "vr": "LO" + }, + { + "desc": "Referring Physician's Name", + "tag1": "(0008,0090)", + "tag2": "", + "value": "", + "vr": "PN" + }, + { + "desc": "Station Name", + "tag1": "(0008,1010)", + "tag2": "", + "value": "CASTMRI", + "vr": "SH" + }, + { + "desc": "Study Description", + "tag1": "(0008,1030)", + "tag2": "", + "value": "MRI_Lumbar", + "vr": "LO" + }, + { + "desc": "Procedure Code Sequence", + "tag1": "(0008,1032)", + "tag2": "(0008,1032)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Code Value", + "tag1": "(0008,1032)", + "tag2": "(0008,0100)", + "value": "015001_RM502", + "vr": "SH" + }, + { + "desc": "Coding Scheme Designator", + "tag1": "(0008,1032)", + "tag2": "(0008,0102)", + "value": "GEIIS", + "vr": "SH" + }, + { + "desc": "Coding Scheme Version", + "tag1": "(0008,1032)", + "tag2": "(0008,0103)", + "value": "0", + "vr": "SH" + }, + { + "desc": "Code Meaning", + "tag1": "(0008,1032)", + "tag2": "(0008,0104)", + "value": "RM COLUMNA LUMBAR", + "vr": "LO" + }, + { + "desc": "Series Description", + "tag1": "(0008,103E)", + "tag2": "", + "value": "SAGITALSTIR", + "vr": "LO" + }, + { + "desc": "Manufacturer's Model Name", + "tag1": "(0008,1090)", + "tag2": "", + "value": "SIGNA EXCITE", + "vr": "LO" + }, + { + "desc": "Referenced Image Sequence", + "tag1": "(0008,1140)", + "tag2": "(0008,1140)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Referenced SOP Class UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1150)", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Referenced SOP Instance UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1155)", + "value": "1.2.840.113619.2.222.2025.1616754.9125.1458715748.26", + "vr": "UI" + }, + { + "desc": "Referenced Image Sequence", + "tag1": "(0008,1140)", + "tag2": "(0008,1140)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Referenced SOP Class UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1150)", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Referenced SOP Instance UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1155)", + "value": "1.2.840.113619.2.222.2025.1616754.9125.1458715748.19", + "vr": "UI" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0009,0010)", + "tag2": "", + "value": "GEMS_IDEN_01", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0009,0011)", + "tag2": "", + "value": "GEIIS", + "vr": "LO" + }, + { + "desc": "Patient's Name", + "tag1": "(0010,0010)", + "tag2": "", + "value": "213117108914127596262799978540518347712", + "vr": "PN" + }, + { + "desc": "Patient ID", + "tag1": "(0010,0020)", + "tag2": "", + "value": "171834704726005099248999303401096937503", + "vr": "LO" + }, + { + "desc": "Patient's Birth Date", + "tag1": "(0010,0030)", + "tag2": "", + "value": "19690513", + "vr": "DA" + }, + { + "desc": "Patient's Sex", + "tag1": "(0010,0040)", + "tag2": "", + "value": "F", + "vr": "CS" + }, + { + "desc": "Patient's Age", + "tag1": "(0010,1010)", + "tag2": "", + "value": "046Y", + "vr": "AS" + }, + { + "desc": "Patient's Weight", + "tag1": "(0010,1030)", + "tag2": "", + "value": "72", + "vr": "DS" + }, + { + "desc": "Additional Patient History", + "tag1": "(0010,21B0)", + "tag2": "", + "value": "", + "vr": "LT" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0011,0010)", + "tag2": "", + "value": "GEMS_PATI_01", + "vr": "LO" + }, + { + "desc": "Scanning Sequence", + "tag1": "(0018,0020)", + "tag2": "", + "value": "RM", + "vr": "CS" + }, + { + "desc": "Sequence Variant", + "tag1": "(0018,0021)", + "tag2": "", + "value": "NONE", + "vr": "CS" + }, + { + "desc": "Scan Options", + "tag1": "(0018,0022)", + "tag2": "", + "value": "FC_FREQ_AX_GEMS\\FC\\SAT_GEMS\\VB_GEMS\\EDR_GEMS\\SEQ_GEMS\\TRF_GEM...", + "vr": "CS" + }, + { + "desc": "MR Acquisition Type", + "tag1": "(0018,0023)", + "tag2": "", + "value": "2D", + "vr": "CS" + }, + { + "desc": "Angio Flag", + "tag1": "(0018,0025)", + "tag2": "", + "value": "N", + "vr": "CS" + }, + { + "desc": "Slice Thickness", + "tag1": "(0018,0050)", + "tag2": "", + "value": "4.5", + "vr": "DS" + }, + { + "desc": "Repetition Time", + "tag1": "(0018,0080)", + "tag2": "", + "value": "4100", + "vr": "DS" + }, + { + "desc": "Echo Time", + "tag1": "(0018,0081)", + "tag2": "", + "value": "42.66", + "vr": "DS" + }, + { + "desc": "Inversion Time", + "tag1": "(0018,0082)", + "tag2": "", + "value": "150", + "vr": "DS" + }, + { + "desc": "Number of Averages", + "tag1": "(0018,0083)", + "tag2": "", + "value": "3", + "vr": "DS" + }, + { + "desc": "Imaging Frequency", + "tag1": "(0018,0084)", + "tag2": "", + "value": "63.869763", + "vr": "DS" + }, + { + "desc": "Imaged Nucleus", + "tag1": "(0018,0085)", + "tag2": "", + "value": "1H", + "vr": "SH" + }, + { + "desc": "Echo Number(s)", + "tag1": "(0018,0086)", + "tag2": "", + "value": "1", + "vr": "IS" + }, + { + "desc": "Magnetic Field Strength", + "tag1": "(0018,0087)", + "tag2": "", + "value": "1.5", + "vr": "DS" + }, + { + "desc": "Spacing Between Slices", + "tag1": "(0018,0088)", + "tag2": "", + "value": "5.5", + "vr": "DS" + }, + { + "desc": "Echo Train Length", + "tag1": "(0018,0091)", + "tag2": "", + "value": "19", + "vr": "IS" + }, + { + "desc": "Percent Sampling", + "tag1": "(0018,0093)", + "tag2": "", + "value": "100", + "vr": "DS" + }, + { + "desc": "Percent Phase Field of View", + "tag1": "(0018,0094)", + "tag2": "", + "value": "90", + "vr": "DS" + }, + { + "desc": "Pixel Bandwidth", + "tag1": "(0018,0095)", + "tag2": "", + "value": "122.07", + "vr": "DS" + }, + { + "desc": "Device Serial Number", + "tag1": "(0018,1000)", + "tag2": "", + "value": "00000000NPV24200", + "vr": "LO" + }, + { + "desc": "Software Version(s)", + "tag1": "(0018,1020)", + "tag2": "", + "value": "11\\LX\\MR Software release:11.1_M4_0818.a", + "vr": "LO" + }, + { + "desc": "Protocol Name", + "tag1": "(0018,1030)", + "tag2": "", + "value": "LUMBAR2012", + "vr": "LO" + }, + { + "desc": "Heart Rate", + "tag1": "(0018,1088)", + "tag2": "", + "value": "0", + "vr": "IS" + }, + { + "desc": "Cardiac Number of Images", + "tag1": "(0018,1090)", + "tag2": "", + "value": "0", + "vr": "IS" + }, + { + "desc": "Trigger Window", + "tag1": "(0018,1094)", + "tag2": "", + "value": "0", + "vr": "IS" + }, + { + "desc": "Reconstruction Diameter", + "tag1": "(0018,1100)", + "tag2": "", + "value": "300", + "vr": "DS" + }, + { + "desc": "Receive Coil Name", + "tag1": "(0018,1250)", + "tag2": "", + "value": "USCTLBOT", + "vr": "SH" + }, + { + "desc": "Acquisition Matrix", + "tag1": "(0018,1310)", + "tag2": "", + "value": "0\\256\\192\\0", + "vr": "US" + }, + { + "desc": "In-plane Phase Encoding Direction", + "tag1": "(0018,1312)", + "tag2": "", + "value": "ROW", + "vr": "CS" + }, + { + "desc": "Flip Angle", + "tag1": "(0018,1314)", + "tag2": "", + "value": "90", + "vr": "DS" + }, + { + "desc": "Variable Flip Angle Flag", + "tag1": "(0018,1315)", + "tag2": "", + "value": "N", + "vr": "CS" + }, + { + "desc": "SAR", + "tag1": "(0018,1316)", + "tag2": "", + "value": "0.834900", + "vr": "DS" + }, + { + "desc": "Patient Position", + "tag1": "(0018,5100)", + "tag2": "", + "value": "HFS", + "vr": "CS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0019,0010)", + "tag2": "", + "value": "GEMS_ACQU_01", + "vr": "LO" + }, + { + "desc": "?", + "tag1": "(0019,10BB)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10BC)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10BD)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10D9)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10DF)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10E0)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "Study Instance UID", + "tag1": "(0020,000D)", + "tag2": "", + "value": "1.2.840.113619.2.182.10808617210140.1458670669.96565", + "vr": "UI" + }, + { + "desc": "Series Instance UID", + "tag1": "(0020,000E)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.9125.1458715748.183", + "vr": "UI" + }, + { + "desc": "Study ID", + "tag1": "(0020,0010)", + "tag2": "", + "value": "", + "vr": "SH" + }, + { + "desc": "Series Number", + "tag1": "(0020,0011)", + "tag2": "", + "value": "4", + "vr": "IS" + }, + { + "desc": "Acquisition Number", + "tag1": "(0020,0012)", + "tag2": "", + "value": "1", + "vr": "IS" + }, + { + "desc": "Instance Number", + "tag1": "(0020,0013)", + "tag2": "", + "value": "6", + "vr": "IS" + }, + { + "desc": "Image Position (Patient)", + "tag1": "(0020,0032)", + "tag2": "", + "value": "-12.5002\\-169.707\\222.878", + "vr": "DS" + }, + { + "desc": "Image Orientation (Patient)", + "tag1": "(0020,0037)", + "tag2": "", + "value": "-0\\1\\0\\-0\\-0\\-1", + "vr": "DS" + }, + { + "desc": "Frame of Reference UID", + "tag1": "(0020,0052)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.9229.1458715506.517", + "vr": "UI" + }, + { + "desc": "Laterality", + "tag1": "(0020,0060)", + "tag2": "", + "value": "", + "vr": "CS" + }, + { + "desc": "Temporal Resolution", + "tag1": "(0020,0110)", + "tag2": "", + "value": "0", + "vr": "DS" + }, + { + "desc": "Position Reference Indicator", + "tag1": "(0020,1040)", + "tag2": "", + "value": "", + "vr": "LO" + }, + { + "desc": "Slice Location", + "tag1": "(0020,1041)", + "tag2": "", + "value": "12.50024414", + "vr": "DS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0021,0010)", + "tag2": "", + "value": "GEMS_RELA_01", + "vr": "LO" + }, + { + "desc": "?", + "tag1": "(0021,105A)", + "tag2": "", + "value": "0", + "vr": "SL" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0023,0010)", + "tag2": "", + "value": "GEMS_STDY_01", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0025,0010)", + "tag2": "", + "value": "GEMS_SERS_01", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0027,0010)", + "tag2": "", + "value": "GEMS_IMAG_01", + "vr": "LO" + }, + { + "desc": "Samples per Pixel", + "tag1": "(0028,0002)", + "tag2": "", + "value": "1", + "vr": "US" + }, + { + "desc": "Photometric Interpretation", + "tag1": "(0028,0004)", + "tag2": "", + "value": "MONOCHROME2", + "vr": "CS" + }, + { + "desc": "Rows", + "tag1": "(0028,0010)", + "tag2": "", + "value": "512", + "vr": "US" + }, + { + "desc": "Columns", + "tag1": "(0028,0011)", + "tag2": "", + "value": "512", + "vr": "US" + }, + { + "desc": "Pixel Spacing", + "tag1": "(0028,0030)", + "tag2": "", + "value": "0.585938\\0.585938", + "vr": "DS" + }, + { + "desc": "Bits Allocated", + "tag1": "(0028,0100)", + "tag2": "", + "value": "16", + "vr": "US" + }, + { + "desc": "Bits Stored", + "tag1": "(0028,0101)", + "tag2": "", + "value": "16", + "vr": "US" + }, + { + "desc": "High Bit", + "tag1": "(0028,0102)", + "tag2": "", + "value": "15", + "vr": "US" + }, + { + "desc": "Pixel Representation", + "tag1": "(0028,0103)", + "tag2": "", + "value": "1", + "vr": "US" + }, + { + "desc": "?", + "tag1": "(0028,0303)", + "tag2": "", + "value": "", + "vr": "CS" + }, + { + "desc": "Window Center", + "tag1": "(0028,1050)", + "tag2": "", + "value": "235", + "vr": "DS" + }, + { + "desc": "Window Width", + "tag1": "(0028,1051)", + "tag2": "", + "value": "470", + "vr": "DS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0029,0010)", + "tag2": "", + "value": "GEMS_IMPS_01", + "vr": "LO" + }, + { + "desc": "Performed Procedure Step Description", + "tag1": "(0040,0254)", + "tag2": "", + "value": "", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0043,0010)", + "tag2": "", + "value": "GEMS_PARM_01", + "vr": "LO" + }, + { + "desc": "?", + "tag1": "(0043,1039)", + "tag2": "", + "value": "0\\32\\0\\0", + "vr": "IS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0903,0010)", + "tag2": "", + "value": "GEIIS PACS", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0905,0010)", + "tag2": "", + "value": "GEIIS", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(7FD1,0010)", + "tag2": "", + "value": "GEIIS", + "vr": "LO" + } + ] + } +} \ No newline at end of file diff --git a/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-2_vp-sag_Stir.nii.gz b/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-2_vp-sag_Stir.nii.gz new file mode 100644 index 0000000..3514e02 Binary files /dev/null and b/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-2_vp-sag_Stir.nii.gz differ diff --git a/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-3_vp-sag_T2w.json b/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-3_vp-sag_T2w.json new file mode 100644 index 0000000..5390f76 --- /dev/null +++ b/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-3_vp-sag_T2w.json @@ -0,0 +1,881 @@ +{ + "ResultSet": { + "Result": [ + { + "desc": "File Meta Information Version", + "tag1": "(0002,0001)", + "tag2": "", + "value": "00\\01", + "vr": "OB" + }, + { + "desc": "Media Storage SOP Class UID", + "tag1": "(0002,0002)", + "tag2": "", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Media Storage SOP Instance UID", + "tag1": "(0002,0003)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.9125.1458715748.104", + "vr": "UI" + }, + { + "desc": "Transfer Syntax UID", + "tag1": "(0002,0010)", + "tag2": "", + "value": "1.2.840.10008.1.2.1", + "vr": "UI" + }, + { + "desc": "Implementation Class UID", + "tag1": "(0002,0012)", + "tag2": "", + "value": "1.2.40.0.13.1.1", + "vr": "UI" + }, + { + "desc": "Implementation Version Name", + "tag1": "(0002,0013)", + "tag2": "", + "value": "dcm4che-2.0", + "vr": "SH" + }, + { + "desc": "Source Application Entity Title", + "tag1": "(0002,0016)", + "tag2": "", + "value": "CTP", + "vr": "AE" + }, + { + "desc": "Specific Character Set", + "tag1": "(0008,0005)", + "tag2": "", + "value": "ISO_IR 100", + "vr": "CS" + }, + { + "desc": "Image Type", + "tag1": "(0008,0008)", + "tag2": "", + "value": "ORIGINAL\\PRIMARY\\OTHER", + "vr": "CS" + }, + { + "desc": "SOP Class UID", + "tag1": "(0008,0016)", + "tag2": "", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "SOP Instance UID", + "tag1": "(0008,0018)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.9125.1458715748.104", + "vr": "UI" + }, + { + "desc": "Study Date", + "tag1": "(0008,0020)", + "tag2": "", + "value": "20160323", + "vr": "DA" + }, + { + "desc": "Series Date", + "tag1": "(0008,0021)", + "tag2": "", + "value": "20160323", + "vr": "DA" + }, + { + "desc": "Acquisition Date", + "tag1": "(0008,0022)", + "tag2": "", + "value": "20160323", + "vr": "DA" + }, + { + "desc": "Content Date", + "tag1": "(0008,0023)", + "tag2": "", + "value": "20160323", + "vr": "DA" + }, + { + "desc": "Study Time", + "tag1": "(0008,0030)", + "tag2": "", + "value": "074907", + "vr": "TM" + }, + { + "desc": "Series Time", + "tag1": "(0008,0031)", + "tag2": "", + "value": "075036", + "vr": "TM" + }, + { + "desc": "Acquisition Time", + "tag1": "(0008,0032)", + "tag2": "", + "value": "075036", + "vr": "TM" + }, + { + "desc": "Content Time", + "tag1": "(0008,0033)", + "tag2": "", + "value": "075036", + "vr": "TM" + }, + { + "desc": "Accession Number", + "tag1": "(0008,0050)", + "tag2": "", + "value": "ceibcs_E19219", + "vr": "SH" + }, + { + "desc": "Modality", + "tag1": "(0008,0060)", + "tag2": "", + "value": "MR", + "vr": "CS" + }, + { + "desc": "Manufacturer", + "tag1": "(0008,0070)", + "tag2": "", + "value": "GE MEDICAL SYSTEMS", + "vr": "LO" + }, + { + "desc": "Referring Physician's Name", + "tag1": "(0008,0090)", + "tag2": "", + "value": "", + "vr": "PN" + }, + { + "desc": "Station Name", + "tag1": "(0008,1010)", + "tag2": "", + "value": "CASTMRI", + "vr": "SH" + }, + { + "desc": "Study Description", + "tag1": "(0008,1030)", + "tag2": "", + "value": "MRI_Lumbar", + "vr": "LO" + }, + { + "desc": "Procedure Code Sequence", + "tag1": "(0008,1032)", + "tag2": "(0008,1032)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Code Value", + "tag1": "(0008,1032)", + "tag2": "(0008,0100)", + "value": "015001_RM502", + "vr": "SH" + }, + { + "desc": "Coding Scheme Designator", + "tag1": "(0008,1032)", + "tag2": "(0008,0102)", + "value": "GEIIS", + "vr": "SH" + }, + { + "desc": "Coding Scheme Version", + "tag1": "(0008,1032)", + "tag2": "(0008,0103)", + "value": "0", + "vr": "SH" + }, + { + "desc": "Code Meaning", + "tag1": "(0008,1032)", + "tag2": "(0008,0104)", + "value": "RM COLUMNA LUMBAR", + "vr": "LO" + }, + { + "desc": "Series Description", + "tag1": "(0008,103E)", + "tag2": "", + "value": "SAGT2LUMBAR", + "vr": "LO" + }, + { + "desc": "Manufacturer's Model Name", + "tag1": "(0008,1090)", + "tag2": "", + "value": "SIGNA EXCITE", + "vr": "LO" + }, + { + "desc": "Referenced Image Sequence", + "tag1": "(0008,1140)", + "tag2": "(0008,1140)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Referenced SOP Class UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1150)", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Referenced SOP Instance UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1155)", + "value": "1.2.840.113619.2.222.2025.1616754.9125.1458715748.26", + "vr": "UI" + }, + { + "desc": "Referenced Image Sequence", + "tag1": "(0008,1140)", + "tag2": "(0008,1140)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Referenced SOP Class UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1150)", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Referenced SOP Instance UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1155)", + "value": "1.2.840.113619.2.222.2025.1616754.9125.1458715748.19", + "vr": "UI" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0009,0010)", + "tag2": "", + "value": "GEMS_IDEN_01", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0009,0011)", + "tag2": "", + "value": "GEIIS", + "vr": "LO" + }, + { + "desc": "Patient's Name", + "tag1": "(0010,0010)", + "tag2": "", + "value": "213117108914127596262799978540518347712", + "vr": "PN" + }, + { + "desc": "Patient ID", + "tag1": "(0010,0020)", + "tag2": "", + "value": "171834704726005099248999303401096937503", + "vr": "LO" + }, + { + "desc": "Patient's Birth Date", + "tag1": "(0010,0030)", + "tag2": "", + "value": "19690513", + "vr": "DA" + }, + { + "desc": "Patient's Sex", + "tag1": "(0010,0040)", + "tag2": "", + "value": "F", + "vr": "CS" + }, + { + "desc": "Patient's Age", + "tag1": "(0010,1010)", + "tag2": "", + "value": "046Y", + "vr": "AS" + }, + { + "desc": "Patient's Weight", + "tag1": "(0010,1030)", + "tag2": "", + "value": "72", + "vr": "DS" + }, + { + "desc": "Additional Patient History", + "tag1": "(0010,21B0)", + "tag2": "", + "value": "", + "vr": "LT" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0011,0010)", + "tag2": "", + "value": "GEMS_PATI_01", + "vr": "LO" + }, + { + "desc": "Scanning Sequence", + "tag1": "(0018,0020)", + "tag2": "", + "value": "SE", + "vr": "CS" + }, + { + "desc": "Sequence Variant", + "tag1": "(0018,0021)", + "tag2": "", + "value": "OSP", + "vr": "CS" + }, + { + "desc": "Scan Options", + "tag1": "(0018,0022)", + "tag2": "", + "value": "SAT_GEMS\\NPW\\VB_GEMS\\TRF_GEMS\\FILTERED_GEMS\\SP", + "vr": "CS" + }, + { + "desc": "MR Acquisition Type", + "tag1": "(0018,0023)", + "tag2": "", + "value": "2D", + "vr": "CS" + }, + { + "desc": "Angio Flag", + "tag1": "(0018,0025)", + "tag2": "", + "value": "N", + "vr": "CS" + }, + { + "desc": "Slice Thickness", + "tag1": "(0018,0050)", + "tag2": "", + "value": "4.5", + "vr": "DS" + }, + { + "desc": "Repetition Time", + "tag1": "(0018,0080)", + "tag2": "", + "value": "3440", + "vr": "DS" + }, + { + "desc": "Echo Time", + "tag1": "(0018,0081)", + "tag2": "", + "value": "110", + "vr": "DS" + }, + { + "desc": "Inversion Time", + "tag1": "(0018,0082)", + "tag2": "", + "value": "0", + "vr": "DS" + }, + { + "desc": "Number of Averages", + "tag1": "(0018,0083)", + "tag2": "", + "value": "2", + "vr": "DS" + }, + { + "desc": "Imaging Frequency", + "tag1": "(0018,0084)", + "tag2": "", + "value": "63.869763", + "vr": "DS" + }, + { + "desc": "Imaged Nucleus", + "tag1": "(0018,0085)", + "tag2": "", + "value": "1H", + "vr": "SH" + }, + { + "desc": "Echo Number(s)", + "tag1": "(0018,0086)", + "tag2": "", + "value": "1", + "vr": "IS" + }, + { + "desc": "Magnetic Field Strength", + "tag1": "(0018,0087)", + "tag2": "", + "value": "1.5", + "vr": "DS" + }, + { + "desc": "Spacing Between Slices", + "tag1": "(0018,0088)", + "tag2": "", + "value": "5.5", + "vr": "DS" + }, + { + "desc": "Echo Train Length", + "tag1": "(0018,0091)", + "tag2": "", + "value": "29", + "vr": "IS" + }, + { + "desc": "Percent Sampling", + "tag1": "(0018,0093)", + "tag2": "", + "value": "100", + "vr": "DS" + }, + { + "desc": "Percent Phase Field of View", + "tag1": "(0018,0094)", + "tag2": "", + "value": "100", + "vr": "DS" + }, + { + "desc": "Pixel Bandwidth", + "tag1": "(0018,0095)", + "tag2": "", + "value": "162.773", + "vr": "DS" + }, + { + "desc": "Device Serial Number", + "tag1": "(0018,1000)", + "tag2": "", + "value": "00000000NPV24200", + "vr": "LO" + }, + { + "desc": "Software Version(s)", + "tag1": "(0018,1020)", + "tag2": "", + "value": "11\\LX\\MR Software release:11.1_M4_0818.a", + "vr": "LO" + }, + { + "desc": "Protocol Name", + "tag1": "(0018,1030)", + "tag2": "", + "value": "LUMBAR2012", + "vr": "LO" + }, + { + "desc": "Heart Rate", + "tag1": "(0018,1088)", + "tag2": "", + "value": "0", + "vr": "IS" + }, + { + "desc": "Cardiac Number of Images", + "tag1": "(0018,1090)", + "tag2": "", + "value": "0", + "vr": "IS" + }, + { + "desc": "Trigger Window", + "tag1": "(0018,1094)", + "tag2": "", + "value": "0", + "vr": "IS" + }, + { + "desc": "Reconstruction Diameter", + "tag1": "(0018,1100)", + "tag2": "", + "value": "300", + "vr": "DS" + }, + { + "desc": "Receive Coil Name", + "tag1": "(0018,1250)", + "tag2": "", + "value": "USCTLBOT", + "vr": "SH" + }, + { + "desc": "Acquisition Matrix", + "tag1": "(0018,1310)", + "tag2": "", + "value": "384\\0\\0\\224", + "vr": "US" + }, + { + "desc": "In-plane Phase Encoding Direction", + "tag1": "(0018,1312)", + "tag2": "", + "value": "COL", + "vr": "CS" + }, + { + "desc": "Flip Angle", + "tag1": "(0018,1314)", + "tag2": "", + "value": "90", + "vr": "DS" + }, + { + "desc": "Variable Flip Angle Flag", + "tag1": "(0018,1315)", + "tag2": "", + "value": "N", + "vr": "CS" + }, + { + "desc": "SAR", + "tag1": "(0018,1316)", + "tag2": "", + "value": "1.222100", + "vr": "DS" + }, + { + "desc": "Patient Position", + "tag1": "(0018,5100)", + "tag2": "", + "value": "HFS", + "vr": "CS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0019,0010)", + "tag2": "", + "value": "GEMS_ACQU_01", + "vr": "LO" + }, + { + "desc": "?", + "tag1": "(0019,10BB)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10BC)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10BD)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10D9)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10DF)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10E0)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "Study Instance UID", + "tag1": "(0020,000D)", + "tag2": "", + "value": "1.2.840.113619.2.182.10808617210140.1458670669.96565", + "vr": "UI" + }, + { + "desc": "Series Instance UID", + "tag1": "(0020,000E)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.9125.1458715748.27", + "vr": "UI" + }, + { + "desc": "Study ID", + "tag1": "(0020,0010)", + "tag2": "", + "value": "", + "vr": "SH" + }, + { + "desc": "Series Number", + "tag1": "(0020,0011)", + "tag2": "", + "value": "2", + "vr": "IS" + }, + { + "desc": "Acquisition Number", + "tag1": "(0020,0012)", + "tag2": "", + "value": "1", + "vr": "IS" + }, + { + "desc": "Instance Number", + "tag1": "(0020,0013)", + "tag2": "", + "value": "12", + "vr": "IS" + }, + { + "desc": "Image Position (Patient)", + "tag1": "(0020,0032)", + "tag2": "", + "value": "20.4998\\-169.707\\222.878", + "vr": "DS" + }, + { + "desc": "Image Orientation (Patient)", + "tag1": "(0020,0037)", + "tag2": "", + "value": "-0\\1\\0\\-0\\-0\\-1", + "vr": "DS" + }, + { + "desc": "Frame of Reference UID", + "tag1": "(0020,0052)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.9229.1458715506.517", + "vr": "UI" + }, + { + "desc": "Laterality", + "tag1": "(0020,0060)", + "tag2": "", + "value": "", + "vr": "CS" + }, + { + "desc": "Temporal Resolution", + "tag1": "(0020,0110)", + "tag2": "", + "value": "0", + "vr": "DS" + }, + { + "desc": "Position Reference Indicator", + "tag1": "(0020,1040)", + "tag2": "", + "value": "", + "vr": "LO" + }, + { + "desc": "Slice Location", + "tag1": "(0020,1041)", + "tag2": "", + "value": "-20.49975586", + "vr": "DS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0021,0010)", + "tag2": "", + "value": "GEMS_RELA_01", + "vr": "LO" + }, + { + "desc": "?", + "tag1": "(0021,105A)", + "tag2": "", + "value": "0", + "vr": "SL" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0023,0010)", + "tag2": "", + "value": "GEMS_STDY_01", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0025,0010)", + "tag2": "", + "value": "GEMS_SERS_01", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0027,0010)", + "tag2": "", + "value": "GEMS_IMAG_01", + "vr": "LO" + }, + { + "desc": "Samples per Pixel", + "tag1": "(0028,0002)", + "tag2": "", + "value": "1", + "vr": "US" + }, + { + "desc": "Photometric Interpretation", + "tag1": "(0028,0004)", + "tag2": "", + "value": "MONOCHROME2", + "vr": "CS" + }, + { + "desc": "Rows", + "tag1": "(0028,0010)", + "tag2": "", + "value": "512", + "vr": "US" + }, + { + "desc": "Columns", + "tag1": "(0028,0011)", + "tag2": "", + "value": "512", + "vr": "US" + }, + { + "desc": "Pixel Spacing", + "tag1": "(0028,0030)", + "tag2": "", + "value": "0.585938\\0.585938", + "vr": "DS" + }, + { + "desc": "Bits Allocated", + "tag1": "(0028,0100)", + "tag2": "", + "value": "16", + "vr": "US" + }, + { + "desc": "Bits Stored", + "tag1": "(0028,0101)", + "tag2": "", + "value": "16", + "vr": "US" + }, + { + "desc": "High Bit", + "tag1": "(0028,0102)", + "tag2": "", + "value": "15", + "vr": "US" + }, + { + "desc": "Pixel Representation", + "tag1": "(0028,0103)", + "tag2": "", + "value": "1", + "vr": "US" + }, + { + "desc": "?", + "tag1": "(0028,0303)", + "tag2": "", + "value": "", + "vr": "CS" + }, + { + "desc": "Window Center", + "tag1": "(0028,1050)", + "tag2": "", + "value": "635", + "vr": "DS" + }, + { + "desc": "Window Width", + "tag1": "(0028,1051)", + "tag2": "", + "value": "1271", + "vr": "DS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0029,0010)", + "tag2": "", + "value": "GEMS_IMPS_01", + "vr": "LO" + }, + { + "desc": "Performed Procedure Step Description", + "tag1": "(0040,0254)", + "tag2": "", + "value": "", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0043,0010)", + "tag2": "", + "value": "GEMS_PARM_01", + "vr": "LO" + }, + { + "desc": "?", + "tag1": "(0043,1039)", + "tag2": "", + "value": "0\\2097152\\0\\0", + "vr": "IS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0903,0010)", + "tag2": "", + "value": "GEIIS PACS", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0905,0010)", + "tag2": "", + "value": "GEIIS", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(7FD1,0010)", + "tag2": "", + "value": "GEIIS", + "vr": "LO" + } + ] + } +} \ No newline at end of file diff --git a/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-3_vp-sag_T2w.nii.gz b/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-3_vp-sag_T2w.nii.gz new file mode 100644 index 0000000..70480d3 Binary files /dev/null and b/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-3_vp-sag_T2w.nii.gz differ diff --git a/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-4_vp-ax_T2w.json b/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-4_vp-ax_T2w.json new file mode 100644 index 0000000..a475cfb --- /dev/null +++ b/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-4_vp-ax_T2w.json @@ -0,0 +1,923 @@ +{ + "ResultSet": { + "Result": [ + { + "desc": "File Meta Information Version", + "tag1": "(0002,0001)", + "tag2": "", + "value": "00\\01", + "vr": "OB" + }, + { + "desc": "Media Storage SOP Class UID", + "tag1": "(0002,0002)", + "tag2": "", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Media Storage SOP Instance UID", + "tag1": "(0002,0003)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.9125.1458715748.346", + "vr": "UI" + }, + { + "desc": "Transfer Syntax UID", + "tag1": "(0002,0010)", + "tag2": "", + "value": "1.2.840.10008.1.2.1", + "vr": "UI" + }, + { + "desc": "Implementation Class UID", + "tag1": "(0002,0012)", + "tag2": "", + "value": "1.2.40.0.13.1.1", + "vr": "UI" + }, + { + "desc": "Implementation Version Name", + "tag1": "(0002,0013)", + "tag2": "", + "value": "dcm4che-2.0", + "vr": "SH" + }, + { + "desc": "Source Application Entity Title", + "tag1": "(0002,0016)", + "tag2": "", + "value": "CTP", + "vr": "AE" + }, + { + "desc": "Specific Character Set", + "tag1": "(0008,0005)", + "tag2": "", + "value": "ISO_IR 100", + "vr": "CS" + }, + { + "desc": "Image Type", + "tag1": "(0008,0008)", + "tag2": "", + "value": "ORIGINAL\\PRIMARY\\OTHER", + "vr": "CS" + }, + { + "desc": "SOP Class UID", + "tag1": "(0008,0016)", + "tag2": "", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "SOP Instance UID", + "tag1": "(0008,0018)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.9125.1458715748.346", + "vr": "UI" + }, + { + "desc": "Study Date", + "tag1": "(0008,0020)", + "tag2": "", + "value": "20160323", + "vr": "DA" + }, + { + "desc": "Series Date", + "tag1": "(0008,0021)", + "tag2": "", + "value": "20160323", + "vr": "DA" + }, + { + "desc": "Acquisition Date", + "tag1": "(0008,0022)", + "tag2": "", + "value": "20160323", + "vr": "DA" + }, + { + "desc": "Content Date", + "tag1": "(0008,0023)", + "tag2": "", + "value": "20160323", + "vr": "DA" + }, + { + "desc": "Study Time", + "tag1": "(0008,0030)", + "tag2": "", + "value": "074907", + "vr": "TM" + }, + { + "desc": "Series Time", + "tag1": "(0008,0031)", + "tag2": "", + "value": "075815", + "vr": "TM" + }, + { + "desc": "Acquisition Time", + "tag1": "(0008,0032)", + "tag2": "", + "value": "075815", + "vr": "TM" + }, + { + "desc": "Content Time", + "tag1": "(0008,0033)", + "tag2": "", + "value": "075815", + "vr": "TM" + }, + { + "desc": "Accession Number", + "tag1": "(0008,0050)", + "tag2": "", + "value": "ceibcs_E19219", + "vr": "SH" + }, + { + "desc": "Modality", + "tag1": "(0008,0060)", + "tag2": "", + "value": "MR", + "vr": "CS" + }, + { + "desc": "Manufacturer", + "tag1": "(0008,0070)", + "tag2": "", + "value": "GE MEDICAL SYSTEMS", + "vr": "LO" + }, + { + "desc": "Referring Physician's Name", + "tag1": "(0008,0090)", + "tag2": "", + "value": "", + "vr": "PN" + }, + { + "desc": "Station Name", + "tag1": "(0008,1010)", + "tag2": "", + "value": "CASTMRI", + "vr": "SH" + }, + { + "desc": "Study Description", + "tag1": "(0008,1030)", + "tag2": "", + "value": "MRI_lUMBAR", + "vr": "LO" + }, + { + "desc": "Procedure Code Sequence", + "tag1": "(0008,1032)", + "tag2": "(0008,1032)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Code Value", + "tag1": "(0008,1032)", + "tag2": "(0008,0100)", + "value": "015001_RM502", + "vr": "SH" + }, + { + "desc": "Coding Scheme Designator", + "tag1": "(0008,1032)", + "tag2": "(0008,0102)", + "value": "GEIIS", + "vr": "SH" + }, + { + "desc": "Coding Scheme Version", + "tag1": "(0008,1032)", + "tag2": "(0008,0103)", + "value": "0", + "vr": "SH" + }, + { + "desc": "Code Meaning", + "tag1": "(0008,1032)", + "tag2": "(0008,0104)", + "value": "RM COLUMNA LUMBAR", + "vr": "LO" + }, + { + "desc": "Series Description", + "tag1": "(0008,103E)", + "tag2": "", + "value": "AXIALT2DISCBASICO", + "vr": "LO" + }, + { + "desc": "Manufacturer's Model Name", + "tag1": "(0008,1090)", + "tag2": "", + "value": "SIGNA EXCITE", + "vr": "LO" + }, + { + "desc": "Referenced Image Sequence", + "tag1": "(0008,1140)", + "tag2": "(0008,1140)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Referenced SOP Class UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1150)", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Referenced SOP Instance UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1155)", + "value": "1.2.840.113619.2.222.2025.1616754.9125.1458715748.98", + "vr": "UI" + }, + { + "desc": "Referenced Image Sequence", + "tag1": "(0008,1140)", + "tag2": "(0008,1140)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Referenced SOP Class UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1150)", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Referenced SOP Instance UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1155)", + "value": "1.2.840.113619.2.222.2025.1616754.9125.1458715748.25", + "vr": "UI" + }, + { + "desc": "Referenced Image Sequence", + "tag1": "(0008,1140)", + "tag2": "(0008,1140)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Referenced SOP Class UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1150)", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Referenced SOP Instance UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1155)", + "value": "1.2.840.113619.2.222.2025.1616754.9125.1458715748.99", + "vr": "UI" + }, + { + "desc": "Referenced Image Sequence", + "tag1": "(0008,1140)", + "tag2": "(0008,1140)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Referenced SOP Class UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1150)", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Referenced SOP Instance UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1155)", + "value": "1.2.840.113619.2.222.2025.1616754.9125.1458715748.19", + "vr": "UI" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0009,0010)", + "tag2": "", + "value": "GEMS_IDEN_01", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0009,0011)", + "tag2": "", + "value": "GEIIS", + "vr": "LO" + }, + { + "desc": "Patient's Name", + "tag1": "(0010,0010)", + "tag2": "", + "value": "213117108914127596262799978540518347712", + "vr": "PN" + }, + { + "desc": "Patient ID", + "tag1": "(0010,0020)", + "tag2": "", + "value": "171834704726005099248999303401096937503", + "vr": "LO" + }, + { + "desc": "Patient's Birth Date", + "tag1": "(0010,0030)", + "tag2": "", + "value": "19690513", + "vr": "DA" + }, + { + "desc": "Patient's Sex", + "tag1": "(0010,0040)", + "tag2": "", + "value": "F", + "vr": "CS" + }, + { + "desc": "Patient's Age", + "tag1": "(0010,1010)", + "tag2": "", + "value": "046Y", + "vr": "AS" + }, + { + "desc": "Patient's Weight", + "tag1": "(0010,1030)", + "tag2": "", + "value": "72", + "vr": "DS" + }, + { + "desc": "Additional Patient History", + "tag1": "(0010,21B0)", + "tag2": "", + "value": "", + "vr": "LT" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0011,0010)", + "tag2": "", + "value": "GEMS_PATI_01", + "vr": "LO" + }, + { + "desc": "Scanning Sequence", + "tag1": "(0018,0020)", + "tag2": "", + "value": "SE", + "vr": "CS" + }, + { + "desc": "Sequence Variant", + "tag1": "(0018,0021)", + "tag2": "", + "value": "NONE", + "vr": "CS" + }, + { + "desc": "Scan Options", + "tag1": "(0018,0022)", + "tag2": "", + "value": "SAT_GEMS\\VB_GEMS\\TRF_GEMS\\FILTERED_GEMS\\SP", + "vr": "CS" + }, + { + "desc": "MR Acquisition Type", + "tag1": "(0018,0023)", + "tag2": "", + "value": "2D", + "vr": "CS" + }, + { + "desc": "Angio Flag", + "tag1": "(0018,0025)", + "tag2": "", + "value": "N", + "vr": "CS" + }, + { + "desc": "Slice Thickness", + "tag1": "(0018,0050)", + "tag2": "", + "value": "3.5", + "vr": "DS" + }, + { + "desc": "Repetition Time", + "tag1": "(0018,0080)", + "tag2": "", + "value": "3400", + "vr": "DS" + }, + { + "desc": "Echo Time", + "tag1": "(0018,0081)", + "tag2": "", + "value": "107.2", + "vr": "DS" + }, + { + "desc": "Inversion Time", + "tag1": "(0018,0082)", + "tag2": "", + "value": "0", + "vr": "DS" + }, + { + "desc": "Number of Averages", + "tag1": "(0018,0083)", + "tag2": "", + "value": "3", + "vr": "DS" + }, + { + "desc": "Imaging Frequency", + "tag1": "(0018,0084)", + "tag2": "", + "value": "63.869753", + "vr": "DS" + }, + { + "desc": "Imaged Nucleus", + "tag1": "(0018,0085)", + "tag2": "", + "value": "1H", + "vr": "SH" + }, + { + "desc": "Echo Number(s)", + "tag1": "(0018,0086)", + "tag2": "", + "value": "1", + "vr": "IS" + }, + { + "desc": "Magnetic Field Strength", + "tag1": "(0018,0087)", + "tag2": "", + "value": "1.5", + "vr": "DS" + }, + { + "desc": "Spacing Between Slices", + "tag1": "(0018,0088)", + "tag2": "", + "value": "4.5", + "vr": "DS" + }, + { + "desc": "Echo Train Length", + "tag1": "(0018,0091)", + "tag2": "", + "value": "29", + "vr": "IS" + }, + { + "desc": "Percent Sampling", + "tag1": "(0018,0093)", + "tag2": "", + "value": "100", + "vr": "DS" + }, + { + "desc": "Percent Phase Field of View", + "tag1": "(0018,0094)", + "tag2": "", + "value": "100", + "vr": "DS" + }, + { + "desc": "Pixel Bandwidth", + "tag1": "(0018,0095)", + "tag2": "", + "value": "162.773", + "vr": "DS" + }, + { + "desc": "Device Serial Number", + "tag1": "(0018,1000)", + "tag2": "", + "value": "00000000NPV24200", + "vr": "LO" + }, + { + "desc": "Software Version(s)", + "tag1": "(0018,1020)", + "tag2": "", + "value": "11\\LX\\MR Software release:11.1_M4_0818.a", + "vr": "LO" + }, + { + "desc": "Protocol Name", + "tag1": "(0018,1030)", + "tag2": "", + "value": "LUMBAR2012", + "vr": "LO" + }, + { + "desc": "Heart Rate", + "tag1": "(0018,1088)", + "tag2": "", + "value": "0", + "vr": "IS" + }, + { + "desc": "Cardiac Number of Images", + "tag1": "(0018,1090)", + "tag2": "", + "value": "0", + "vr": "IS" + }, + { + "desc": "Trigger Window", + "tag1": "(0018,1094)", + "tag2": "", + "value": "0", + "vr": "IS" + }, + { + "desc": "Reconstruction Diameter", + "tag1": "(0018,1100)", + "tag2": "", + "value": "200", + "vr": "DS" + }, + { + "desc": "Receive Coil Name", + "tag1": "(0018,1250)", + "tag2": "", + "value": "USCTLBOT", + "vr": "SH" + }, + { + "desc": "Acquisition Matrix", + "tag1": "(0018,1310)", + "tag2": "", + "value": "288\\0\\0\\224", + "vr": "US" + }, + { + "desc": "In-plane Phase Encoding Direction", + "tag1": "(0018,1312)", + "tag2": "", + "value": "COL", + "vr": "CS" + }, + { + "desc": "Flip Angle", + "tag1": "(0018,1314)", + "tag2": "", + "value": "90", + "vr": "DS" + }, + { + "desc": "Variable Flip Angle Flag", + "tag1": "(0018,1315)", + "tag2": "", + "value": "N", + "vr": "CS" + }, + { + "desc": "SAR", + "tag1": "(0018,1316)", + "tag2": "", + "value": "1.236500", + "vr": "DS" + }, + { + "desc": "Patient Position", + "tag1": "(0018,5100)", + "tag2": "", + "value": "HFS", + "vr": "CS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0019,0010)", + "tag2": "", + "value": "GEMS_ACQU_01", + "vr": "LO" + }, + { + "desc": "?", + "tag1": "(0019,10BB)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10BC)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10BD)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10D9)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10DF)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10E0)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "Study Instance UID", + "tag1": "(0020,000D)", + "tag2": "", + "value": "1.2.840.113619.2.182.10808617210140.1458670669.96565", + "vr": "UI" + }, + { + "desc": "Series Instance UID", + "tag1": "(0020,000E)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.9125.1458715748.261", + "vr": "UI" + }, + { + "desc": "Study ID", + "tag1": "(0020,0010)", + "tag2": "", + "value": "", + "vr": "SH" + }, + { + "desc": "Series Number", + "tag1": "(0020,0011)", + "tag2": "", + "value": "5", + "vr": "IS" + }, + { + "desc": "Acquisition Number", + "tag1": "(0020,0012)", + "tag2": "", + "value": "1", + "vr": "IS" + }, + { + "desc": "Instance Number", + "tag1": "(0020,0013)", + "tag2": "", + "value": "16", + "vr": "IS" + }, + { + "desc": "Image Position (Patient)", + "tag1": "(0020,0032)", + "tag2": "", + "value": "-106.805\\-110.059\\71.0907", + "vr": "DS" + }, + { + "desc": "Image Orientation (Patient)", + "tag1": "(0020,0037)", + "tag2": "", + "value": "1\\-0\\0\\-0\\0.993135\\0.116978", + "vr": "DS" + }, + { + "desc": "Frame of Reference UID", + "tag1": "(0020,0052)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.9229.1458715506.517", + "vr": "UI" + }, + { + "desc": "Laterality", + "tag1": "(0020,0060)", + "tag2": "", + "value": "", + "vr": "CS" + }, + { + "desc": "Temporal Resolution", + "tag1": "(0020,0110)", + "tag2": "", + "value": "0", + "vr": "DS" + }, + { + "desc": "Position Reference Indicator", + "tag1": "(0020,1040)", + "tag2": "", + "value": "", + "vr": "LO" + }, + { + "desc": "Slice Location", + "tag1": "(0020,1041)", + "tag2": "", + "value": "82.76560974", + "vr": "DS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0021,0010)", + "tag2": "", + "value": "GEMS_RELA_01", + "vr": "LO" + }, + { + "desc": "?", + "tag1": "(0021,105A)", + "tag2": "", + "value": "0", + "vr": "SL" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0023,0010)", + "tag2": "", + "value": "GEMS_STDY_01", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0025,0010)", + "tag2": "", + "value": "GEMS_SERS_01", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0027,0010)", + "tag2": "", + "value": "GEMS_IMAG_01", + "vr": "LO" + }, + { + "desc": "Samples per Pixel", + "tag1": "(0028,0002)", + "tag2": "", + "value": "1", + "vr": "US" + }, + { + "desc": "Photometric Interpretation", + "tag1": "(0028,0004)", + "tag2": "", + "value": "MONOCHROME2", + "vr": "CS" + }, + { + "desc": "Rows", + "tag1": "(0028,0010)", + "tag2": "", + "value": "512", + "vr": "US" + }, + { + "desc": "Columns", + "tag1": "(0028,0011)", + "tag2": "", + "value": "512", + "vr": "US" + }, + { + "desc": "Pixel Spacing", + "tag1": "(0028,0030)", + "tag2": "", + "value": "0.390625\\0.390625", + "vr": "DS" + }, + { + "desc": "Bits Allocated", + "tag1": "(0028,0100)", + "tag2": "", + "value": "16", + "vr": "US" + }, + { + "desc": "Bits Stored", + "tag1": "(0028,0101)", + "tag2": "", + "value": "16", + "vr": "US" + }, + { + "desc": "High Bit", + "tag1": "(0028,0102)", + "tag2": "", + "value": "15", + "vr": "US" + }, + { + "desc": "Pixel Representation", + "tag1": "(0028,0103)", + "tag2": "", + "value": "1", + "vr": "US" + }, + { + "desc": "?", + "tag1": "(0028,0303)", + "tag2": "", + "value": "", + "vr": "CS" + }, + { + "desc": "Window Center", + "tag1": "(0028,1050)", + "tag2": "", + "value": "473", + "vr": "DS" + }, + { + "desc": "Window Width", + "tag1": "(0028,1051)", + "tag2": "", + "value": "947", + "vr": "DS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0029,0010)", + "tag2": "", + "value": "GEMS_IMPS_01", + "vr": "LO" + }, + { + "desc": "Performed Procedure Step Description", + "tag1": "(0040,0254)", + "tag2": "", + "value": "", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0043,0010)", + "tag2": "", + "value": "GEMS_PARM_01", + "vr": "LO" + }, + { + "desc": "?", + "tag1": "(0043,1039)", + "tag2": "", + "value": "0\\2097152\\0\\0", + "vr": "IS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0903,0010)", + "tag2": "", + "value": "GEIIS PACS", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0905,0010)", + "tag2": "", + "value": "GEIIS", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(7FD1,0010)", + "tag2": "", + "value": "GEIIS", + "vr": "LO" + } + ] + } +} \ No newline at end of file diff --git a/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-4_vp-ax_T2w.nii.gz b/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-4_vp-ax_T2w.nii.gz new file mode 100644 index 0000000..bae62c8 Binary files /dev/null and b/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-4_vp-ax_T2w.nii.gz differ diff --git a/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-2_run-4_vp-ax_T2w.nii.gz b/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-2_run-4_vp-ax_T2w.nii.gz new file mode 100644 index 0000000..935f376 Binary files /dev/null and b/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-2_run-4_vp-ax_T2w.nii.gz differ diff --git a/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-3_run-4_vp-ax_T2w.nii.gz b/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-3_run-4_vp-ax_T2w.nii.gz new file mode 100644 index 0000000..a935549 Binary files /dev/null and b/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-3_run-4_vp-ax_T2w.nii.gz differ diff --git a/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-4_run-4_vp-ax_T2w.nii.gz b/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-4_run-4_vp-ax_T2w.nii.gz new file mode 100644 index 0000000..2ed0178 Binary files /dev/null and b/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-4_run-4_vp-ax_T2w.nii.gz differ diff --git a/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-5_run-4_vp-ax_T2w.nii.gz b/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-5_run-4_vp-ax_T2w.nii.gz new file mode 100644 index 0000000..c271b8c Binary files /dev/null and b/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-5_run-4_vp-ax_T2w.nii.gz differ diff --git a/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-6_run-4_vp-ax_T2w.nii.gz b/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-6_run-4_vp-ax_T2w.nii.gz new file mode 100644 index 0000000..070e439 Binary files /dev/null and b/data/examples/MRI_Lumbar/sub-1/ses-1/mr/anat/sub-1_ses-1_bp-lsspine_acq-6_run-4_vp-ax_T2w.nii.gz differ diff --git a/data/examples/MRI_Lumbar/sub-1/ses-1/sub-1_ses-1_scans.tsv b/data/examples/MRI_Lumbar/sub-1/ses-1/sub-1_ses-1_scans.tsv new file mode 100644 index 0000000..2af8213 --- /dev/null +++ b/data/examples/MRI_Lumbar/sub-1/ses-1/sub-1_ses-1_scans.tsv @@ -0,0 +1,5 @@ +filename slides plane Manufacturer (0008,0070) Series Description (0008,103E) Manufacturer's Model Name (0008,1090) Patient ID (0010,0020) Patient's Sex (0010,0040) Patient's Age (0010,1010) Patient's Weight (0010,1030) Scanning Sequence (0018,0020) Sequence Variant (0018,0021) Scan Options (0018,0022) MR Acquisition Type (0018,0023) Slice Thickness (0018,0050) Repetition Time (0018,0080) Echo Time (0018,0081) Inversion Time (0018,0082) Imaging Frequency (0018,0084) Magnetic Field Strength (0018,0087) Manufacturer's Model Name (0008,1090) Spacing Between Slices (0018,0088) Echo Train Length (0018,0091) Percent Sampling (0018,0093) Pixel Bandwidth (0018,0095) Flip Angle (0018,1314) Patient Position (0018,5100) Image Position (Patient) (0020,0032) Image Orientation (Patient) (0020,0037) Position Reference Indicator (0020,1040) Slice Location (0020,1041) Rows (0028,0010) Columns (0028,0011) Pixel Spacing (0028,0030) Bits Allocated (0028,0100) Number of Averages (0018,0083) Echo Number(s) (0018,0086) (0018,9461) +mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-2_vp-sag_Stir.nii.gz 12 Sag GE MEDICAL SYSTEMS SAGITALSTIR SIGNA EXCITE 171834704726005099248999303401096937503 F 046Y 72 RM NONE FC_FREQ_AX_GEMS\FC\SAT_GEMS\VB_GEMS\EDR_GEMS\SEQ_GEMS\TRF_GEM... 2D 4.5 4100 42.66 150 63.869763 1.5 SIGNA EXCITE 5.5 19 100 122.07 90 HFS -12.5002\-169.707\222.878 -0\1\0\-0\-0\-1 12.50024414 512 512 0.585938\0.585938 16 3 1 None +mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-3_vp-sag_T2w.nii.gz 12 Sag GE MEDICAL SYSTEMS SAGT2LUMBAR SIGNA EXCITE 171834704726005099248999303401096937503 F 046Y 72 SE OSP SAT_GEMS\NPW\VB_GEMS\TRF_GEMS\FILTERED_GEMS\SP 2D 4.5 3440 110 0 63.869763 1.5 SIGNA EXCITE 5.5 29 100 162.773 90 HFS 20.4998\-169.707\222.878 -0\1\0\-0\-0\-1 -20.49975586 512 512 0.585938\0.585938 16 2 1 None +mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-1_vp-sag_T1w.nii.gz 12 Sag GE MEDICAL SYSTEMS SAGT1LUMBAR SIGNA EXCITE 171834704726005099248999303401096937503 F 046Y 72 RM NONE FC_FREQ_AX_GEMS\FC\SAT_GEMS\VB_GEMS\TRF_GEMS\FILTERED_GEMS\SP 2D 4.5 400 15.072 0 63.869763 1.5 SIGNA EXCITE 5.5 4 100 139.492 90 HFS 3.99976\-169.707\222.878 -0\1\0\-0\-0\-1 -3.999755859 512 512 0.585938\0.585938 16 3 1 None +mr/anat/sub-1_ses-1_bp-lsspine_acq-1_run-4_vp-ax_T2w.nii.gz,mr/anat/sub-1_ses-1_bp-lsspine_acq-3_run-4_vp-ax_T2w.nii.gz,mr/anat/sub-1_ses-1_bp-lsspine_acq-4_run-4_vp-ax_T2w.nii.gz,mr/anat/sub-1_ses-1_bp-lsspine_acq-5_run-4_vp-ax_T2w.nii.gz,mr/anat/sub-1_ses-1_bp-lsspine_acq-6_run-4_vp-ax_T2w.nii.gz,mr/anat/sub-1_ses-1_bp-lsspine_acq-2_run-4_vp-ax_T2w.nii.gz 24 GE MEDICAL SYSTEMS AXIALT2DISCBASICO SIGNA EXCITE 171834704726005099248999303401096937503 F 046Y 72 SE NONE SAT_GEMS\VB_GEMS\TRF_GEMS\FILTERED_GEMS\SP 2D 3.5 3400 107.2 0 63.869753 1.5 SIGNA EXCITE 4.5 29 100 162.773 90 HFS -106.805\-110.059\71.0907 1\-0\0\-0\0.993135\0.116978 82.76560974 512 512 0.390625\0.390625 16 3 1 None diff --git a/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-1_vp-sag_T1w.json b/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-1_vp-sag_T1w.json new file mode 100644 index 0000000..9c536e6 --- /dev/null +++ b/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-1_vp-sag_T1w.json @@ -0,0 +1,881 @@ +{ + "ResultSet": { + "Result": [ + { + "desc": "File Meta Information Version", + "tag1": "(0002,0001)", + "tag2": "", + "value": "00\\01", + "vr": "OB" + }, + { + "desc": "Media Storage SOP Class UID", + "tag1": "(0002,0002)", + "tag2": "", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Media Storage SOP Instance UID", + "tag1": "(0002,0003)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.15477.1466833583.475", + "vr": "UI" + }, + { + "desc": "Transfer Syntax UID", + "tag1": "(0002,0010)", + "tag2": "", + "value": "1.2.840.10008.1.2.1", + "vr": "UI" + }, + { + "desc": "Implementation Class UID", + "tag1": "(0002,0012)", + "tag2": "", + "value": "1.2.40.0.13.1.1", + "vr": "UI" + }, + { + "desc": "Implementation Version Name", + "tag1": "(0002,0013)", + "tag2": "", + "value": "dcm4che-2.0", + "vr": "SH" + }, + { + "desc": "Source Application Entity Title", + "tag1": "(0002,0016)", + "tag2": "", + "value": "CTP", + "vr": "AE" + }, + { + "desc": "Specific Character Set", + "tag1": "(0008,0005)", + "tag2": "", + "value": "ISO_IR 100", + "vr": "CS" + }, + { + "desc": "Image Type", + "tag1": "(0008,0008)", + "tag2": "", + "value": "ORIGINAL\\PRIMARY\\OTHER", + "vr": "CS" + }, + { + "desc": "SOP Class UID", + "tag1": "(0008,0016)", + "tag2": "", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "SOP Instance UID", + "tag1": "(0008,0018)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.15477.1466833583.475", + "vr": "UI" + }, + { + "desc": "Study Date", + "tag1": "(0008,0020)", + "tag2": "", + "value": "20160625", + "vr": "DA" + }, + { + "desc": "Series Date", + "tag1": "(0008,0021)", + "tag2": "", + "value": "20160625", + "vr": "DA" + }, + { + "desc": "Acquisition Date", + "tag1": "(0008,0022)", + "tag2": "", + "value": "20160625", + "vr": "DA" + }, + { + "desc": "Content Date", + "tag1": "(0008,0023)", + "tag2": "", + "value": "20160625", + "vr": "DA" + }, + { + "desc": "Study Time", + "tag1": "(0008,0030)", + "tag2": "", + "value": "134718", + "vr": "TM" + }, + { + "desc": "Series Time", + "tag1": "(0008,0031)", + "tag2": "", + "value": "135056", + "vr": "TM" + }, + { + "desc": "Acquisition Time", + "tag1": "(0008,0032)", + "tag2": "", + "value": "135056", + "vr": "TM" + }, + { + "desc": "Content Time", + "tag1": "(0008,0033)", + "tag2": "", + "value": "135056", + "vr": "TM" + }, + { + "desc": "Accession Number", + "tag1": "(0008,0050)", + "tag2": "", + "value": "ceibcs_E19348", + "vr": "SH" + }, + { + "desc": "Modality", + "tag1": "(0008,0060)", + "tag2": "", + "value": "MR", + "vr": "CS" + }, + { + "desc": "Manufacturer", + "tag1": "(0008,0070)", + "tag2": "", + "value": "GE MEDICAL SYSTEMS", + "vr": "LO" + }, + { + "desc": "Referring Physician's Name", + "tag1": "(0008,0090)", + "tag2": "", + "value": "", + "vr": "PN" + }, + { + "desc": "Station Name", + "tag1": "(0008,1010)", + "tag2": "", + "value": "CASTMRI", + "vr": "SH" + }, + { + "desc": "Study Description", + "tag1": "(0008,1030)", + "tag2": "", + "value": "MRI_Lumbar", + "vr": "LO" + }, + { + "desc": "Procedure Code Sequence", + "tag1": "(0008,1032)", + "tag2": "(0008,1032)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Code Value", + "tag1": "(0008,1032)", + "tag2": "(0008,0100)", + "value": "015001_RM816", + "vr": "SH" + }, + { + "desc": "Coding Scheme Designator", + "tag1": "(0008,1032)", + "tag2": "(0008,0102)", + "value": "GEIIS", + "vr": "SH" + }, + { + "desc": "Coding Scheme Version", + "tag1": "(0008,1032)", + "tag2": "(0008,0103)", + "value": "0", + "vr": "SH" + }, + { + "desc": "Code Meaning", + "tag1": "(0008,1032)", + "tag2": "(0008,0104)", + "value": "RM LUMBAR", + "vr": "LO" + }, + { + "desc": "Series Description", + "tag1": "(0008,103E)", + "tag2": "", + "value": "SAGT1LUMBAR", + "vr": "LO" + }, + { + "desc": "Manufacturer's Model Name", + "tag1": "(0008,1090)", + "tag2": "", + "value": "SIGNA EXCITE", + "vr": "LO" + }, + { + "desc": "Referenced Image Sequence", + "tag1": "(0008,1140)", + "tag2": "(0008,1140)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Referenced SOP Class UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1150)", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Referenced SOP Instance UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1155)", + "value": "1.2.840.113619.2.222.2025.1616754.15477.1466833583.320", + "vr": "UI" + }, + { + "desc": "Referenced Image Sequence", + "tag1": "(0008,1140)", + "tag2": "(0008,1140)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Referenced SOP Class UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1150)", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Referenced SOP Instance UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1155)", + "value": "1.2.840.113619.2.222.2025.1616754.15477.1466833583.314", + "vr": "UI" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0009,0010)", + "tag2": "", + "value": "GEMS_IDEN_01", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0009,0011)", + "tag2": "", + "value": "GEIIS", + "vr": "LO" + }, + { + "desc": "Patient's Name", + "tag1": "(0010,0010)", + "tag2": "", + "value": "90070970630437776381142865766563279659", + "vr": "PN" + }, + { + "desc": "Patient ID", + "tag1": "(0010,0020)", + "tag2": "", + "value": "35180663179348213717850348575679254082", + "vr": "LO" + }, + { + "desc": "Patient's Birth Date", + "tag1": "(0010,0030)", + "tag2": "", + "value": "19960802", + "vr": "DA" + }, + { + "desc": "Patient's Sex", + "tag1": "(0010,0040)", + "tag2": "", + "value": "F", + "vr": "CS" + }, + { + "desc": "Patient's Age", + "tag1": "(0010,1010)", + "tag2": "", + "value": "019Y", + "vr": "AS" + }, + { + "desc": "Patient's Weight", + "tag1": "(0010,1030)", + "tag2": "", + "value": "65", + "vr": "DS" + }, + { + "desc": "Additional Patient History", + "tag1": "(0010,21B0)", + "tag2": "", + "value": "", + "vr": "LT" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0011,0010)", + "tag2": "", + "value": "GEMS_PATI_01", + "vr": "LO" + }, + { + "desc": "Scanning Sequence", + "tag1": "(0018,0020)", + "tag2": "", + "value": "RM", + "vr": "CS" + }, + { + "desc": "Sequence Variant", + "tag1": "(0018,0021)", + "tag2": "", + "value": "OSP", + "vr": "CS" + }, + { + "desc": "Scan Options", + "tag1": "(0018,0022)", + "tag2": "", + "value": "FC_FREQ_AX_GEMS\\FC\\NPW\\VB_GEMS\\TRF_GEMS\\FILTERED_GEMS", + "vr": "CS" + }, + { + "desc": "MR Acquisition Type", + "tag1": "(0018,0023)", + "tag2": "", + "value": "2D", + "vr": "CS" + }, + { + "desc": "Angio Flag", + "tag1": "(0018,0025)", + "tag2": "", + "value": "N", + "vr": "CS" + }, + { + "desc": "Slice Thickness", + "tag1": "(0018,0050)", + "tag2": "", + "value": "4.5", + "vr": "DS" + }, + { + "desc": "Repetition Time", + "tag1": "(0018,0080)", + "tag2": "", + "value": "300", + "vr": "DS" + }, + { + "desc": "Echo Time", + "tag1": "(0018,0081)", + "tag2": "", + "value": "14.976", + "vr": "DS" + }, + { + "desc": "Inversion Time", + "tag1": "(0018,0082)", + "tag2": "", + "value": "0", + "vr": "DS" + }, + { + "desc": "Number of Averages", + "tag1": "(0018,0083)", + "tag2": "", + "value": "1", + "vr": "DS" + }, + { + "desc": "Imaging Frequency", + "tag1": "(0018,0084)", + "tag2": "", + "value": "63.869726", + "vr": "DS" + }, + { + "desc": "Imaged Nucleus", + "tag1": "(0018,0085)", + "tag2": "", + "value": "1H", + "vr": "SH" + }, + { + "desc": "Echo Number(s)", + "tag1": "(0018,0086)", + "tag2": "", + "value": "1", + "vr": "IS" + }, + { + "desc": "Magnetic Field Strength", + "tag1": "(0018,0087)", + "tag2": "", + "value": "1.5", + "vr": "DS" + }, + { + "desc": "Spacing Between Slices", + "tag1": "(0018,0088)", + "tag2": "", + "value": "5.5", + "vr": "DS" + }, + { + "desc": "Echo Train Length", + "tag1": "(0018,0091)", + "tag2": "", + "value": "4", + "vr": "IS" + }, + { + "desc": "Percent Sampling", + "tag1": "(0018,0093)", + "tag2": "", + "value": "100", + "vr": "DS" + }, + { + "desc": "Percent Phase Field of View", + "tag1": "(0018,0094)", + "tag2": "", + "value": "100", + "vr": "DS" + }, + { + "desc": "Pixel Bandwidth", + "tag1": "(0018,0095)", + "tag2": "", + "value": "139.492", + "vr": "DS" + }, + { + "desc": "Device Serial Number", + "tag1": "(0018,1000)", + "tag2": "", + "value": "00000000NPV24200", + "vr": "LO" + }, + { + "desc": "Software Version(s)", + "tag1": "(0018,1020)", + "tag2": "", + "value": "11\\LX\\MR Software release:11.1_M4_0818.a", + "vr": "LO" + }, + { + "desc": "Protocol Name", + "tag1": "(0018,1030)", + "tag2": "", + "value": "LUMBAR", + "vr": "LO" + }, + { + "desc": "Heart Rate", + "tag1": "(0018,1088)", + "tag2": "", + "value": "0", + "vr": "IS" + }, + { + "desc": "Cardiac Number of Images", + "tag1": "(0018,1090)", + "tag2": "", + "value": "0", + "vr": "IS" + }, + { + "desc": "Trigger Window", + "tag1": "(0018,1094)", + "tag2": "", + "value": "0", + "vr": "IS" + }, + { + "desc": "Reconstruction Diameter", + "tag1": "(0018,1100)", + "tag2": "", + "value": "320", + "vr": "DS" + }, + { + "desc": "Receive Coil Name", + "tag1": "(0018,1250)", + "tag2": "", + "value": "USCTLBOT", + "vr": "SH" + }, + { + "desc": "Acquisition Matrix", + "tag1": "(0018,1310)", + "tag2": "", + "value": "320\\0\\0\\224", + "vr": "US" + }, + { + "desc": "In-plane Phase Encoding Direction", + "tag1": "(0018,1312)", + "tag2": "", + "value": "COL", + "vr": "CS" + }, + { + "desc": "Flip Angle", + "tag1": "(0018,1314)", + "tag2": "", + "value": "90", + "vr": "DS" + }, + { + "desc": "Variable Flip Angle Flag", + "tag1": "(0018,1315)", + "tag2": "", + "value": "N", + "vr": "CS" + }, + { + "desc": "SAR", + "tag1": "(0018,1316)", + "tag2": "", + "value": "1.119700", + "vr": "DS" + }, + { + "desc": "Patient Position", + "tag1": "(0018,5100)", + "tag2": "", + "value": "HFS", + "vr": "CS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0019,0010)", + "tag2": "", + "value": "GEMS_ACQU_01", + "vr": "LO" + }, + { + "desc": "?", + "tag1": "(0019,10BB)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10BC)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10BD)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10D9)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10DF)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10E0)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "Study Instance UID", + "tag1": "(0020,000D)", + "tag2": "", + "value": "1.2.840.113619.2.182.10808617210140.1466503585.135941", + "vr": "UI" + }, + { + "desc": "Series Instance UID", + "tag1": "(0020,000E)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.15477.1466833583.400", + "vr": "UI" + }, + { + "desc": "Study ID", + "tag1": "(0020,0010)", + "tag2": "", + "value": "", + "vr": "SH" + }, + { + "desc": "Series Number", + "tag1": "(0020,0011)", + "tag2": "", + "value": "3", + "vr": "IS" + }, + { + "desc": "Acquisition Number", + "tag1": "(0020,0012)", + "tag2": "", + "value": "1", + "vr": "IS" + }, + { + "desc": "Instance Number", + "tag1": "(0020,0013)", + "tag2": "", + "value": "8", + "vr": "IS" + }, + { + "desc": "Image Position (Patient)", + "tag1": "(0020,0032)", + "tag2": "", + "value": "-3.09914\\-173.346\\194.882", + "vr": "DS" + }, + { + "desc": "Image Orientation (Patient)", + "tag1": "(0020,0037)", + "tag2": "", + "value": "-0\\1\\0\\0.0100102\\-0\\-0.99995", + "vr": "DS" + }, + { + "desc": "Frame of Reference UID", + "tag1": "(0020,0052)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.15543.1466833318.370", + "vr": "UI" + }, + { + "desc": "Laterality", + "tag1": "(0020,0060)", + "tag2": "", + "value": "", + "vr": "CS" + }, + { + "desc": "Temporal Resolution", + "tag1": "(0020,0110)", + "tag2": "", + "value": "0", + "vr": "DS" + }, + { + "desc": "Position Reference Indicator", + "tag1": "(0020,1040)", + "tag2": "", + "value": "", + "vr": "LO" + }, + { + "desc": "Slice Location", + "tag1": "(0020,1041)", + "tag2": "", + "value": "1.500656366", + "vr": "DS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0021,0010)", + "tag2": "", + "value": "GEMS_RELA_01", + "vr": "LO" + }, + { + "desc": "?", + "tag1": "(0021,105A)", + "tag2": "", + "value": "0", + "vr": "SL" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0023,0010)", + "tag2": "", + "value": "GEMS_STDY_01", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0025,0010)", + "tag2": "", + "value": "GEMS_SERS_01", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0027,0010)", + "tag2": "", + "value": "GEMS_IMAG_01", + "vr": "LO" + }, + { + "desc": "Samples per Pixel", + "tag1": "(0028,0002)", + "tag2": "", + "value": "1", + "vr": "US" + }, + { + "desc": "Photometric Interpretation", + "tag1": "(0028,0004)", + "tag2": "", + "value": "MONOCHROME2", + "vr": "CS" + }, + { + "desc": "Rows", + "tag1": "(0028,0010)", + "tag2": "", + "value": "512", + "vr": "US" + }, + { + "desc": "Columns", + "tag1": "(0028,0011)", + "tag2": "", + "value": "512", + "vr": "US" + }, + { + "desc": "Pixel Spacing", + "tag1": "(0028,0030)", + "tag2": "", + "value": "0.624993\\0.625", + "vr": "DS" + }, + { + "desc": "Bits Allocated", + "tag1": "(0028,0100)", + "tag2": "", + "value": "16", + "vr": "US" + }, + { + "desc": "Bits Stored", + "tag1": "(0028,0101)", + "tag2": "", + "value": "16", + "vr": "US" + }, + { + "desc": "High Bit", + "tag1": "(0028,0102)", + "tag2": "", + "value": "15", + "vr": "US" + }, + { + "desc": "Pixel Representation", + "tag1": "(0028,0103)", + "tag2": "", + "value": "1", + "vr": "US" + }, + { + "desc": "?", + "tag1": "(0028,0303)", + "tag2": "", + "value": "", + "vr": "CS" + }, + { + "desc": "Window Center", + "tag1": "(0028,1050)", + "tag2": "", + "value": "507", + "vr": "DS" + }, + { + "desc": "Window Width", + "tag1": "(0028,1051)", + "tag2": "", + "value": "1014", + "vr": "DS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0029,0010)", + "tag2": "", + "value": "GEMS_IMPS_01", + "vr": "LO" + }, + { + "desc": "Performed Procedure Step Description", + "tag1": "(0040,0254)", + "tag2": "", + "value": "", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0043,0010)", + "tag2": "", + "value": "GEMS_PARM_01", + "vr": "LO" + }, + { + "desc": "?", + "tag1": "(0043,1039)", + "tag2": "", + "value": "0\\0\\0\\0", + "vr": "IS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0903,0010)", + "tag2": "", + "value": "GEIIS PACS", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0905,0010)", + "tag2": "", + "value": "GEIIS", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(7FD1,0010)", + "tag2": "", + "value": "GEIIS", + "vr": "LO" + } + ] + } +} \ No newline at end of file diff --git a/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-1_vp-sag_T1w.nii.gz b/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-1_vp-sag_T1w.nii.gz new file mode 100644 index 0000000..affed3a Binary files /dev/null and b/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-1_vp-sag_T1w.nii.gz differ diff --git a/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-2_vp-sag_Stir.json b/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-2_vp-sag_Stir.json new file mode 100644 index 0000000..cc82d1c --- /dev/null +++ b/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-2_vp-sag_Stir.json @@ -0,0 +1,881 @@ +{ + "ResultSet": { + "Result": [ + { + "desc": "File Meta Information Version", + "tag1": "(0002,0001)", + "tag2": "", + "value": "00\\01", + "vr": "OB" + }, + { + "desc": "Media Storage SOP Class UID", + "tag1": "(0002,0002)", + "tag2": "", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Media Storage SOP Instance UID", + "tag1": "(0002,0003)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.15477.1466833583.553", + "vr": "UI" + }, + { + "desc": "Transfer Syntax UID", + "tag1": "(0002,0010)", + "tag2": "", + "value": "1.2.840.10008.1.2.1", + "vr": "UI" + }, + { + "desc": "Implementation Class UID", + "tag1": "(0002,0012)", + "tag2": "", + "value": "1.2.40.0.13.1.1", + "vr": "UI" + }, + { + "desc": "Implementation Version Name", + "tag1": "(0002,0013)", + "tag2": "", + "value": "dcm4che-2.0", + "vr": "SH" + }, + { + "desc": "Source Application Entity Title", + "tag1": "(0002,0016)", + "tag2": "", + "value": "CTP", + "vr": "AE" + }, + { + "desc": "Specific Character Set", + "tag1": "(0008,0005)", + "tag2": "", + "value": "ISO_IR 100", + "vr": "CS" + }, + { + "desc": "Image Type", + "tag1": "(0008,0008)", + "tag2": "", + "value": "ORIGINAL\\PRIMARY\\OTHER", + "vr": "CS" + }, + { + "desc": "SOP Class UID", + "tag1": "(0008,0016)", + "tag2": "", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "SOP Instance UID", + "tag1": "(0008,0018)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.15477.1466833583.553", + "vr": "UI" + }, + { + "desc": "Study Date", + "tag1": "(0008,0020)", + "tag2": "", + "value": "20160625", + "vr": "DA" + }, + { + "desc": "Series Date", + "tag1": "(0008,0021)", + "tag2": "", + "value": "20160625", + "vr": "DA" + }, + { + "desc": "Acquisition Date", + "tag1": "(0008,0022)", + "tag2": "", + "value": "20160625", + "vr": "DA" + }, + { + "desc": "Content Date", + "tag1": "(0008,0023)", + "tag2": "", + "value": "20160625", + "vr": "DA" + }, + { + "desc": "Study Time", + "tag1": "(0008,0030)", + "tag2": "", + "value": "134718", + "vr": "TM" + }, + { + "desc": "Series Time", + "tag1": "(0008,0031)", + "tag2": "", + "value": "135219", + "vr": "TM" + }, + { + "desc": "Acquisition Time", + "tag1": "(0008,0032)", + "tag2": "", + "value": "135219", + "vr": "TM" + }, + { + "desc": "Content Time", + "tag1": "(0008,0033)", + "tag2": "", + "value": "135219", + "vr": "TM" + }, + { + "desc": "Accession Number", + "tag1": "(0008,0050)", + "tag2": "", + "value": "ceibcs_E19348", + "vr": "SH" + }, + { + "desc": "Modality", + "tag1": "(0008,0060)", + "tag2": "", + "value": "MR", + "vr": "CS" + }, + { + "desc": "Manufacturer", + "tag1": "(0008,0070)", + "tag2": "", + "value": "GE MEDICAL SYSTEMS", + "vr": "LO" + }, + { + "desc": "Referring Physician's Name", + "tag1": "(0008,0090)", + "tag2": "", + "value": "", + "vr": "PN" + }, + { + "desc": "Station Name", + "tag1": "(0008,1010)", + "tag2": "", + "value": "CASTMRI", + "vr": "SH" + }, + { + "desc": "Study Description", + "tag1": "(0008,1030)", + "tag2": "", + "value": "MRI_Lumbar", + "vr": "LO" + }, + { + "desc": "Procedure Code Sequence", + "tag1": "(0008,1032)", + "tag2": "(0008,1032)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Code Value", + "tag1": "(0008,1032)", + "tag2": "(0008,0100)", + "value": "015001_RM816", + "vr": "SH" + }, + { + "desc": "Coding Scheme Designator", + "tag1": "(0008,1032)", + "tag2": "(0008,0102)", + "value": "GEIIS", + "vr": "SH" + }, + { + "desc": "Coding Scheme Version", + "tag1": "(0008,1032)", + "tag2": "(0008,0103)", + "value": "0", + "vr": "SH" + }, + { + "desc": "Code Meaning", + "tag1": "(0008,1032)", + "tag2": "(0008,0104)", + "value": "RM LUMBAR", + "vr": "LO" + }, + { + "desc": "Series Description", + "tag1": "(0008,103E)", + "tag2": "", + "value": "SAGITALSTIR", + "vr": "LO" + }, + { + "desc": "Manufacturer's Model Name", + "tag1": "(0008,1090)", + "tag2": "", + "value": "SIGNA EXCITE", + "vr": "LO" + }, + { + "desc": "Referenced Image Sequence", + "tag1": "(0008,1140)", + "tag2": "(0008,1140)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Referenced SOP Class UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1150)", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Referenced SOP Instance UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1155)", + "value": "1.2.840.113619.2.222.2025.1616754.15477.1466833583.320", + "vr": "UI" + }, + { + "desc": "Referenced Image Sequence", + "tag1": "(0008,1140)", + "tag2": "(0008,1140)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Referenced SOP Class UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1150)", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Referenced SOP Instance UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1155)", + "value": "1.2.840.113619.2.222.2025.1616754.15477.1466833583.314", + "vr": "UI" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0009,0010)", + "tag2": "", + "value": "GEMS_IDEN_01", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0009,0011)", + "tag2": "", + "value": "GEIIS", + "vr": "LO" + }, + { + "desc": "Patient's Name", + "tag1": "(0010,0010)", + "tag2": "", + "value": "90070970630437776381142865766563279659", + "vr": "PN" + }, + { + "desc": "Patient ID", + "tag1": "(0010,0020)", + "tag2": "", + "value": "35180663179348213717850348575679254082", + "vr": "LO" + }, + { + "desc": "Patient's Birth Date", + "tag1": "(0010,0030)", + "tag2": "", + "value": "19960802", + "vr": "DA" + }, + { + "desc": "Patient's Sex", + "tag1": "(0010,0040)", + "tag2": "", + "value": "F", + "vr": "CS" + }, + { + "desc": "Patient's Age", + "tag1": "(0010,1010)", + "tag2": "", + "value": "019Y", + "vr": "AS" + }, + { + "desc": "Patient's Weight", + "tag1": "(0010,1030)", + "tag2": "", + "value": "65", + "vr": "DS" + }, + { + "desc": "Additional Patient History", + "tag1": "(0010,21B0)", + "tag2": "", + "value": "", + "vr": "LT" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0011,0010)", + "tag2": "", + "value": "GEMS_PATI_01", + "vr": "LO" + }, + { + "desc": "Scanning Sequence", + "tag1": "(0018,0020)", + "tag2": "", + "value": "RM", + "vr": "CS" + }, + { + "desc": "Sequence Variant", + "tag1": "(0018,0021)", + "tag2": "", + "value": "NONE", + "vr": "CS" + }, + { + "desc": "Scan Options", + "tag1": "(0018,0022)", + "tag2": "", + "value": "FC_FREQ_AX_GEMS\\FC\\SAT_GEMS\\VB_GEMS\\EDR_GEMS\\SEQ_GEMS\\TRF_GEM...", + "vr": "CS" + }, + { + "desc": "MR Acquisition Type", + "tag1": "(0018,0023)", + "tag2": "", + "value": "2D", + "vr": "CS" + }, + { + "desc": "Angio Flag", + "tag1": "(0018,0025)", + "tag2": "", + "value": "N", + "vr": "CS" + }, + { + "desc": "Slice Thickness", + "tag1": "(0018,0050)", + "tag2": "", + "value": "4.5", + "vr": "DS" + }, + { + "desc": "Repetition Time", + "tag1": "(0018,0080)", + "tag2": "", + "value": "4100", + "vr": "DS" + }, + { + "desc": "Echo Time", + "tag1": "(0018,0081)", + "tag2": "", + "value": "42.444", + "vr": "DS" + }, + { + "desc": "Inversion Time", + "tag1": "(0018,0082)", + "tag2": "", + "value": "150", + "vr": "DS" + }, + { + "desc": "Number of Averages", + "tag1": "(0018,0083)", + "tag2": "", + "value": "3", + "vr": "DS" + }, + { + "desc": "Imaging Frequency", + "tag1": "(0018,0084)", + "tag2": "", + "value": "63.869729", + "vr": "DS" + }, + { + "desc": "Imaged Nucleus", + "tag1": "(0018,0085)", + "tag2": "", + "value": "1H", + "vr": "SH" + }, + { + "desc": "Echo Number(s)", + "tag1": "(0018,0086)", + "tag2": "", + "value": "1", + "vr": "IS" + }, + { + "desc": "Magnetic Field Strength", + "tag1": "(0018,0087)", + "tag2": "", + "value": "1.5", + "vr": "DS" + }, + { + "desc": "Spacing Between Slices", + "tag1": "(0018,0088)", + "tag2": "", + "value": "5.5", + "vr": "DS" + }, + { + "desc": "Echo Train Length", + "tag1": "(0018,0091)", + "tag2": "", + "value": "19", + "vr": "IS" + }, + { + "desc": "Percent Sampling", + "tag1": "(0018,0093)", + "tag2": "", + "value": "100", + "vr": "DS" + }, + { + "desc": "Percent Phase Field of View", + "tag1": "(0018,0094)", + "tag2": "", + "value": "90", + "vr": "DS" + }, + { + "desc": "Pixel Bandwidth", + "tag1": "(0018,0095)", + "tag2": "", + "value": "122.07", + "vr": "DS" + }, + { + "desc": "Device Serial Number", + "tag1": "(0018,1000)", + "tag2": "", + "value": "00000000NPV24200", + "vr": "LO" + }, + { + "desc": "Software Version(s)", + "tag1": "(0018,1020)", + "tag2": "", + "value": "11\\LX\\MR Software release:11.1_M4_0818.a", + "vr": "LO" + }, + { + "desc": "Protocol Name", + "tag1": "(0018,1030)", + "tag2": "", + "value": "LUMBAR", + "vr": "LO" + }, + { + "desc": "Heart Rate", + "tag1": "(0018,1088)", + "tag2": "", + "value": "0", + "vr": "IS" + }, + { + "desc": "Cardiac Number of Images", + "tag1": "(0018,1090)", + "tag2": "", + "value": "0", + "vr": "IS" + }, + { + "desc": "Trigger Window", + "tag1": "(0018,1094)", + "tag2": "", + "value": "0", + "vr": "IS" + }, + { + "desc": "Reconstruction Diameter", + "tag1": "(0018,1100)", + "tag2": "", + "value": "320", + "vr": "DS" + }, + { + "desc": "Receive Coil Name", + "tag1": "(0018,1250)", + "tag2": "", + "value": "USCTLBOT", + "vr": "SH" + }, + { + "desc": "Acquisition Matrix", + "tag1": "(0018,1310)", + "tag2": "", + "value": "0\\256\\192\\0", + "vr": "US" + }, + { + "desc": "In-plane Phase Encoding Direction", + "tag1": "(0018,1312)", + "tag2": "", + "value": "ROW", + "vr": "CS" + }, + { + "desc": "Flip Angle", + "tag1": "(0018,1314)", + "tag2": "", + "value": "90", + "vr": "DS" + }, + { + "desc": "Variable Flip Angle Flag", + "tag1": "(0018,1315)", + "tag2": "", + "value": "N", + "vr": "CS" + }, + { + "desc": "SAR", + "tag1": "(0018,1316)", + "tag2": "", + "value": "0.794900", + "vr": "DS" + }, + { + "desc": "Patient Position", + "tag1": "(0018,5100)", + "tag2": "", + "value": "HFS", + "vr": "CS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0019,0010)", + "tag2": "", + "value": "GEMS_ACQU_01", + "vr": "LO" + }, + { + "desc": "?", + "tag1": "(0019,10BB)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10BC)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10BD)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10D9)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10DF)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10E0)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "Study Instance UID", + "tag1": "(0020,000D)", + "tag2": "", + "value": "1.2.840.113619.2.182.10808617210140.1466503585.135941", + "vr": "UI" + }, + { + "desc": "Series Instance UID", + "tag1": "(0020,000E)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.15477.1466833583.478", + "vr": "UI" + }, + { + "desc": "Study ID", + "tag1": "(0020,0010)", + "tag2": "", + "value": "", + "vr": "SH" + }, + { + "desc": "Series Number", + "tag1": "(0020,0011)", + "tag2": "", + "value": "4", + "vr": "IS" + }, + { + "desc": "Acquisition Number", + "tag1": "(0020,0012)", + "tag2": "", + "value": "1", + "vr": "IS" + }, + { + "desc": "Instance Number", + "tag1": "(0020,0013)", + "tag2": "", + "value": "10", + "vr": "IS" + }, + { + "desc": "Image Position (Patient)", + "tag1": "(0020,0032)", + "tag2": "", + "value": "7.90031\\-173.346\\194.992", + "vr": "DS" + }, + { + "desc": "Image Orientation (Patient)", + "tag1": "(0020,0037)", + "tag2": "", + "value": "-0\\1\\0\\0.0100102\\-0\\-0.99995", + "vr": "DS" + }, + { + "desc": "Frame of Reference UID", + "tag1": "(0020,0052)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.15543.1466833318.370", + "vr": "UI" + }, + { + "desc": "Laterality", + "tag1": "(0020,0060)", + "tag2": "", + "value": "", + "vr": "CS" + }, + { + "desc": "Temporal Resolution", + "tag1": "(0020,0110)", + "tag2": "", + "value": "0", + "vr": "DS" + }, + { + "desc": "Position Reference Indicator", + "tag1": "(0020,1040)", + "tag2": "", + "value": "", + "vr": "LO" + }, + { + "desc": "Slice Location", + "tag1": "(0020,1041)", + "tag2": "", + "value": "-9.498793602", + "vr": "DS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0021,0010)", + "tag2": "", + "value": "GEMS_RELA_01", + "vr": "LO" + }, + { + "desc": "?", + "tag1": "(0021,105A)", + "tag2": "", + "value": "0", + "vr": "SL" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0023,0010)", + "tag2": "", + "value": "GEMS_STDY_01", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0025,0010)", + "tag2": "", + "value": "GEMS_SERS_01", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0027,0010)", + "tag2": "", + "value": "GEMS_IMAG_01", + "vr": "LO" + }, + { + "desc": "Samples per Pixel", + "tag1": "(0028,0002)", + "tag2": "", + "value": "1", + "vr": "US" + }, + { + "desc": "Photometric Interpretation", + "tag1": "(0028,0004)", + "tag2": "", + "value": "MONOCHROME2", + "vr": "CS" + }, + { + "desc": "Rows", + "tag1": "(0028,0010)", + "tag2": "", + "value": "512", + "vr": "US" + }, + { + "desc": "Columns", + "tag1": "(0028,0011)", + "tag2": "", + "value": "512", + "vr": "US" + }, + { + "desc": "Pixel Spacing", + "tag1": "(0028,0030)", + "tag2": "", + "value": "0.624993\\0.625", + "vr": "DS" + }, + { + "desc": "Bits Allocated", + "tag1": "(0028,0100)", + "tag2": "", + "value": "16", + "vr": "US" + }, + { + "desc": "Bits Stored", + "tag1": "(0028,0101)", + "tag2": "", + "value": "16", + "vr": "US" + }, + { + "desc": "High Bit", + "tag1": "(0028,0102)", + "tag2": "", + "value": "15", + "vr": "US" + }, + { + "desc": "Pixel Representation", + "tag1": "(0028,0103)", + "tag2": "", + "value": "1", + "vr": "US" + }, + { + "desc": "?", + "tag1": "(0028,0303)", + "tag2": "", + "value": "", + "vr": "CS" + }, + { + "desc": "Window Center", + "tag1": "(0028,1050)", + "tag2": "", + "value": "197", + "vr": "DS" + }, + { + "desc": "Window Width", + "tag1": "(0028,1051)", + "tag2": "", + "value": "395", + "vr": "DS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0029,0010)", + "tag2": "", + "value": "GEMS_IMPS_01", + "vr": "LO" + }, + { + "desc": "Performed Procedure Step Description", + "tag1": "(0040,0254)", + "tag2": "", + "value": "", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0043,0010)", + "tag2": "", + "value": "GEMS_PARM_01", + "vr": "LO" + }, + { + "desc": "?", + "tag1": "(0043,1039)", + "tag2": "", + "value": "0\\32\\0\\0", + "vr": "IS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0903,0010)", + "tag2": "", + "value": "GEIIS PACS", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0905,0010)", + "tag2": "", + "value": "GEIIS", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(7FD1,0010)", + "tag2": "", + "value": "GEIIS", + "vr": "LO" + } + ] + } +} \ No newline at end of file diff --git a/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-2_vp-sag_Stir.nii.gz b/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-2_vp-sag_Stir.nii.gz new file mode 100644 index 0000000..7a32abd Binary files /dev/null and b/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-2_vp-sag_Stir.nii.gz differ diff --git a/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-3_vp-sag_T2w.json b/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-3_vp-sag_T2w.json new file mode 100644 index 0000000..e66ba6c --- /dev/null +++ b/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-3_vp-sag_T2w.json @@ -0,0 +1,881 @@ +{ + "ResultSet": { + "Result": [ + { + "desc": "File Meta Information Version", + "tag1": "(0002,0001)", + "tag2": "", + "value": "00\\01", + "vr": "OB" + }, + { + "desc": "Media Storage SOP Class UID", + "tag1": "(0002,0002)", + "tag2": "", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Media Storage SOP Instance UID", + "tag1": "(0002,0003)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.15477.1466833583.399", + "vr": "UI" + }, + { + "desc": "Transfer Syntax UID", + "tag1": "(0002,0010)", + "tag2": "", + "value": "1.2.840.10008.1.2.1", + "vr": "UI" + }, + { + "desc": "Implementation Class UID", + "tag1": "(0002,0012)", + "tag2": "", + "value": "1.2.40.0.13.1.1", + "vr": "UI" + }, + { + "desc": "Implementation Version Name", + "tag1": "(0002,0013)", + "tag2": "", + "value": "dcm4che-2.0", + "vr": "SH" + }, + { + "desc": "Source Application Entity Title", + "tag1": "(0002,0016)", + "tag2": "", + "value": "CTP", + "vr": "AE" + }, + { + "desc": "Specific Character Set", + "tag1": "(0008,0005)", + "tag2": "", + "value": "ISO_IR 100", + "vr": "CS" + }, + { + "desc": "Image Type", + "tag1": "(0008,0008)", + "tag2": "", + "value": "ORIGINAL\\PRIMARY\\OTHER", + "vr": "CS" + }, + { + "desc": "SOP Class UID", + "tag1": "(0008,0016)", + "tag2": "", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "SOP Instance UID", + "tag1": "(0008,0018)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.15477.1466833583.399", + "vr": "UI" + }, + { + "desc": "Study Date", + "tag1": "(0008,0020)", + "tag2": "", + "value": "20160625", + "vr": "DA" + }, + { + "desc": "Series Date", + "tag1": "(0008,0021)", + "tag2": "", + "value": "20160625", + "vr": "DA" + }, + { + "desc": "Acquisition Date", + "tag1": "(0008,0022)", + "tag2": "", + "value": "20160625", + "vr": "DA" + }, + { + "desc": "Content Date", + "tag1": "(0008,0023)", + "tag2": "", + "value": "20160625", + "vr": "DA" + }, + { + "desc": "Study Time", + "tag1": "(0008,0030)", + "tag2": "", + "value": "134718", + "vr": "TM" + }, + { + "desc": "Series Time", + "tag1": "(0008,0031)", + "tag2": "", + "value": "134818", + "vr": "TM" + }, + { + "desc": "Acquisition Time", + "tag1": "(0008,0032)", + "tag2": "", + "value": "134818", + "vr": "TM" + }, + { + "desc": "Content Time", + "tag1": "(0008,0033)", + "tag2": "", + "value": "134818", + "vr": "TM" + }, + { + "desc": "Accession Number", + "tag1": "(0008,0050)", + "tag2": "", + "value": "ceibcs_E19348", + "vr": "SH" + }, + { + "desc": "Modality", + "tag1": "(0008,0060)", + "tag2": "", + "value": "MR", + "vr": "CS" + }, + { + "desc": "Manufacturer", + "tag1": "(0008,0070)", + "tag2": "", + "value": "GE MEDICAL SYSTEMS", + "vr": "LO" + }, + { + "desc": "Referring Physician's Name", + "tag1": "(0008,0090)", + "tag2": "", + "value": "", + "vr": "PN" + }, + { + "desc": "Station Name", + "tag1": "(0008,1010)", + "tag2": "", + "value": "CASTMRI", + "vr": "SH" + }, + { + "desc": "Study Description", + "tag1": "(0008,1030)", + "tag2": "", + "value": "MRI_LUMBAR", + "vr": "LO" + }, + { + "desc": "Procedure Code Sequence", + "tag1": "(0008,1032)", + "tag2": "(0008,1032)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Code Value", + "tag1": "(0008,1032)", + "tag2": "(0008,0100)", + "value": "015001_RM816", + "vr": "SH" + }, + { + "desc": "Coding Scheme Designator", + "tag1": "(0008,1032)", + "tag2": "(0008,0102)", + "value": "GEIIS", + "vr": "SH" + }, + { + "desc": "Coding Scheme Version", + "tag1": "(0008,1032)", + "tag2": "(0008,0103)", + "value": "0", + "vr": "SH" + }, + { + "desc": "Code Meaning", + "tag1": "(0008,1032)", + "tag2": "(0008,0104)", + "value": "RM LUMBAR", + "vr": "LO" + }, + { + "desc": "Series Description", + "tag1": "(0008,103E)", + "tag2": "", + "value": "SAGT2LUMBAR", + "vr": "LO" + }, + { + "desc": "Manufacturer's Model Name", + "tag1": "(0008,1090)", + "tag2": "", + "value": "SIGNA EXCITE", + "vr": "LO" + }, + { + "desc": "Referenced Image Sequence", + "tag1": "(0008,1140)", + "tag2": "(0008,1140)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Referenced SOP Class UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1150)", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Referenced SOP Instance UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1155)", + "value": "1.2.840.113619.2.222.2025.1616754.15477.1466833583.320", + "vr": "UI" + }, + { + "desc": "Referenced Image Sequence", + "tag1": "(0008,1140)", + "tag2": "(0008,1140)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Referenced SOP Class UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1150)", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Referenced SOP Instance UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1155)", + "value": "1.2.840.113619.2.222.2025.1616754.15477.1466833583.314", + "vr": "UI" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0009,0010)", + "tag2": "", + "value": "GEMS_IDEN_01", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0009,0011)", + "tag2": "", + "value": "GEIIS", + "vr": "LO" + }, + { + "desc": "Patient's Name", + "tag1": "(0010,0010)", + "tag2": "", + "value": "90070970630437776381142865766563279659", + "vr": "PN" + }, + { + "desc": "Patient ID", + "tag1": "(0010,0020)", + "tag2": "", + "value": "35180663179348213717850348575679254082", + "vr": "LO" + }, + { + "desc": "Patient's Birth Date", + "tag1": "(0010,0030)", + "tag2": "", + "value": "19960802", + "vr": "DA" + }, + { + "desc": "Patient's Sex", + "tag1": "(0010,0040)", + "tag2": "", + "value": "F", + "vr": "CS" + }, + { + "desc": "Patient's Age", + "tag1": "(0010,1010)", + "tag2": "", + "value": "019Y", + "vr": "AS" + }, + { + "desc": "Patient's Weight", + "tag1": "(0010,1030)", + "tag2": "", + "value": "65", + "vr": "DS" + }, + { + "desc": "Additional Patient History", + "tag1": "(0010,21B0)", + "tag2": "", + "value": "", + "vr": "LT" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0011,0010)", + "tag2": "", + "value": "GEMS_PATI_01", + "vr": "LO" + }, + { + "desc": "Scanning Sequence", + "tag1": "(0018,0020)", + "tag2": "", + "value": "SE", + "vr": "CS" + }, + { + "desc": "Sequence Variant", + "tag1": "(0018,0021)", + "tag2": "", + "value": "OSP", + "vr": "CS" + }, + { + "desc": "Scan Options", + "tag1": "(0018,0022)", + "tag2": "", + "value": "NPW\\VB_GEMS\\TRF_GEMS\\FILTERED_GEMS", + "vr": "CS" + }, + { + "desc": "MR Acquisition Type", + "tag1": "(0018,0023)", + "tag2": "", + "value": "2D", + "vr": "CS" + }, + { + "desc": "Angio Flag", + "tag1": "(0018,0025)", + "tag2": "", + "value": "N", + "vr": "CS" + }, + { + "desc": "Slice Thickness", + "tag1": "(0018,0050)", + "tag2": "", + "value": "4.5", + "vr": "DS" + }, + { + "desc": "Repetition Time", + "tag1": "(0018,0080)", + "tag2": "", + "value": "3260", + "vr": "DS" + }, + { + "desc": "Echo Time", + "tag1": "(0018,0081)", + "tag2": "", + "value": "109.9", + "vr": "DS" + }, + { + "desc": "Inversion Time", + "tag1": "(0018,0082)", + "tag2": "", + "value": "0", + "vr": "DS" + }, + { + "desc": "Number of Averages", + "tag1": "(0018,0083)", + "tag2": "", + "value": "2", + "vr": "DS" + }, + { + "desc": "Imaging Frequency", + "tag1": "(0018,0084)", + "tag2": "", + "value": "63.869726", + "vr": "DS" + }, + { + "desc": "Imaged Nucleus", + "tag1": "(0018,0085)", + "tag2": "", + "value": "1H", + "vr": "SH" + }, + { + "desc": "Echo Number(s)", + "tag1": "(0018,0086)", + "tag2": "", + "value": "1", + "vr": "IS" + }, + { + "desc": "Magnetic Field Strength", + "tag1": "(0018,0087)", + "tag2": "", + "value": "1.5", + "vr": "DS" + }, + { + "desc": "Spacing Between Slices", + "tag1": "(0018,0088)", + "tag2": "", + "value": "5.5", + "vr": "DS" + }, + { + "desc": "Echo Train Length", + "tag1": "(0018,0091)", + "tag2": "", + "value": "29", + "vr": "IS" + }, + { + "desc": "Percent Sampling", + "tag1": "(0018,0093)", + "tag2": "", + "value": "100", + "vr": "DS" + }, + { + "desc": "Percent Phase Field of View", + "tag1": "(0018,0094)", + "tag2": "", + "value": "100", + "vr": "DS" + }, + { + "desc": "Pixel Bandwidth", + "tag1": "(0018,0095)", + "tag2": "", + "value": "162.773", + "vr": "DS" + }, + { + "desc": "Device Serial Number", + "tag1": "(0018,1000)", + "tag2": "", + "value": "00000000NPV24200", + "vr": "LO" + }, + { + "desc": "Software Version(s)", + "tag1": "(0018,1020)", + "tag2": "", + "value": "11\\LX\\MR Software release:11.1_M4_0818.a", + "vr": "LO" + }, + { + "desc": "Protocol Name", + "tag1": "(0018,1030)", + "tag2": "", + "value": "LUMBAR", + "vr": "LO" + }, + { + "desc": "Heart Rate", + "tag1": "(0018,1088)", + "tag2": "", + "value": "0", + "vr": "IS" + }, + { + "desc": "Cardiac Number of Images", + "tag1": "(0018,1090)", + "tag2": "", + "value": "0", + "vr": "IS" + }, + { + "desc": "Trigger Window", + "tag1": "(0018,1094)", + "tag2": "", + "value": "0", + "vr": "IS" + }, + { + "desc": "Reconstruction Diameter", + "tag1": "(0018,1100)", + "tag2": "", + "value": "320", + "vr": "DS" + }, + { + "desc": "Receive Coil Name", + "tag1": "(0018,1250)", + "tag2": "", + "value": "USCTLBOT", + "vr": "SH" + }, + { + "desc": "Acquisition Matrix", + "tag1": "(0018,1310)", + "tag2": "", + "value": "384\\0\\0\\224", + "vr": "US" + }, + { + "desc": "In-plane Phase Encoding Direction", + "tag1": "(0018,1312)", + "tag2": "", + "value": "COL", + "vr": "CS" + }, + { + "desc": "Flip Angle", + "tag1": "(0018,1314)", + "tag2": "", + "value": "90", + "vr": "DS" + }, + { + "desc": "Variable Flip Angle Flag", + "tag1": "(0018,1315)", + "tag2": "", + "value": "N", + "vr": "CS" + }, + { + "desc": "SAR", + "tag1": "(0018,1316)", + "tag2": "", + "value": "1.203500", + "vr": "DS" + }, + { + "desc": "Patient Position", + "tag1": "(0018,5100)", + "tag2": "", + "value": "HFS", + "vr": "CS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0019,0010)", + "tag2": "", + "value": "GEMS_ACQU_01", + "vr": "LO" + }, + { + "desc": "?", + "tag1": "(0019,10BB)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10BC)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10BD)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10D9)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10DF)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10E0)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "Study Instance UID", + "tag1": "(0020,000D)", + "tag2": "", + "value": "1.2.840.113619.2.182.10808617210140.1466503585.135941", + "vr": "UI" + }, + { + "desc": "Series Instance UID", + "tag1": "(0020,000E)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.15477.1466833583.322", + "vr": "UI" + }, + { + "desc": "Study ID", + "tag1": "(0020,0010)", + "tag2": "", + "value": "", + "vr": "SH" + }, + { + "desc": "Series Number", + "tag1": "(0020,0011)", + "tag2": "", + "value": "2", + "vr": "IS" + }, + { + "desc": "Acquisition Number", + "tag1": "(0020,0012)", + "tag2": "", + "value": "1", + "vr": "IS" + }, + { + "desc": "Instance Number", + "tag1": "(0020,0013)", + "tag2": "", + "value": "12", + "vr": "IS" + }, + { + "desc": "Image Position (Patient)", + "tag1": "(0020,0032)", + "tag2": "", + "value": "18.8998\\-173.346\\195.102", + "vr": "DS" + }, + { + "desc": "Image Orientation (Patient)", + "tag1": "(0020,0037)", + "tag2": "", + "value": "-0\\1\\0\\0.0100102\\-0\\-0.99995", + "vr": "DS" + }, + { + "desc": "Frame of Reference UID", + "tag1": "(0020,0052)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.15543.1466833318.370", + "vr": "UI" + }, + { + "desc": "Laterality", + "tag1": "(0020,0060)", + "tag2": "", + "value": "", + "vr": "CS" + }, + { + "desc": "Temporal Resolution", + "tag1": "(0020,0110)", + "tag2": "", + "value": "0", + "vr": "DS" + }, + { + "desc": "Position Reference Indicator", + "tag1": "(0020,1040)", + "tag2": "", + "value": "", + "vr": "LO" + }, + { + "desc": "Slice Location", + "tag1": "(0020,1041)", + "tag2": "", + "value": "-20.49824333", + "vr": "DS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0021,0010)", + "tag2": "", + "value": "GEMS_RELA_01", + "vr": "LO" + }, + { + "desc": "?", + "tag1": "(0021,105A)", + "tag2": "", + "value": "0", + "vr": "SL" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0023,0010)", + "tag2": "", + "value": "GEMS_STDY_01", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0025,0010)", + "tag2": "", + "value": "GEMS_SERS_01", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0027,0010)", + "tag2": "", + "value": "GEMS_IMAG_01", + "vr": "LO" + }, + { + "desc": "Samples per Pixel", + "tag1": "(0028,0002)", + "tag2": "", + "value": "1", + "vr": "US" + }, + { + "desc": "Photometric Interpretation", + "tag1": "(0028,0004)", + "tag2": "", + "value": "MONOCHROME2", + "vr": "CS" + }, + { + "desc": "Rows", + "tag1": "(0028,0010)", + "tag2": "", + "value": "512", + "vr": "US" + }, + { + "desc": "Columns", + "tag1": "(0028,0011)", + "tag2": "", + "value": "512", + "vr": "US" + }, + { + "desc": "Pixel Spacing", + "tag1": "(0028,0030)", + "tag2": "", + "value": "0.624993\\0.625", + "vr": "DS" + }, + { + "desc": "Bits Allocated", + "tag1": "(0028,0100)", + "tag2": "", + "value": "16", + "vr": "US" + }, + { + "desc": "Bits Stored", + "tag1": "(0028,0101)", + "tag2": "", + "value": "16", + "vr": "US" + }, + { + "desc": "High Bit", + "tag1": "(0028,0102)", + "tag2": "", + "value": "15", + "vr": "US" + }, + { + "desc": "Pixel Representation", + "tag1": "(0028,0103)", + "tag2": "", + "value": "1", + "vr": "US" + }, + { + "desc": "?", + "tag1": "(0028,0303)", + "tag2": "", + "value": "", + "vr": "CS" + }, + { + "desc": "Window Center", + "tag1": "(0028,1050)", + "tag2": "", + "value": "628", + "vr": "DS" + }, + { + "desc": "Window Width", + "tag1": "(0028,1051)", + "tag2": "", + "value": "1257", + "vr": "DS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0029,0010)", + "tag2": "", + "value": "GEMS_IMPS_01", + "vr": "LO" + }, + { + "desc": "Performed Procedure Step Description", + "tag1": "(0040,0254)", + "tag2": "", + "value": "", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0043,0010)", + "tag2": "", + "value": "GEMS_PARM_01", + "vr": "LO" + }, + { + "desc": "?", + "tag1": "(0043,1039)", + "tag2": "", + "value": "0\\2097152\\0\\0", + "vr": "IS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0903,0010)", + "tag2": "", + "value": "GEIIS PACS", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0905,0010)", + "tag2": "", + "value": "GEIIS", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(7FD1,0010)", + "tag2": "", + "value": "GEIIS", + "vr": "LO" + } + ] + } +} \ No newline at end of file diff --git a/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-3_vp-sag_T2w.nii.gz b/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-3_vp-sag_T2w.nii.gz new file mode 100644 index 0000000..bb0412c Binary files /dev/null and b/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-3_vp-sag_T2w.nii.gz differ diff --git a/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-4_vp-ax_T2w.json b/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-4_vp-ax_T2w.json new file mode 100644 index 0000000..d49ed32 --- /dev/null +++ b/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-4_vp-ax_T2w.json @@ -0,0 +1,902 @@ +{ + "ResultSet": { + "Result": [ + { + "desc": "File Meta Information Version", + "tag1": "(0002,0001)", + "tag2": "", + "value": "00\\01", + "vr": "OB" + }, + { + "desc": "Media Storage SOP Class UID", + "tag1": "(0002,0002)", + "tag2": "", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Media Storage SOP Instance UID", + "tag1": "(0002,0003)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.15477.1466833583.625", + "vr": "UI" + }, + { + "desc": "Transfer Syntax UID", + "tag1": "(0002,0010)", + "tag2": "", + "value": "1.2.840.10008.1.2.1", + "vr": "UI" + }, + { + "desc": "Implementation Class UID", + "tag1": "(0002,0012)", + "tag2": "", + "value": "1.2.40.0.13.1.1", + "vr": "UI" + }, + { + "desc": "Implementation Version Name", + "tag1": "(0002,0013)", + "tag2": "", + "value": "dcm4che-2.0", + "vr": "SH" + }, + { + "desc": "Source Application Entity Title", + "tag1": "(0002,0016)", + "tag2": "", + "value": "CTP", + "vr": "AE" + }, + { + "desc": "Specific Character Set", + "tag1": "(0008,0005)", + "tag2": "", + "value": "ISO_IR 100", + "vr": "CS" + }, + { + "desc": "Image Type", + "tag1": "(0008,0008)", + "tag2": "", + "value": "ORIGINAL\\PRIMARY\\OTHER", + "vr": "CS" + }, + { + "desc": "SOP Class UID", + "tag1": "(0008,0016)", + "tag2": "", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "SOP Instance UID", + "tag1": "(0008,0018)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.15477.1466833583.625", + "vr": "UI" + }, + { + "desc": "Study Date", + "tag1": "(0008,0020)", + "tag2": "", + "value": "20160625", + "vr": "DA" + }, + { + "desc": "Series Date", + "tag1": "(0008,0021)", + "tag2": "", + "value": "20160625", + "vr": "DA" + }, + { + "desc": "Acquisition Date", + "tag1": "(0008,0022)", + "tag2": "", + "value": "20160625", + "vr": "DA" + }, + { + "desc": "Content Date", + "tag1": "(0008,0023)", + "tag2": "", + "value": "20160625", + "vr": "DA" + }, + { + "desc": "Study Time", + "tag1": "(0008,0030)", + "tag2": "", + "value": "134718", + "vr": "TM" + }, + { + "desc": "Series Time", + "tag1": "(0008,0031)", + "tag2": "", + "value": "135556", + "vr": "TM" + }, + { + "desc": "Acquisition Time", + "tag1": "(0008,0032)", + "tag2": "", + "value": "135556", + "vr": "TM" + }, + { + "desc": "Content Time", + "tag1": "(0008,0033)", + "tag2": "", + "value": "135556", + "vr": "TM" + }, + { + "desc": "Accession Number", + "tag1": "(0008,0050)", + "tag2": "", + "value": "ceibcs_E19348", + "vr": "SH" + }, + { + "desc": "Modality", + "tag1": "(0008,0060)", + "tag2": "", + "value": "MR", + "vr": "CS" + }, + { + "desc": "Manufacturer", + "tag1": "(0008,0070)", + "tag2": "", + "value": "GE MEDICAL SYSTEMS", + "vr": "LO" + }, + { + "desc": "Referring Physician's Name", + "tag1": "(0008,0090)", + "tag2": "", + "value": "", + "vr": "PN" + }, + { + "desc": "Station Name", + "tag1": "(0008,1010)", + "tag2": "", + "value": "CASTMRI", + "vr": "SH" + }, + { + "desc": "Study Description", + "tag1": "(0008,1030)", + "tag2": "", + "value": "MRI_Lumbar", + "vr": "LO" + }, + { + "desc": "Procedure Code Sequence", + "tag1": "(0008,1032)", + "tag2": "(0008,1032)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Code Value", + "tag1": "(0008,1032)", + "tag2": "(0008,0100)", + "value": "015001_RM816", + "vr": "SH" + }, + { + "desc": "Coding Scheme Designator", + "tag1": "(0008,1032)", + "tag2": "(0008,0102)", + "value": "GEIIS", + "vr": "SH" + }, + { + "desc": "Coding Scheme Version", + "tag1": "(0008,1032)", + "tag2": "(0008,0103)", + "value": "0", + "vr": "SH" + }, + { + "desc": "Code Meaning", + "tag1": "(0008,1032)", + "tag2": "(0008,0104)", + "value": "RM LUMBAR", + "vr": "LO" + }, + { + "desc": "Series Description", + "tag1": "(0008,103E)", + "tag2": "", + "value": "AXIALT2DISCBASICO", + "vr": "LO" + }, + { + "desc": "Manufacturer's Model Name", + "tag1": "(0008,1090)", + "tag2": "", + "value": "SIGNA EXCITE", + "vr": "LO" + }, + { + "desc": "Referenced Image Sequence", + "tag1": "(0008,1140)", + "tag2": "(0008,1140)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Referenced SOP Class UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1150)", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Referenced SOP Instance UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1155)", + "value": "1.2.840.113619.2.222.2025.1616754.15477.1466833583.393", + "vr": "UI" + }, + { + "desc": "Referenced Image Sequence", + "tag1": "(0008,1140)", + "tag2": "(0008,1140)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Referenced SOP Class UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1150)", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Referenced SOP Instance UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1155)", + "value": "1.2.840.113619.2.222.2025.1616754.15477.1466833583.320", + "vr": "UI" + }, + { + "desc": "Referenced Image Sequence", + "tag1": "(0008,1140)", + "tag2": "(0008,1140)", + "value": "", + "vr": "SQ" + }, + { + "desc": "Referenced SOP Class UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1150)", + "value": "1.2.840.10008.5.1.4.1.1.4", + "vr": "UI" + }, + { + "desc": "Referenced SOP Instance UID", + "tag1": "(0008,1140)", + "tag2": "(0008,1155)", + "value": "1.2.840.113619.2.222.2025.1616754.15477.1466833583.314", + "vr": "UI" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0009,0010)", + "tag2": "", + "value": "GEMS_IDEN_01", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0009,0011)", + "tag2": "", + "value": "GEIIS", + "vr": "LO" + }, + { + "desc": "Patient's Name", + "tag1": "(0010,0010)", + "tag2": "", + "value": "90070970630437776381142865766563279659", + "vr": "PN" + }, + { + "desc": "Patient ID", + "tag1": "(0010,0020)", + "tag2": "", + "value": "35180663179348213717850348575679254082", + "vr": "LO" + }, + { + "desc": "Patient's Birth Date", + "tag1": "(0010,0030)", + "tag2": "", + "value": "19960802", + "vr": "DA" + }, + { + "desc": "Patient's Sex", + "tag1": "(0010,0040)", + "tag2": "", + "value": "F", + "vr": "CS" + }, + { + "desc": "Patient's Age", + "tag1": "(0010,1010)", + "tag2": "", + "value": "019Y", + "vr": "AS" + }, + { + "desc": "Patient's Weight", + "tag1": "(0010,1030)", + "tag2": "", + "value": "65", + "vr": "DS" + }, + { + "desc": "Additional Patient History", + "tag1": "(0010,21B0)", + "tag2": "", + "value": "", + "vr": "LT" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0011,0010)", + "tag2": "", + "value": "GEMS_PATI_01", + "vr": "LO" + }, + { + "desc": "Scanning Sequence", + "tag1": "(0018,0020)", + "tag2": "", + "value": "SE", + "vr": "CS" + }, + { + "desc": "Sequence Variant", + "tag1": "(0018,0021)", + "tag2": "", + "value": "NONE", + "vr": "CS" + }, + { + "desc": "Scan Options", + "tag1": "(0018,0022)", + "tag2": "", + "value": "VB_GEMS\\TRF_GEMS\\FILTERED_GEMS", + "vr": "CS" + }, + { + "desc": "MR Acquisition Type", + "tag1": "(0018,0023)", + "tag2": "", + "value": "2D", + "vr": "CS" + }, + { + "desc": "Angio Flag", + "tag1": "(0018,0025)", + "tag2": "", + "value": "N", + "vr": "CS" + }, + { + "desc": "Slice Thickness", + "tag1": "(0018,0050)", + "tag2": "", + "value": "3.5", + "vr": "DS" + }, + { + "desc": "Repetition Time", + "tag1": "(0018,0080)", + "tag2": "", + "value": "2700", + "vr": "DS" + }, + { + "desc": "Echo Time", + "tag1": "(0018,0081)", + "tag2": "", + "value": "108.7", + "vr": "DS" + }, + { + "desc": "Inversion Time", + "tag1": "(0018,0082)", + "tag2": "", + "value": "0", + "vr": "DS" + }, + { + "desc": "Number of Averages", + "tag1": "(0018,0083)", + "tag2": "", + "value": "3", + "vr": "DS" + }, + { + "desc": "Imaging Frequency", + "tag1": "(0018,0084)", + "tag2": "", + "value": "63.869712", + "vr": "DS" + }, + { + "desc": "Imaged Nucleus", + "tag1": "(0018,0085)", + "tag2": "", + "value": "1H", + "vr": "SH" + }, + { + "desc": "Echo Number(s)", + "tag1": "(0018,0086)", + "tag2": "", + "value": "1", + "vr": "IS" + }, + { + "desc": "Magnetic Field Strength", + "tag1": "(0018,0087)", + "tag2": "", + "value": "1.5", + "vr": "DS" + }, + { + "desc": "Spacing Between Slices", + "tag1": "(0018,0088)", + "tag2": "", + "value": "4.5", + "vr": "DS" + }, + { + "desc": "Echo Train Length", + "tag1": "(0018,0091)", + "tag2": "", + "value": "29", + "vr": "IS" + }, + { + "desc": "Percent Sampling", + "tag1": "(0018,0093)", + "tag2": "", + "value": "100", + "vr": "DS" + }, + { + "desc": "Percent Phase Field of View", + "tag1": "(0018,0094)", + "tag2": "", + "value": "100", + "vr": "DS" + }, + { + "desc": "Pixel Bandwidth", + "tag1": "(0018,0095)", + "tag2": "", + "value": "162.773", + "vr": "DS" + }, + { + "desc": "Device Serial Number", + "tag1": "(0018,1000)", + "tag2": "", + "value": "00000000NPV24200", + "vr": "LO" + }, + { + "desc": "Software Version(s)", + "tag1": "(0018,1020)", + "tag2": "", + "value": "11\\LX\\MR Software release:11.1_M4_0818.a", + "vr": "LO" + }, + { + "desc": "Protocol Name", + "tag1": "(0018,1030)", + "tag2": "", + "value": "LUMBAR", + "vr": "LO" + }, + { + "desc": "Heart Rate", + "tag1": "(0018,1088)", + "tag2": "", + "value": "0", + "vr": "IS" + }, + { + "desc": "Cardiac Number of Images", + "tag1": "(0018,1090)", + "tag2": "", + "value": "0", + "vr": "IS" + }, + { + "desc": "Trigger Window", + "tag1": "(0018,1094)", + "tag2": "", + "value": "0", + "vr": "IS" + }, + { + "desc": "Reconstruction Diameter", + "tag1": "(0018,1100)", + "tag2": "", + "value": "200", + "vr": "DS" + }, + { + "desc": "Receive Coil Name", + "tag1": "(0018,1250)", + "tag2": "", + "value": "USCTLBOT", + "vr": "SH" + }, + { + "desc": "Acquisition Matrix", + "tag1": "(0018,1310)", + "tag2": "", + "value": "288\\0\\0\\224", + "vr": "US" + }, + { + "desc": "In-plane Phase Encoding Direction", + "tag1": "(0018,1312)", + "tag2": "", + "value": "COL", + "vr": "CS" + }, + { + "desc": "Flip Angle", + "tag1": "(0018,1314)", + "tag2": "", + "value": "90", + "vr": "DS" + }, + { + "desc": "Variable Flip Angle Flag", + "tag1": "(0018,1315)", + "tag2": "", + "value": "N", + "vr": "CS" + }, + { + "desc": "SAR", + "tag1": "(0018,1316)", + "tag2": "", + "value": "1.211100", + "vr": "DS" + }, + { + "desc": "Patient Position", + "tag1": "(0018,5100)", + "tag2": "", + "value": "HFS", + "vr": "CS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0019,0010)", + "tag2": "", + "value": "GEMS_ACQU_01", + "vr": "LO" + }, + { + "desc": "?", + "tag1": "(0019,10BB)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10BC)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10BD)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10D9)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10DF)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "?", + "tag1": "(0019,10E0)", + "tag2": "", + "value": "0.000000", + "vr": "DS" + }, + { + "desc": "Study Instance UID", + "tag1": "(0020,000D)", + "tag2": "", + "value": "1.2.840.113619.2.182.10808617210140.1466503585.135941", + "vr": "UI" + }, + { + "desc": "Series Instance UID", + "tag1": "(0020,000E)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.15477.1466833583.556", + "vr": "UI" + }, + { + "desc": "Study ID", + "tag1": "(0020,0010)", + "tag2": "", + "value": "", + "vr": "SH" + }, + { + "desc": "Series Number", + "tag1": "(0020,0011)", + "tag2": "", + "value": "5", + "vr": "IS" + }, + { + "desc": "Acquisition Number", + "tag1": "(0020,0012)", + "tag2": "", + "value": "1", + "vr": "IS" + }, + { + "desc": "Instance Number", + "tag1": "(0020,0013)", + "tag2": "", + "value": "7", + "vr": "IS" + }, + { + "desc": "Image Position (Patient)", + "tag1": "(0020,0032)", + "tag2": "", + "value": "-112.807\\-101.522\\84.9648", + "vr": "DS" + }, + { + "desc": "Image Orientation (Patient)", + "tag1": "(0020,0037)", + "tag2": "", + "value": "0.99995\\-0\\0.0100102\\0.00170901\\0.985191\\-0.171452", + "vr": "DS" + }, + { + "desc": "Frame of Reference UID", + "tag1": "(0020,0052)", + "tag2": "", + "value": "1.2.840.113619.2.222.2025.1616754.15543.1466833318.370", + "vr": "UI" + }, + { + "desc": "Laterality", + "tag1": "(0020,0060)", + "tag2": "", + "value": "", + "vr": "CS" + }, + { + "desc": "Temporal Resolution", + "tag1": "(0020,0110)", + "tag2": "", + "value": "0", + "vr": "DS" + }, + { + "desc": "Position Reference Indicator", + "tag1": "(0020,1040)", + "tag2": "", + "value": "", + "vr": "LO" + }, + { + "desc": "Slice Location", + "tag1": "(0020,1041)", + "tag2": "", + "value": "68.85205078", + "vr": "DS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0021,0010)", + "tag2": "", + "value": "GEMS_RELA_01", + "vr": "LO" + }, + { + "desc": "?", + "tag1": "(0021,105A)", + "tag2": "", + "value": "0", + "vr": "SL" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0023,0010)", + "tag2": "", + "value": "GEMS_STDY_01", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0025,0010)", + "tag2": "", + "value": "GEMS_SERS_01", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0027,0010)", + "tag2": "", + "value": "GEMS_IMAG_01", + "vr": "LO" + }, + { + "desc": "Samples per Pixel", + "tag1": "(0028,0002)", + "tag2": "", + "value": "1", + "vr": "US" + }, + { + "desc": "Photometric Interpretation", + "tag1": "(0028,0004)", + "tag2": "", + "value": "MONOCHROME2", + "vr": "CS" + }, + { + "desc": "Rows", + "tag1": "(0028,0010)", + "tag2": "", + "value": "512", + "vr": "US" + }, + { + "desc": "Columns", + "tag1": "(0028,0011)", + "tag2": "", + "value": "512", + "vr": "US" + }, + { + "desc": "Pixel Spacing", + "tag1": "(0028,0030)", + "tag2": "", + "value": "0.390628\\0.390621", + "vr": "DS" + }, + { + "desc": "Bits Allocated", + "tag1": "(0028,0100)", + "tag2": "", + "value": "16", + "vr": "US" + }, + { + "desc": "Bits Stored", + "tag1": "(0028,0101)", + "tag2": "", + "value": "16", + "vr": "US" + }, + { + "desc": "High Bit", + "tag1": "(0028,0102)", + "tag2": "", + "value": "15", + "vr": "US" + }, + { + "desc": "Pixel Representation", + "tag1": "(0028,0103)", + "tag2": "", + "value": "1", + "vr": "US" + }, + { + "desc": "?", + "tag1": "(0028,0303)", + "tag2": "", + "value": "", + "vr": "CS" + }, + { + "desc": "Window Center", + "tag1": "(0028,1050)", + "tag2": "", + "value": "453", + "vr": "DS" + }, + { + "desc": "Window Width", + "tag1": "(0028,1051)", + "tag2": "", + "value": "907", + "vr": "DS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0029,0010)", + "tag2": "", + "value": "GEMS_IMPS_01", + "vr": "LO" + }, + { + "desc": "Performed Procedure Step Description", + "tag1": "(0040,0254)", + "tag2": "", + "value": "", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0043,0010)", + "tag2": "", + "value": "GEMS_PARM_01", + "vr": "LO" + }, + { + "desc": "?", + "tag1": "(0043,1039)", + "tag2": "", + "value": "0\\2097152\\0\\0", + "vr": "IS" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0903,0010)", + "tag2": "", + "value": "GEIIS PACS", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(0905,0010)", + "tag2": "", + "value": "GEIIS", + "vr": "LO" + }, + { + "desc": "Private Creator Data Element", + "tag1": "(7FD1,0010)", + "tag2": "", + "value": "GEIIS", + "vr": "LO" + } + ] + } +} \ No newline at end of file diff --git a/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-4_vp-ax_T2w.nii.gz b/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-4_vp-ax_T2w.nii.gz new file mode 100644 index 0000000..36778b3 Binary files /dev/null and b/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-4_vp-ax_T2w.nii.gz differ diff --git a/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-2_run-4_vp-ax_T2w.nii.gz b/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-2_run-4_vp-ax_T2w.nii.gz new file mode 100644 index 0000000..b2bdeb0 Binary files /dev/null and b/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-2_run-4_vp-ax_T2w.nii.gz differ diff --git a/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-3_run-4_vp-ax_T2w.nii.gz b/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-3_run-4_vp-ax_T2w.nii.gz new file mode 100644 index 0000000..27a08dd Binary files /dev/null and b/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-3_run-4_vp-ax_T2w.nii.gz differ diff --git a/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-4_run-4__vp-ax_T2w.nii.gz b/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-4_run-4__vp-ax_T2w.nii.gz new file mode 100644 index 0000000..4df388c Binary files /dev/null and b/data/examples/MRI_Lumbar/sub-2/ses-1/mr/anat/sub-2_ses-1_bp-lsspine_acq-4_run-4__vp-ax_T2w.nii.gz differ diff --git a/data/examples/MRI_Lumbar/sub-2/ses-1/sub-2_ses-1_scans.tsv b/data/examples/MRI_Lumbar/sub-2/ses-1/sub-2_ses-1_scans.tsv new file mode 100644 index 0000000..1f574ba --- /dev/null +++ b/data/examples/MRI_Lumbar/sub-2/ses-1/sub-2_ses-1_scans.tsv @@ -0,0 +1,5 @@ +filename slides plane Manufacturer (0008,0070) Series Description (0008,103E) Manufacturer's Model Name (0008,1090) Patient ID (0010,0020) Patient's Sex (0010,0040) Patient's Age (0010,1010) Patient's Weight (0010,1030) Scanning Sequence (0018,0020) Sequence Variant (0018,0021) Scan Options (0018,0022) MR Acquisition Type (0018,0023) Slice Thickness (0018,0050) Repetition Time (0018,0080) Echo Time (0018,0081) Inversion Time (0018,0082) Imaging Frequency (0018,0084) Magnetic Field Strength (0018,0087) Manufacturer's Model Name (0008,1090) Spacing Between Slices (0018,0088) Echo Train Length (0018,0091) Percent Sampling (0018,0093) Pixel Bandwidth (0018,0095) Flip Angle (0018,1314) Patient Position (0018,5100) Image Position (Patient) (0020,0032) Image Orientation (Patient) (0020,0037) Position Reference Indicator (0020,1040) Slice Location (0020,1041) Rows (0028,0010) Columns (0028,0011) Pixel Spacing (0028,0030) Bits Allocated (0028,0100) Number of Averages (0018,0083) Echo Number(s) (0018,0086) (0018,9461) +mr/anat/sub-2_ses-1_bp-lsspine_acq-3_run-4_vp-ax_T2w.nii.gz,mr/anat/sub-2_bp-lsspine_ses-1_acq-1_run-4_vp-ax_T2w.nii.gz,mr/anat/sub-2_ses-1_bp-lsspine_acq-4_run-4_vp-ax_T2w.nii.gz,mr/anat/sub-2_ses-1_bp-lsspine_acq-2_run-4_vp-ax_T2w.nii.gz 20 Tra GE MEDICAL SYSTEMS AXIALT2DISCBASICO SIGNA EXCITE 35180663179348213717850348575679254082 F 019Y 65 SE NONE VB_GEMS\TRF_GEMS\FILTERED_GEMS 2D 3.5 2700 108.7 0 63.869712 1.5 SIGNA EXCITE 4.5 29 100 162.773 90 HFS -112.807\-101.522\84.9648 0.99995\-0\0.0100102\0.00170901\0.985191\-0.171452 68.85205078 512 512 0.390628\0.390621 16 3 1 None +mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-1_vp-sag_T1w.nii.gz 12 Sag GE MEDICAL SYSTEMS SAGT1LUMBAR SIGNA EXCITE 35180663179348213717850348575679254082 F 019Y 65 RM OSP FC_FREQ_AX_GEMS\FC\NPW\VB_GEMS\TRF_GEMS\FILTERED_GEMS 2D 4.5 300 14.976 0 63.869726 1.5 SIGNA EXCITE 5.5 4 100 139.492 90 HFS -3.09914\-173.346\194.882 -0\1\0\0.0100102\-0\-0.99995 1.500656366 512 512 0.624993\0.625 16 1 1 None +mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-2_vp-sag_Stir.nii.gz 12 Sag GE MEDICAL SYSTEMS SAGITALSTIR SIGNA EXCITE 35180663179348213717850348575679254082 F 019Y 65 RM NONE FC_FREQ_AX_GEMS\FC\SAT_GEMS\VB_GEMS\EDR_GEMS\SEQ_GEMS\TRF_GEM... 2D 4.5 4100 42.444 150 63.869729 1.5 SIGNA EXCITE 5.5 19 100 122.07 90 HFS 7.90031\-173.346\194.992 -0\1\0\0.0100102\-0\-0.99995 -9.498793602 512 512 0.624993\0.625 16 3 1 None +mr/anat/sub-2_ses-1_bp-lsspine_acq-1_run-3_vp-sag_T2w.nii.gz 12 Sag GE MEDICAL SYSTEMS SAGT2LUMBAR SIGNA EXCITE 35180663179348213717850348575679254082 F 019Y 65 SE OSP NPW\VB_GEMS\TRF_GEMS\FILTERED_GEMS 2D 4.5 3260 109.9 0 63.869726 1.5 SIGNA EXCITE 5.5 29 100 162.773 90 HFS 18.8998\-173.346\195.102 -0\1\0\0.0100102\-0\-0.99995 -20.49824333 512 512 0.624993\0.625 16 2 1 None diff --git a/data/examples/RX_Thorax/CHANGES.txt b/data/examples/RX_Thorax/CHANGES.txt new file mode 100644 index 0000000..310e84b --- /dev/null +++ b/data/examples/RX_Thorax/CHANGES.txt @@ -0,0 +1,9 @@ +1.0.1 2017-08-27 + - DICOM information. +1.0.0 2016-05-26 + - Initial release. + +AUTHOR + - Aurelia Bustos + +COPYRIGHT AND LICENSE diff --git a/data/examples/RX_Thorax/README.txt b/data/examples/RX_Thorax/README.txt new file mode 100644 index 0000000..e69de29 diff --git a/data/examples/RX_Thorax/dataset_description.json b/data/examples/RX_Thorax/dataset_description.json new file mode 100644 index 0000000..c6b7087 --- /dev/null +++ b/data/examples/RX_Thorax/dataset_description.json @@ -0,0 +1,6 @@ +{ + "Name": "RX_Thorax", + "BIDSVersion": "1.1.0", + "MIDSVersion": "1.0.0", + "License": "CC BY 4.0" +} \ No newline at end of file diff --git a/data/examples/RX_Thorax/participants.tsv b/data/examples/RX_Thorax/participants.tsv new file mode 100644 index 0000000..fdd0e5d --- /dev/null +++ b/data/examples/RX_Thorax/participants.tsv @@ -0,0 +1,3 @@ +participant_id age gender control +sub-2 57 F 0 +sub-1 54 F 0 \ No newline at end of file diff --git a/data/examples/RX_Thorax/sub-1/ses-1/rx/sub-1_ses-1_bp-thorax_vp_ap_dx.nii.gz b/data/examples/RX_Thorax/sub-1/ses-1/rx/sub-1_ses-1_bp-thorax_vp_ap_dx.nii.gz new file mode 100644 index 0000000..20fee41 Binary files /dev/null and b/data/examples/RX_Thorax/sub-1/ses-1/rx/sub-1_ses-1_bp-thorax_vp_ap_dx.nii.gz differ diff --git a/data/examples/RX_Thorax/sub-1/ses-1/rx/sub-1_ses-1_bp-thorax_vp_ap_dx.nii.json b/data/examples/RX_Thorax/sub-1/ses-1/rx/sub-1_ses-1_bp-thorax_vp_ap_dx.nii.json new file mode 100644 index 0000000..5feb60d --- /dev/null +++ b/data/examples/RX_Thorax/sub-1/ses-1/rx/sub-1_ses-1_bp-thorax_vp_ap_dx.nii.json @@ -0,0 +1 @@ +{"ResultSet":{"Result":[{"tag1":"(0002,0001)","vr":"OB","value":"00\\01","tag2":"","desc":"File Meta Information Version"},{"tag1":"(0002,0002)","vr":"UI","value":"1.2.840.10008.5.1.4.1.1.1.1","tag2":"","desc":"Media Storage SOP Class UID"},{"tag1":"(0002,0003)","vr":"UI","value":"1.3.46.670589.30.36.0.1.72567767433727.1485247623251.2","tag2":"","desc":"Media Storage SOP Instance UID"},{"tag1":"(0002,0010)","vr":"UI","value":"1.2.840.10008.1.2.1","tag2":"","desc":"Transfer Syntax UID"},{"tag1":"(0002,0012)","vr":"UI","value":"1.2.40.0.13.1.1","tag2":"","desc":"Implementation Class UID"},{"tag1":"(0002,0013)","vr":"SH","value":"dcm4che-2.0","tag2":"","desc":"Implementation Version Name"},{"tag1":"(0002,0016)","vr":"AE","value":"CTP","tag2":"","desc":"Source Application Entity Title"},{"tag1":"(0008,0005)","vr":"CS","value":"ISO_IR 100","tag2":"","desc":"Specific Character Set"},{"tag1":"(0008,0008)","vr":"CS","value":"ORIGINAL\\PRIMARY\\","tag2":"","desc":"Image Type"},{"tag1":"(0008,0016)","vr":"UI","value":"1.2.840.10008.5.1.4.1.1.1.1","tag2":"","desc":"SOP Class UID"},{"tag1":"(0008,0018)","vr":"UI","value":"1.3.46.670589.30.36.0.1.72567767433727.1485247623251.2","tag2":"","desc":"SOP Instance UID"},{"tag1":"(0008,0020)","vr":"DA","value":"20170124","tag2":"","desc":"Study Date"},{"tag1":"(0008,0021)","vr":"DA","value":"20170124","tag2":"","desc":"Series Date"},{"tag1":"(0008,0022)","vr":"DA","value":"20170124","tag2":"","desc":"Acquisition Date"},{"tag1":"(0008,0023)","vr":"DA","value":"20170124","tag2":"","desc":"Content Date"},{"tag1":"(0008,0030)","vr":"TM","value":"094646.541000","tag2":"","desc":"Study Time"},{"tag1":"(0008,0031)","vr":"TM","value":"094649.000000","tag2":"","desc":"Series Time"},{"tag1":"(0008,0032)","vr":"TM","value":"094650","tag2":"","desc":"Acquisition Time"},{"tag1":"(0008,0033)","vr":"TM","value":"094650","tag2":"","desc":"Content Time"},{"tag1":"(0008,0050)","vr":"SH","value":"","tag2":"","desc":"Accession Number"},{"tag1":"(0008,0060)","vr":"CS","value":"DX","tag2":"","desc":"Modality"},{"tag1":"(0008,0068)","vr":"CS","value":"FOR PRESENTATION","tag2":"","desc":"Presentation Intent Type"},{"tag1":"(0008,0070)","vr":"LO","value":"Philips Medical Systems","tag2":"","desc":"Manufacturer"},{"tag1":"(0008,0090)","vr":"PN","value":"","tag2":"","desc":"Referring Physician’s Name"},{"tag1":"(0008,1010)","vr":"SH","value":"SJDIDI01","tag2":"","desc":"Station Name"},{"tag1":"(0008,1030)","vr":"LO","value":"padchest_ds17","tag2":"","desc":"Study Description"},{"tag1":"(0008,1032)","vr":"SQ","value":"","tag2":"(0008,1032)","desc":"Procedure Code Sequence"},{"tag1":"(0008,1032)","vr":"SH","value":"3061010101001030","tag2":"(0008,0100)","desc":"Code Value"},{"tag1":"(0008,1032)","vr":"SH","value":"CCG_CSTemp","tag2":"(0008,0102)","desc":"Coding Scheme Designator"},{"tag1":"(0008,1032)","vr":"LO","value":"RX TORAX, PA O AP","tag2":"(0008,0104)","desc":"Code Meaning"},{"tag1":"(0008,103E)","vr":"LO","value":"T�rax","tag2":"","desc":"Series Description"},{"tag1":"(0008,1090)","vr":"LO","value":"DigitalDiagnost","tag2":"","desc":"Manufacturer’s Model Name"},{"tag1":"(0008,1110)","vr":"SQ","value":"","tag2":"(0008,1110)","desc":"Referenced Study Sequence"},{"tag1":"(0008,1110)","vr":"UI","value":"1.2.840.100008.3.1.2.3.1","tag2":"(0008,1150)","desc":"Referenced SOP Class UID"},{"tag1":"(0008,1110)","vr":"UI","value":"1.2.840.113619.2.182.10808617219229.1484672322.853647","tag2":"(0008,1155)","desc":"Referenced SOP Instance UID"},{"tag1":"(0008,1111)","vr":"SQ","value":"","tag2":"(0008,1111)","desc":"Referenced Performed Procedure Step Sequence"},{"tag1":"(0008,1111)","vr":"UI","value":"1.2.840.10008.3.1.2.3.3","tag2":"(0008,1150)","desc":"Referenced SOP Class UID"},{"tag1":"(0008,1111)","vr":"UI","value":"1.3.46.670589.30.36.0.1.72567767433727.1485212877727.1","tag2":"(0008,1155)","desc":"Referenced SOP Instance UID"},{"tag1":"(0008,3010)","vr":"UI","value":"1.3.46.670589.30.36.0.1.72567767433727.1485247606412.1","tag2":"","desc":"Irradiation Event UID"},{"tag1":"(0009,0010)","vr":"LO","value":"GEIIS","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(0010,0010)","vr":"PN","value":"100002652742762245719447501824197948584","tag2":"","desc":"Patient’s Name"},{"tag1":"(0010,0020)","vr":"LO","value":"125374151943505747025890313053997514922","tag2":"","desc":"Patient ID"},{"tag1":"(0010,0030)","vr":"DA","value":"19530920","tag2":"","desc":"Patient’s Birth Date"},{"tag1":"(0010,0040)","vr":"CS","value":"F","tag2":"","desc":"Patient’s Sex"},{"tag1":"(0010,1010)","vr":"AS","value":"063Y","tag2":"","desc":"Patient’s Age"},{"tag1":"(0010,1020)","vr":"DS","value":"0","tag2":"","desc":"Patient’s Size"},{"tag1":"(0010,1030)","vr":"DS","value":"0","tag2":"","desc":"Patient’s Weight"},{"tag1":"(0010,2000)","vr":"LO","value":"","tag2":"","desc":"Medical Alerts"},{"tag1":"(0010,2110)","vr":"LO","value":"","tag2":"","desc":"Allergies"},{"tag1":"(0010,2160)","vr":"SH","value":"","tag2":"","desc":"Ethnic Group"},{"tag1":"(0010,21B0)","vr":"LT","value":"","tag2":"","desc":"Additional Patient History"},{"tag1":"(0010,21C0)","vr":"US","value":"4","tag2":"","desc":"Pregnancy Status"},{"tag1":"(0018,0015)","vr":"CS","value":"CHEST","tag2":"","desc":"Body Part Examined"},{"tag1":"(0018,0060)","vr":"DS","value":"125","tag2":"","desc":"KVP"},{"tag1":"(0018,1000)","vr":"LO","value":"72567767433727","tag2":"","desc":"Device Serial Number"},{"tag1":"(0018,1020)","vr":"LO","value":"4.1.3.2","tag2":"","desc":"Software Version(s)"},{"tag1":"(0018,1030)","vr":"LO","value":"T�rax","tag2":"","desc":"Protocol Name"},{"tag1":"(0018,1050)","vr":"DS","value":"0.148","tag2":"","desc":"Spatial Resolution"},{"tag1":"(0018,1110)","vr":"DS","value":"1808","tag2":"","desc":"Distance Source to Detector"},{"tag1":"(0018,1111)","vr":"DS","value":"1754","tag2":"","desc":"Distance Source to Patient"},{"tag1":"(0018,1114)","vr":"DS","value":"0.99395272127526","tag2":"","desc":"Estimated Radiographic Magnification Factor"},{"tag1":"(0018,1150)","vr":"IS","value":"5","tag2":"","desc":"Exposure Time"},{"tag1":"(0018,1152)","vr":"IS","value":"1","tag2":"","desc":"Exposure"},{"tag1":"(0018,1153)","vr":"IS","value":"1200","tag2":"","desc":"Exposure in µAs"},{"tag1":"(0018,115E)","vr":"DS","value":"0.384","tag2":"","desc":"Image and Fluoroscopy Area Dose Product"},{"tag1":"(0018,1164)","vr":"DS","value":"0.148\\0.148","tag2":"","desc":"Imager Pixel Spacing"},{"tag1":"(0018,1166)","vr":"CS","value":"IN","tag2":"","desc":"Grid"},{"tag1":"(0018,1400)","vr":"LO","value":"","tag2":"","desc":"Acquisition Device Processing Description"},{"tag1":"(0018,1405)","vr":"IS","value":"369","tag2":"","desc":"Relative X-Ray Exposure"},{"tag1":"(0018,1411)","vr":"DS","value":"369","tag2":"","desc":"Exposure Index"},{"tag1":"(0018,1508)","vr":"CS","value":"NONE","tag2":"","desc":"Positioner Type"},{"tag1":"(0018,1600)","vr":"CS","value":"POLYGONAL","tag2":"","desc":"Shutter Shape"},{"tag1":"(0018,1620)","vr":"IS","value":"0\\2777\\0\\0\\2278\\0\\2278\\2777","tag2":"","desc":"Vertices of the Polygonal Shutter"},{"tag1":"(0018,1700)","vr":"CS","value":"RECTANGULAR","tag2":"","desc":"Collimator Shape"},{"tag1":"(0018,1702)","vr":"IS","value":"0","tag2":"","desc":"Collimator Left Vertical Edge"},{"tag1":"(0018,1704)","vr":"IS","value":"2777","tag2":"","desc":"Collimator Right Vertical Edge"},{"tag1":"(0018,1706)","vr":"IS","value":"0","tag2":"","desc":"Collimator Upper Horizontal Edge"},{"tag1":"(0018,1708)","vr":"IS","value":"2278","tag2":"","desc":"Collimator Lower Horizontal Edge"},{"tag1":"(0018,5101)","vr":"CS","value":"PA","tag2":"","desc":"View Position"},{"tag1":"(0018,7001)","vr":"DS","value":"32.7","tag2":"","desc":"Detector Temperature"},{"tag1":"(0018,7004)","vr":"CS","value":"SCINTILLATOR","tag2":"","desc":"Detector Type"},{"tag1":"(0018,7008)","vr":"LT","value":"SingleShot1s","tag2":"","desc":"Detector Mode"},{"tag1":"(0018,700A)","vr":"SH","value":"SN1546U4","tag2":"","desc":"Detector ID"},{"tag1":"(0018,700C)","vr":"DA","value":"20170102","tag2":"","desc":"Date of Last Detector Calibration"},{"tag1":"(0018,700E)","vr":"TM","value":"091930","tag2":"","desc":"Time of Last Detector Calibration"},{"tag1":"(0018,7012)","vr":"DS","value":"180517.087","tag2":"","desc":"Detector Time Since Last Exposure"},{"tag1":"(0018,702A)","vr":"LO","value":"TRIXELL","tag2":"","desc":"Detector Manufacturer Name"},{"tag1":"(0018,702B)","vr":"LO","value":"PIXIUM4343RC","tag2":"","desc":"Detector Manufacturer’s Model Name"},{"tag1":"(0018,7030)","vr":"DS","value":"0\\0","tag2":"","desc":"Field of View Origin"},{"tag1":"(0018,7032)","vr":"DS","value":"0","tag2":"","desc":"Field of View Rotation"},{"tag1":"(0018,7034)","vr":"CS","value":"YES","tag2":"","desc":"Field of View Horizontal Flip"},{"tag1":"(0018,7050)","vr":"CS","value":"COPPER\\ALUMINIUM","tag2":"","desc":"Filter Material"},{"tag1":"(0018,7062)","vr":"LT","value":"3","tag2":"","desc":"Exposure Control Mode Description"},{"tag1":"(0018,8150)","vr":"DS","value":"5100","tag2":"","desc":"Exposure Time in µS"},{"tag1":"(0020,000D)","vr":"UI","value":"1.2.840.113619.2.182.10808617219229.1484672322.853647","tag2":"","desc":"Study Instance UID"},{"tag1":"(0020,000E)","vr":"UI","value":"1.3.46.670589.30.36.0.1.72567767433727.1485247623321.1","tag2":"","desc":"Series Instance UID"},{"tag1":"(0020,0010)","vr":"SH","value":"","tag2":"","desc":"Study ID"},{"tag1":"(0020,0011)","vr":"IS","value":"1","tag2":"","desc":"Series Number"},{"tag1":"(0020,0013)","vr":"IS","value":"1","tag2":"","desc":"Instance Number"},{"tag1":"(0020,0020)","vr":"CS","value":"L\\F","tag2":"","desc":"Patient Orientation"},{"tag1":"(0020,0062)","vr":"CS","value":"","tag2":"","desc":"Image Laterality"},{"tag1":"(0028,0002)","vr":"US","value":"1","tag2":"","desc":"Samples per Pixel"},{"tag1":"(0028,0004)","vr":"CS","value":"MONOCHROME2","tag2":"","desc":"Photometric Interpretation"},{"tag1":"(0028,0010)","vr":"US","value":"2279","tag2":"","desc":"Rows"},{"tag1":"(0028,0011)","vr":"US","value":"2778","tag2":"","desc":"Columns"},{"tag1":"(0028,0030)","vr":"DS","value":"0.1489004424779\\0.1489004424779","tag2":"","desc":"Pixel Spacing"},{"tag1":"(0028,0100)","vr":"US","value":"16","tag2":"","desc":"Bits Allocated"},{"tag1":"(0028,0101)","vr":"US","value":"12","tag2":"","desc":"Bits Stored"},{"tag1":"(0028,0102)","vr":"US","value":"11","tag2":"","desc":"High Bit"},{"tag1":"(0028,0103)","vr":"US","value":"0","tag2":"","desc":"Pixel Representation"},{"tag1":"(0028,0300)","vr":"CS","value":"NO","tag2":"","desc":"Quality Control Image"},{"tag1":"(0028,0301)","vr":"CS","value":"NO","tag2":"","desc":"Burned In Annotation"},{"tag1":"(0028,0303)","vr":"CS","value":"","tag2":"","desc":"Longitudinal Temporal Information Modified"},{"tag1":"(0028,1040)","vr":"CS","value":"LOG","tag2":"","desc":"Pixel Intensity Relationship"},{"tag1":"(0028,1041)","vr":"SS","value":"-1","tag2":"","desc":"Pixel Intensity Relationship Sign"},{"tag1":"(0028,1050)","vr":"DS","value":"2047.5","tag2":"","desc":"Window Center"},{"tag1":"(0028,1051)","vr":"DS","value":"4095","tag2":"","desc":"Window Width"},{"tag1":"(0028,1052)","vr":"DS","value":"0","tag2":"","desc":"Rescale Intercept"},{"tag1":"(0028,1053)","vr":"DS","value":"1","tag2":"","desc":"Rescale Slope"},{"tag1":"(0028,1054)","vr":"LO","value":"US","tag2":"","desc":"Rescale Type"},{"tag1":"(0028,2110)","vr":"CS","value":"00","tag2":"","desc":"Lossy Image Compression"},{"tag1":"(0032,1060)","vr":"LO","value":"","tag2":"","desc":"Requested Procedure Description"},{"tag1":"(0032,1064)","vr":"SQ","value":"","tag2":"(0032,1064)","desc":"Requested Procedure Code Sequence"},{"tag1":"(0032,1064)","vr":"SH","value":"3061010101001030","tag2":"(0008,0100)","desc":"Code Value"},{"tag1":"(0032,1064)","vr":"SH","value":"CCG_CSTemp","tag2":"(0008,0102)","desc":"Coding Scheme Designator"},{"tag1":"(0032,1064)","vr":"LO","value":"RX T�RAX, PA","tag2":"(0008,0104)","desc":"Code Meaning"},{"tag1":"(0040,0241)","vr":"AE","value":"SJDIDI01","tag2":"","desc":"Performed Station AE Title"},{"tag1":"(0040,0244)","vr":"DA","value":"20170124","tag2":"","desc":"Performed Procedure Step Start Date"},{"tag1":"(0040,0245)","vr":"TM","value":"094646.541000","tag2":"","desc":"Performed Procedure Step Start Time"},{"tag1":"(0040,0250)","vr":"DA","value":"20170124","tag2":"","desc":"Performed Procedure Step End Date"},{"tag1":"(0040,0251)","vr":"TM","value":"094703.214000","tag2":"","desc":"Performed Procedure Step End Time"},{"tag1":"(0040,0252)","vr":"CS","value":"","tag2":"","desc":"Performed Procedure Step Status"},{"tag1":"(0040,0254)","vr":"LO","value":"","tag2":"","desc":"Performed Procedure Step Description"},{"tag1":"(0040,0275)","vr":"SQ","value":"","tag2":"(0040,0275)","desc":"Request Attributes Sequence"},{"tag1":"(0040,0275)","vr":"SH","value":"0123410005305389","tag2":"(0040,1001)","desc":"Requested Procedure ID"},{"tag1":"(0040,0301)","vr":"US","value":"1","tag2":"","desc":"Total Number of Exposures"},{"tag1":"(0040,0302)","vr":"US","value":"0","tag2":"","desc":"Entrance Dose"},{"tag1":"(0040,1002)","vr":"LO","value":"","tag2":"","desc":"Reason for the Requested Procedure"},{"tag1":"(0040,1003)","vr":"SH","value":"","tag2":"","desc":"Requested Procedure Priority"},{"tag1":"(0040,1400)","vr":"LT","value":"","tag2":"","desc":"Requested Procedure Comments"},{"tag1":"(0040,2001)","vr":"LO","value":"","tag2":"","desc":"Reason for the Imaging Service Request"},{"tag1":"(0040,2004)","vr":"DA","value":"","tag2":"","desc":"Issue Date of Imaging Service Request"},{"tag1":"(0040,2017)","vr":"LO","value":"","tag2":"","desc":"Filler Order Number / Imaging Service Request"},{"tag1":"(0040,2400)","vr":"LT","value":"","tag2":"","desc":"Imaging Service Request Comments"},{"tag1":"(0040,8302)","vr":"DS","value":"0.043","tag2":"","desc":"Entrance Dose in mGy"},{"tag1":"(0903,0010)","vr":"LO","value":"GEIIS PACS","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(0905,0010)","vr":"LO","value":"GEIIS","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(2001,0010)","vr":"LO","value":"Philips Imaging DD 001","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(2001,0011)","vr":"LO","value":"Philips Imaging DD 002","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(2001,0090)","vr":"LO","value":"Philips Imaging DD 129","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(200B,0010)","vr":"LO","value":"Philips RAD Imaging DD 001","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(200B,0070)","vr":"LO","value":"Philips RAD Imaging DD 097","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(200B,0072)","vr":"LO","value":"Philips RAD Imaging DD 099","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(2050,0020)","vr":"CS","value":"IDENTITY","tag2":"","desc":"Presentation LUT Shape"},{"tag1":"(7FD1,0010)","vr":"LO","value":"GEIIS","tag2":"","desc":"Private Creator Data Element"}]}} \ No newline at end of file diff --git a/data/examples/RX_Thorax/sub-1/ses-1/sub-1_ses-1_scans.tsv b/data/examples/RX_Thorax/sub-1/ses-1/sub-1_ses-1_scans.tsv new file mode 100644 index 0000000..9ba107b --- /dev/null +++ b/data/examples/RX_Thorax/sub-1/ses-1/sub-1_ses-1_scans.tsv @@ -0,0 +1,2 @@ +filename Manufacturer (0008,0070) Series Description (0008,103E) Manufacturer’s Model Name (0008,1090) Patient ID (0010,0020) Patient’s Sex (0010,0040) Patient’s Age (0010,1010) Patient’s Weight (0010,1030) Scanning Sequence (0018,0020) Sequence Variant (0018,0021) Scan Options (0018,0022) MR Acquisition Type (0018,0023) Slice Thickness (0018,0050) Repetition Time (0018,0080) Echo Time (0018,0081) (0018,0082) Imaging Frequency (0018,0084) Magnetic Field Strength (0018,0087) Manufacturer’s Model Name (0008,1090) Spacing Between Slices (0018,0088) Echo Train Length (0018,0091) Percent Sampling (0018,0093) Pixel Bandwidth (0018,0095) Flip Angle (0018,1314) Patient Position (0018,5100) Image Position (Patient) (0020,0032) Image Orientation (Patient) (0020,0037) Position Reference Indicator (0020,1040) Slice Location (0020,1041) Rows (0028,0010) Columns (0028,0011) Pixel Spacing (0028,0030) Bits Allocated (0028,0100) Number of Averages (0018,0083) Echo Number(s) (0018,0086) (0018,9461) +rx/sub-1_ses-1_bp-thorax_vp_ap_dx.nii.gz GE MEDICAL SYSTEMS Thorax_AP OPTIMA 332424083962373450045181767823697702475 F 057Y 80 GR SS\SP\SK FAST_GEMS\EDR_GEMS\PFF 3D 1 6.816 1.984 None 63.867408 1.5 OPTIMA MR360 0.5 1 100 244.141 12 HFS -139.453\-147.422\39.1247 1\-0\0\-0\1\0 39.12474823 256 256 1.0938\1.0938 16 2 1 None diff --git a/data/examples/RX_Thorax/sub-1/ses-2/rx/sub-1_ses-2_bp-thorax_bp-ap_cr.json b/data/examples/RX_Thorax/sub-1/ses-2/rx/sub-1_ses-2_bp-thorax_bp-ap_cr.json new file mode 100644 index 0000000..cf69fb9 --- /dev/null +++ b/data/examples/RX_Thorax/sub-1/ses-2/rx/sub-1_ses-2_bp-thorax_bp-ap_cr.json @@ -0,0 +1 @@ +{"ResultSet":{"Result":[{"tag1":"(0002,0001)","vr":"OB","value":"00\\01","tag2":"","desc":"File Meta Information Version"},{"tag1":"(0002,0002)","vr":"UI","value":"1.2.840.10008.5.1.4.1.1.1","tag2":"","desc":"Media Storage SOP Class UID"},{"tag1":"(0002,0003)","vr":"UI","value":"2.16.840.1.113669.6.4.0.1255808290671.2010109121521807.0.1","tag2":"","desc":"Media Storage SOP Instance UID"},{"tag1":"(0002,0010)","vr":"UI","value":"1.2.840.10008.1.2.1","tag2":"","desc":"Transfer Syntax UID"},{"tag1":"(0002,0012)","vr":"UI","value":"1.2.40.0.13.1.1","tag2":"","desc":"Implementation Class UID"},{"tag1":"(0002,0013)","vr":"SH","value":"dcm4che-2.0","tag2":"","desc":"Implementation Version Name"},{"tag1":"(0002,0016)","vr":"AE","value":"GDCMSCU","tag2":"","desc":"Source Application Entity Title"},{"tag1":"(0008,0005)","vr":"CS","value":"ISO_IR 100","tag2":"","desc":"Specific Character Set"},{"tag1":"(0008,0008)","vr":"CS","value":"DERIVED\\PRIMARY","tag2":"","desc":"Image Type"},{"tag1":"(0008,0016)","vr":"UI","value":"1.2.840.10008.5.1.4.1.1.1","tag2":"","desc":"SOP Class UID"},{"tag1":"(0008,0018)","vr":"UI","value":"2.16.840.1.113669.6.4.0.1255808290671.2010109121521807.0.1","tag2":"","desc":"SOP Instance UID"},{"tag1":"(0008,0020)","vr":"DA","value":"20100422","tag2":"","desc":"Study Date"},{"tag1":"(0008,0022)","vr":"DA","value":"20100422","tag2":"","desc":"Acquisition Date"},{"tag1":"(0008,0030)","vr":"TM","value":"091614","tag2":"","desc":"Study Time"},{"tag1":"(0008,0032)","vr":"TM","value":"091655","tag2":"","desc":"Acquisition Time"},{"tag1":"(0008,0050)","vr":"SH","value":"","tag2":"","desc":"Accession Number"},{"tag1":"(0008,0060)","vr":"CS","value":"CR","tag2":"","desc":"Modality"},{"tag1":"(0008,0070)","vr":"LO","value":"Imaging Dynamics Company Ltd.","tag2":"","desc":"Manufacturer"},{"tag1":"(0008,0090)","vr":"PN","value":"","tag2":"","desc":"Referring Physician’s Name"},{"tag1":"(0008,1010)","vr":"SH","value":"SJTD","tag2":"","desc":"Station Name"},{"tag1":"(0008,1030)","vr":"LO","value":"padchest_ds17","tag2":"","desc":"Study Description"},{"tag1":"(0008,1032)","vr":"SQ","value":"","tag2":"(0008,1032)","desc":"Procedure Code Sequence"},{"tag1":"(0008,1032)","vr":"SH","value":"012341_G0.12","tag2":"(0008,0100)","desc":"Code Value"},{"tag1":"(0008,1032)","vr":"SH","value":"GEIIS","tag2":"(0008,0102)","desc":"Coding Scheme Designator"},{"tag1":"(0008,1032)","vr":"SH","value":"0","tag2":"(0008,0103)","desc":"Coding Scheme Version"},{"tag1":"(0008,1032)","vr":"LO","value":"TORAX PREOPERATORIO","tag2":"(0008,0104)","desc":"Code Meaning"},{"tag1":"(0008,103E)","vr":"LO","value":"","tag2":"","desc":"Series Description"},{"tag1":"(0008,2112)","vr":"SQ","value":"","tag2":"(0008,2112)","desc":"Source Image Sequence"},{"tag1":"(0008,2112)","vr":"UI","value":"1.2.840.10008.5.1.4.1.1.1","tag2":"(0008,1150)","desc":"Referenced SOP Class UID"},{"tag1":"(0008,2112)","vr":"UI","value":"2.16.840.1.113669.6.4.0.1255808290671.2010109121521807.0.0","tag2":"(0008,1155)","desc":"Referenced SOP Instance UID"},{"tag1":"(0009,0010)","vr":"LO","value":"GEIIS","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(0010,0010)","vr":"PN","value":"100002652742762245719447501824197948584","tag2":"","desc":"Patient’s Name"},{"tag1":"(0010,0020)","vr":"LO","value":"125374151943505747025890313053997514922","tag2":"","desc":"Patient ID"},{"tag1":"(0010,0030)","vr":"DA","value":"19530920","tag2":"","desc":"Patient’s Birth Date"},{"tag1":"(0010,0040)","vr":"CS","value":"F","tag2":"","desc":"Patient’s Sex"},{"tag1":"(0010,2000)","vr":"LO","value":"","tag2":"","desc":"Medical Alerts"},{"tag1":"(0010,2110)","vr":"LO","value":"","tag2":"","desc":"Allergies"},{"tag1":"(0018,0015)","vr":"CS","value":"TORAX PREOPERATO","tag2":"","desc":"Body Part Examined"},{"tag1":"(0018,0060)","vr":"DS","value":"125","tag2":"","desc":"KVP"},{"tag1":"(0018,1020)","vr":"LO","value":"2.1.149","tag2":"","desc":"Software Version(s)"},{"tag1":"(0018,1030)","vr":"LO","value":"","tag2":"","desc":"Protocol Name"},{"tag1":"(0018,1150)","vr":"IS","value":"10","tag2":"","desc":"Exposure Time"},{"tag1":"(0018,1151)","vr":"IS","value":"320","tag2":"","desc":"X-Ray Tube Current"},{"tag1":"(0018,1152)","vr":"IS","value":"3","tag2":"","desc":"Exposure"},{"tag1":"(0018,1153)","vr":"IS","value":"3200","tag2":"","desc":"Exposure in µAs"},{"tag1":"(0018,115E)","vr":"DS","value":"0","tag2":"","desc":"Image and Fluoroscopy Area Dose Product"},{"tag1":"(0018,1164)","vr":"DS","value":"0.216\\0.216","tag2":"","desc":"Imager Pixel Spacing"},{"tag1":"(0018,1405)","vr":"IS","value":"-0.5","tag2":"","desc":"Relative X-Ray Exposure"},{"tag1":"(0018,5101)","vr":"CS","value":"POSTERO_ANTERIOR","tag2":"","desc":"View Position"},{"tag1":"(0018,6000)","vr":"DS","value":"400","tag2":"","desc":"Sensitivity"},{"tag1":"(0018,7060)","vr":"CS","value":"MANUAL","tag2":"","desc":"Exposure Control Mode"},{"tag1":"(0018,8150)","vr":"DS","value":"10000","tag2":"","desc":"Exposure Time in µS"},{"tag1":"(0018,8151)","vr":"DS","value":"320000","tag2":"","desc":"X-Ray Tube Current in µA"},{"tag1":"(0020,000D)","vr":"UI","value":"2.16.840.1.113669.6.4.0.1255808290671.2010109121521807","tag2":"","desc":"Study Instance UID"},{"tag1":"(0020,000E)","vr":"UI","value":"2.16.840.1.113669.6.4.0.1255808290671.2010109121521807.0.1","tag2":"","desc":"Series Instance UID"},{"tag1":"(0020,0010)","vr":"SH","value":"","tag2":"","desc":"Study ID"},{"tag1":"(0020,0011)","vr":"IS","value":"1","tag2":"","desc":"Series Number"},{"tag1":"(0020,0013)","vr":"IS","value":"235799","tag2":"","desc":"Instance Number"},{"tag1":"(0028,0002)","vr":"US","value":"1","tag2":"","desc":"Samples per Pixel"},{"tag1":"(0028,0004)","vr":"CS","value":"MONOCHROME2","tag2":"","desc":"Photometric Interpretation"},{"tag1":"(0028,0006)","vr":"US","value":"0","tag2":"","desc":"Planar Configuration"},{"tag1":"(0028,0010)","vr":"US","value":"1464","tag2":"","desc":"Rows"},{"tag1":"(0028,0011)","vr":"US","value":"1576","tag2":"","desc":"Columns"},{"tag1":"(0028,0030)","vr":"DS","value":"0.216\\0.216","tag2":"","desc":"Pixel Spacing"},{"tag1":"(0028,0100)","vr":"US","value":"16","tag2":"","desc":"Bits Allocated"},{"tag1":"(0028,0101)","vr":"US","value":"12","tag2":"","desc":"Bits Stored"},{"tag1":"(0028,0102)","vr":"US","value":"11","tag2":"","desc":"High Bit"},{"tag1":"(0028,0103)","vr":"US","value":"0","tag2":"","desc":"Pixel Representation"},{"tag1":"(0028,0303)","vr":"CS","value":"","tag2":"","desc":"Longitudinal Temporal Information Modified"},{"tag1":"(0028,1050)","vr":"DS","value":"1561","tag2":"","desc":"Window Center"},{"tag1":"(0028,1051)","vr":"DS","value":"2536","tag2":"","desc":"Window Width"},{"tag1":"(0028,1052)","vr":"DS","value":"0","tag2":"","desc":"Rescale Intercept"},{"tag1":"(0028,1053)","vr":"DS","value":"1","tag2":"","desc":"Rescale Slope"},{"tag1":"(0028,1054)","vr":"LO","value":"US","tag2":"","desc":"Rescale Type"},{"tag1":"(0040,0254)","vr":"LO","value":"","tag2":"","desc":"Performed Procedure Step Description"},{"tag1":"(0040,0275)","vr":"SQ","value":"","tag2":"(0040,0275)","desc":"Request Attributes Sequence"},{"tag1":"(0040,0275)","vr":"SH","value":"0123410003818272","tag2":"(0040,1001)","desc":"Requested Procedure ID"},{"tag1":"(0903,0010)","vr":"LO","value":"GEIIS PACS","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(0905,0010)","vr":"LO","value":"GEIIS","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(4321,0010)","vr":"LO","value":"Imaging Dynamics Company Ltd.","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(7FD1,0010)","vr":"LO","value":"GEIIS","tag2":"","desc":"Private Creator Data Element"}]}} \ No newline at end of file diff --git a/data/examples/RX_Thorax/sub-1/ses-2/rx/sub-1_ses-2_bp-thorax_bp-ap_cr.nii.gz b/data/examples/RX_Thorax/sub-1/ses-2/rx/sub-1_ses-2_bp-thorax_bp-ap_cr.nii.gz new file mode 100644 index 0000000..7000b84 Binary files /dev/null and b/data/examples/RX_Thorax/sub-1/ses-2/rx/sub-1_ses-2_bp-thorax_bp-ap_cr.nii.gz differ diff --git a/data/examples/RX_Thorax/sub-1/ses-2/sub-1_ses-2_scans.tsv b/data/examples/RX_Thorax/sub-1/ses-2/sub-1_ses-2_scans.tsv new file mode 100644 index 0000000..235b340 --- /dev/null +++ b/data/examples/RX_Thorax/sub-1/ses-2/sub-1_ses-2_scans.tsv @@ -0,0 +1,2 @@ +filename Manufacturer (0008,0070) Series Description (0008,103E) Manufacturer’s Model Name (0008,1090) Patient ID (0010,0020) Patient’s Sex (0010,0040) Patient’s Age (0010,1010) Patient’s Weight (0010,1030) Scanning Sequence (0018,0020) Sequence Variant (0018,0021) Scan Options (0018,0022) MR Acquisition Type (0018,0023) Slice Thickness (0018,0050) Repetition Time (0018,0080) Echo Time (0018,0081) (0018,0082) Imaging Frequency (0018,0084) Magnetic Field Strength (0018,0087) Manufacturer’s Model Name (0008,1090) Spacing Between Slices (0018,0088) Echo Train Length (0018,0091) Percent Sampling (0018,0093) Pixel Bandwidth (0018,0095) Flip Angle (0018,1314) Patient Position (0018,5100) Image Position (Patient) (0020,0032) Image Orientation (Patient) (0020,0037) Position Reference Indicator (0020,1040) Slice Location (0020,1041) Rows (0028,0010) Columns (0028,0011) Pixel Spacing (0028,0030) Bits Allocated (0028,0100) Number of Averages (0018,0083) Echo Number(s) (0018,0086) (0018,9461) +dx/sub-1_ses-1_bp-thorax_vp_ap_cr.nii.gz GE MEDICAL SYSTEMS Thorax AP OPTIMA 332424083962373450045181767823697702475 F 057Y 80 GR SS\SP\SK FAST_GEMS\EDR_GEMS\PFF 3D 1 6.816 1.984 None 63.867408 1.5 OPTIMA MR360 0.5 1 100 244.141 12 HFS -139.453\-147.422\39.1247 1\-0\0\-0\1\0 39.12474823 256 256 1.0938\1.0938 16 2 1 None diff --git a/data/examples/RX_Thorax/sub-2/rx/sub-2_ses-1_bp-thorax_vp-ap_dx.json b/data/examples/RX_Thorax/sub-2/rx/sub-2_ses-1_bp-thorax_vp-ap_dx.json new file mode 100644 index 0000000..099a8a8 --- /dev/null +++ b/data/examples/RX_Thorax/sub-2/rx/sub-2_ses-1_bp-thorax_vp-ap_dx.json @@ -0,0 +1 @@ +{"ResultSet":{"Result":[{"tag1":"(0002,0001)","vr":"OB","value":"00\\01","tag2":"","desc":"File Meta Information Version"},{"tag1":"(0002,0002)","vr":"UI","value":"1.2.840.10008.5.1.4.1.1.1.1","tag2":"","desc":"Media Storage SOP Class UID"},{"tag1":"(0002,0003)","vr":"UI","value":"1.3.46.670589.30.36.0.1.72567767433727.1508740832189.2","tag2":"","desc":"Media Storage SOP Instance UID"},{"tag1":"(0002,0010)","vr":"UI","value":"1.2.840.10008.1.2.1","tag2":"","desc":"Transfer Syntax UID"},{"tag1":"(0002,0012)","vr":"UI","value":"1.2.40.0.13.1.1","tag2":"","desc":"Implementation Class UID"},{"tag1":"(0002,0013)","vr":"SH","value":"dcm4che-2.0","tag2":"","desc":"Implementation Version Name"},{"tag1":"(0002,0016)","vr":"AE","value":"CTP","tag2":"","desc":"Source Application Entity Title"},{"tag1":"(0008,0005)","vr":"CS","value":"ISO_IR 100","tag2":"","desc":"Specific Character Set"},{"tag1":"(0008,0008)","vr":"CS","value":"ORIGINAL\\PRIMARY\\","tag2":"","desc":"Image Type"},{"tag1":"(0008,0016)","vr":"UI","value":"1.2.840.10008.5.1.4.1.1.1.1","tag2":"","desc":"SOP Class UID"},{"tag1":"(0008,0018)","vr":"UI","value":"1.3.46.670589.30.36.0.1.72567767433727.1508740832189.2","tag2":"","desc":"SOP Instance UID"},{"tag1":"(0008,0020)","vr":"DA","value":"20171023","tag2":"","desc":"Study Date"},{"tag1":"(0008,0021)","vr":"DA","value":"20171023","tag2":"","desc":"Series Date"},{"tag1":"(0008,0022)","vr":"DA","value":"20171023","tag2":"","desc":"Acquisition Date"},{"tag1":"(0008,0023)","vr":"DA","value":"20171023","tag2":"","desc":"Content Date"},{"tag1":"(0008,0030)","vr":"TM","value":"083836.209000","tag2":"","desc":"Study Time"},{"tag1":"(0008,0031)","vr":"TM","value":"083839.000000","tag2":"","desc":"Series Time"},{"tag1":"(0008,0032)","vr":"TM","value":"083916","tag2":"","desc":"Acquisition Time"},{"tag1":"(0008,0033)","vr":"TM","value":"083916","tag2":"","desc":"Content Time"},{"tag1":"(0008,0050)","vr":"SH","value":"","tag2":"","desc":"Accession Number"},{"tag1":"(0008,0060)","vr":"CS","value":"DX","tag2":"","desc":"Modality"},{"tag1":"(0008,0068)","vr":"CS","value":"FOR PRESENTATION","tag2":"","desc":"Presentation Intent Type"},{"tag1":"(0008,0070)","vr":"LO","value":"Philips Medical Systems","tag2":"","desc":"Manufacturer"},{"tag1":"(0008,0090)","vr":"PN","value":"","tag2":"","desc":"Referring Physician’s Name"},{"tag1":"(0008,1010)","vr":"SH","value":"SJDIDI01","tag2":"","desc":"Station Name"},{"tag1":"(0008,1030)","vr":"LO","value":"padchest_ds17","tag2":"","desc":"Study Description"},{"tag1":"(0008,1032)","vr":"SQ","value":"","tag2":"(0008,1032)","desc":"Procedure Code Sequence"},{"tag1":"(0008,1032)","vr":"SH","value":"3061010101001040","tag2":"(0008,0100)","desc":"Code Value"},{"tag1":"(0008,1032)","vr":"SH","value":"CCG_CSTemp","tag2":"(0008,0102)","desc":"Coding Scheme Designator"},{"tag1":"(0008,1032)","vr":"LO","value":"RX TORAX PA Y LAT","tag2":"(0008,0104)","desc":"Code Meaning"},{"tag1":"(0008,103E)","vr":"LO","value":"Trax","tag2":"","desc":"Series Description"},{"tag1":"(0008,1090)","vr":"LO","value":"DigitalDiagnost","tag2":"","desc":"Manufacturer’s Model Name"},{"tag1":"(0008,1110)","vr":"SQ","value":"","tag2":"(0008,1110)","desc":"Referenced Study Sequence"},{"tag1":"(0008,1110)","vr":"UI","value":"1.2.840.100008.3.1.2.3.1","tag2":"(0008,1150)","desc":"Referenced SOP Class UID"},{"tag1":"(0008,1110)","vr":"UI","value":"1.2.840.113619.2.182.10808617219229.1508740222.1172960","tag2":"(0008,1155)","desc":"Referenced SOP Instance UID"},{"tag1":"(0008,1111)","vr":"SQ","value":"","tag2":"(0008,1111)","desc":"Referenced Performed Procedure Step Sequence"},{"tag1":"(0008,1111)","vr":"UI","value":"1.2.840.10008.3.1.2.3.3","tag2":"(0008,1150)","desc":"Referenced SOP Class UID"},{"tag1":"(0008,1111)","vr":"UI","value":"1.3.46.670589.30.36.0.1.72567767433727.1508740652038.1","tag2":"(0008,1155)","desc":"Referenced SOP Instance UID"},{"tag1":"(0008,3010)","vr":"UI","value":"1.3.46.670589.30.36.0.1.72567767433727.1508740752489.1","tag2":"","desc":"Irradiation Event UID"},{"tag1":"(0009,0010)","vr":"LO","value":"GEIIS","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(0010,0010)","vr":"PN","value":"100008301845755693600822040133468866003","tag2":"","desc":"Patient’s Name"},{"tag1":"(0010,0020)","vr":"LO","value":"117677712752528732526839762067921423608","tag2":"","desc":"Patient ID"},{"tag1":"(0010,0030)","vr":"DA","value":"19631102","tag2":"","desc":"Patient’s Birth Date"},{"tag1":"(0010,0040)","vr":"CS","value":"F","tag2":"","desc":"Patient’s Sex"},{"tag1":"(0010,1010)","vr":"AS","value":"053Y","tag2":"","desc":"Patient’s Age"},{"tag1":"(0010,1020)","vr":"DS","value":"0","tag2":"","desc":"Patient’s Size"},{"tag1":"(0010,1030)","vr":"DS","value":"0","tag2":"","desc":"Patient’s Weight"},{"tag1":"(0010,2000)","vr":"LO","value":"","tag2":"","desc":"Medical Alerts"},{"tag1":"(0010,2110)","vr":"LO","value":"","tag2":"","desc":"Allergies"},{"tag1":"(0010,2160)","vr":"SH","value":"","tag2":"","desc":"Ethnic Group"},{"tag1":"(0010,21B0)","vr":"LT","value":"","tag2":"","desc":"Additional Patient History"},{"tag1":"(0010,21C0)","vr":"US","value":"4","tag2":"","desc":"Pregnancy Status"},{"tag1":"(0018,0015)","vr":"CS","value":"CHEST","tag2":"","desc":"Body Part Examined"},{"tag1":"(0018,0060)","vr":"DS","value":"125","tag2":"","desc":"KVP"},{"tag1":"(0018,1000)","vr":"LO","value":"72567767433727","tag2":"","desc":"Device Serial Number"},{"tag1":"(0018,1020)","vr":"LO","value":"4.1.3.2","tag2":"","desc":"Software Version(s)"},{"tag1":"(0018,1030)","vr":"LO","value":"Trax","tag2":"","desc":"Protocol Name"},{"tag1":"(0018,1050)","vr":"DS","value":"0.148","tag2":"","desc":"Spatial Resolution"},{"tag1":"(0018,1110)","vr":"DS","value":"1807","tag2":"","desc":"Distance Source to Detector"},{"tag1":"(0018,1111)","vr":"DS","value":"1753","tag2":"","desc":"Distance Source to Patient"},{"tag1":"(0018,1114)","vr":"DS","value":"0.99394939493971","tag2":"","desc":"Estimated Radiographic Magnification Factor"},{"tag1":"(0018,1150)","vr":"IS","value":"5","tag2":"","desc":"Exposure Time"},{"tag1":"(0018,1152)","vr":"IS","value":"1","tag2":"","desc":"Exposure"},{"tag1":"(0018,1153)","vr":"IS","value":"1400","tag2":"","desc":"Exposure in µAs"},{"tag1":"(0018,115E)","vr":"DS","value":"0.59","tag2":"","desc":"Image and Fluoroscopy Area Dose Product"},{"tag1":"(0018,1164)","vr":"DS","value":"0.148\\0.148","tag2":"","desc":"Imager Pixel Spacing"},{"tag1":"(0018,1166)","vr":"CS","value":"IN","tag2":"","desc":"Grid"},{"tag1":"(0018,1400)","vr":"LO","value":"","tag2":"","desc":"Acquisition Device Processing Description"},{"tag1":"(0018,1405)","vr":"IS","value":"391","tag2":"","desc":"Relative X-Ray Exposure"},{"tag1":"(0018,1411)","vr":"DS","value":"391","tag2":"","desc":"Exposure Index"},{"tag1":"(0018,1508)","vr":"CS","value":"NONE","tag2":"","desc":"Positioner Type"},{"tag1":"(0018,1600)","vr":"CS","value":"POLYGONAL","tag2":"","desc":"Shutter Shape"},{"tag1":"(0018,1620)","vr":"IS","value":"103\\2064\\128\\0\\2829\\0\\2829\\2064","tag2":"","desc":"Vertices of the Polygonal Shutter"},{"tag1":"(0018,1700)","vr":"CS","value":"RECTANGULAR","tag2":"","desc":"Collimator Shape"},{"tag1":"(0018,1702)","vr":"IS","value":"0","tag2":"","desc":"Collimator Left Vertical Edge"},{"tag1":"(0018,1704)","vr":"IS","value":"2389","tag2":"","desc":"Collimator Right Vertical Edge"},{"tag1":"(0018,1706)","vr":"IS","value":"0","tag2":"","desc":"Collimator Upper Horizontal Edge"},{"tag1":"(0018,1708)","vr":"IS","value":"2829","tag2":"","desc":"Collimator Lower Horizontal Edge"},{"tag1":"(0018,5101)","vr":"CS","value":"LL","tag2":"","desc":"View Position"},{"tag1":"(0018,7001)","vr":"DS","value":"31.3","tag2":"","desc":"Detector Temperature"},{"tag1":"(0018,7004)","vr":"CS","value":"SCINTILLATOR","tag2":"","desc":"Detector Type"},{"tag1":"(0018,7008)","vr":"LT","value":"SingleShot1s","tag2":"","desc":"Detector Mode"},{"tag1":"(0018,700A)","vr":"SH","value":"SN1546U4","tag2":"","desc":"Detector ID"},{"tag1":"(0018,700C)","vr":"DA","value":"20171018","tag2":"","desc":"Date of Last Detector Calibration"},{"tag1":"(0018,700E)","vr":"TM","value":"082323","tag2":"","desc":"Time of Last Detector Calibration"},{"tag1":"(0018,7012)","vr":"DS","value":"36403.63","tag2":"","desc":"Detector Time Since Last Exposure"},{"tag1":"(0018,702A)","vr":"LO","value":"TRIXELL","tag2":"","desc":"Detector Manufacturer Name"},{"tag1":"(0018,702B)","vr":"LO","value":"PIXIUM4343RC","tag2":"","desc":"Detector Manufacturer’s Model Name"},{"tag1":"(0018,7030)","vr":"DS","value":"0\\0","tag2":"","desc":"Field of View Origin"},{"tag1":"(0018,7032)","vr":"DS","value":"0","tag2":"","desc":"Field of View Rotation"},{"tag1":"(0018,7034)","vr":"CS","value":"YES","tag2":"","desc":"Field of View Horizontal Flip"},{"tag1":"(0018,7050)","vr":"CS","value":"COPPER\\ALUMINIUM","tag2":"","desc":"Filter Material"},{"tag1":"(0018,7062)","vr":"LT","value":"4","tag2":"","desc":"Exposure Control Mode Description"},{"tag1":"(0018,8150)","vr":"DS","value":"5000","tag2":"","desc":"Exposure Time in µS"},{"tag1":"(0020,000D)","vr":"UI","value":"1.2.840.113619.2.182.10808617219229.1508740222.1172960","tag2":"","desc":"Study Instance UID"},{"tag1":"(0020,000E)","vr":"UI","value":"1.3.46.670589.30.36.0.1.72567767433727.1508740832187.1","tag2":"","desc":"Series Instance UID"},{"tag1":"(0020,0010)","vr":"SH","value":"","tag2":"","desc":"Study ID"},{"tag1":"(0020,0011)","vr":"IS","value":"1","tag2":"","desc":"Series Number"},{"tag1":"(0020,0013)","vr":"IS","value":"2","tag2":"","desc":"Instance Number"},{"tag1":"(0020,0020)","vr":"CS","value":"A\\F","tag2":"","desc":"Patient Orientation"},{"tag1":"(0020,0062)","vr":"CS","value":"","tag2":"","desc":"Image Laterality"},{"tag1":"(0028,0002)","vr":"US","value":"1","tag2":"","desc":"Samples per Pixel"},{"tag1":"(0028,0004)","vr":"CS","value":"MONOCHROME2","tag2":"","desc":"Photometric Interpretation"},{"tag1":"(0028,0010)","vr":"US","value":"2830","tag2":"","desc":"Rows"},{"tag1":"(0028,0011)","vr":"US","value":"2390","tag2":"","desc":"Columns"},{"tag1":"(0028,0030)","vr":"DS","value":"0.1489009407858\\0.1489009407858","tag2":"","desc":"Pixel Spacing"},{"tag1":"(0028,0100)","vr":"US","value":"16","tag2":"","desc":"Bits Allocated"},{"tag1":"(0028,0101)","vr":"US","value":"12","tag2":"","desc":"Bits Stored"},{"tag1":"(0028,0102)","vr":"US","value":"11","tag2":"","desc":"High Bit"},{"tag1":"(0028,0103)","vr":"US","value":"0","tag2":"","desc":"Pixel Representation"},{"tag1":"(0028,0300)","vr":"CS","value":"NO","tag2":"","desc":"Quality Control Image"},{"tag1":"(0028,0301)","vr":"CS","value":"NO","tag2":"","desc":"Burned In Annotation"},{"tag1":"(0028,0303)","vr":"CS","value":"","tag2":"","desc":"Longitudinal Temporal Information Modified"},{"tag1":"(0028,1040)","vr":"CS","value":"LOG","tag2":"","desc":"Pixel Intensity Relationship"},{"tag1":"(0028,1041)","vr":"SS","value":"-1","tag2":"","desc":"Pixel Intensity Relationship Sign"},{"tag1":"(0028,1050)","vr":"DS","value":"2047.5","tag2":"","desc":"Window Center"},{"tag1":"(0028,1051)","vr":"DS","value":"4095","tag2":"","desc":"Window Width"},{"tag1":"(0028,1052)","vr":"DS","value":"0","tag2":"","desc":"Rescale Intercept"},{"tag1":"(0028,1053)","vr":"DS","value":"1","tag2":"","desc":"Rescale Slope"},{"tag1":"(0028,1054)","vr":"LO","value":"US","tag2":"","desc":"Rescale Type"},{"tag1":"(0028,2110)","vr":"CS","value":"00","tag2":"","desc":"Lossy Image Compression"},{"tag1":"(0032,1060)","vr":"LO","value":"","tag2":"","desc":"Requested Procedure Description"},{"tag1":"(0032,1064)","vr":"SQ","value":"","tag2":"(0032,1064)","desc":"Requested Procedure Code Sequence"},{"tag1":"(0032,1064)","vr":"SH","value":"3061010101001040","tag2":"(0008,0100)","desc":"Code Value"},{"tag1":"(0032,1064)","vr":"SH","value":"CCG_CSTemp","tag2":"(0008,0102)","desc":"Coding Scheme Designator"},{"tag1":"(0032,1064)","vr":"LO","value":"RX T�RAX, PA Y LAT","tag2":"(0008,0104)","desc":"Code Meaning"},{"tag1":"(0040,0241)","vr":"AE","value":"SJDIDI01","tag2":"","desc":"Performed Station AE Title"},{"tag1":"(0040,0244)","vr":"DA","value":"20171023","tag2":"","desc":"Performed Procedure Step Start Date"},{"tag1":"(0040,0245)","vr":"TM","value":"083836.209000","tag2":"","desc":"Performed Procedure Step Start Time"},{"tag1":"(0040,0250)","vr":"DA","value":"20171023","tag2":"","desc":"Performed Procedure Step End Date"},{"tag1":"(0040,0251)","vr":"TM","value":"084032.059000","tag2":"","desc":"Performed Procedure Step End Time"},{"tag1":"(0040,0252)","vr":"CS","value":"","tag2":"","desc":"Performed Procedure Step Status"},{"tag1":"(0040,0254)","vr":"LO","value":"","tag2":"","desc":"Performed Procedure Step Description"},{"tag1":"(0040,0301)","vr":"US","value":"2","tag2":"","desc":"Total Number of Exposures"},{"tag1":"(0040,0302)","vr":"US","value":"0","tag2":"","desc":"Entrance Dose"},{"tag1":"(0040,1002)","vr":"LO","value":"","tag2":"","desc":"Reason for the Requested Procedure"},{"tag1":"(0040,1003)","vr":"SH","value":"","tag2":"","desc":"Requested Procedure Priority"},{"tag1":"(0040,1400)","vr":"LT","value":"","tag2":"","desc":"Requested Procedure Comments"},{"tag1":"(0040,2001)","vr":"LO","value":"","tag2":"","desc":"Reason for the Imaging Service Request"},{"tag1":"(0040,2004)","vr":"DA","value":"","tag2":"","desc":"Issue Date of Imaging Service Request"},{"tag1":"(0040,2017)","vr":"LO","value":"","tag2":"","desc":"Filler Order Number / Imaging Service Request"},{"tag1":"(0040,2400)","vr":"LT","value":"","tag2":"","desc":"Imaging Service Request Comments"},{"tag1":"(0040,8302)","vr":"DS","value":"0.077","tag2":"","desc":"Entrance Dose in mGy"},{"tag1":"(0903,0010)","vr":"LO","value":"GEIIS PACS","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(0905,0010)","vr":"LO","value":"GEIIS","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(2001,0010)","vr":"LO","value":"Philips Imaging DD 001","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(2001,0011)","vr":"LO","value":"Philips Imaging DD 002","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(2001,0090)","vr":"LO","value":"Philips Imaging DD 129","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(200B,0010)","vr":"LO","value":"Philips RAD Imaging DD 001","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(200B,0070)","vr":"LO","value":"Philips RAD Imaging DD 097","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(200B,0072)","vr":"LO","value":"Philips RAD Imaging DD 099","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(2050,0020)","vr":"CS","value":"IDENTITY","tag2":"","desc":"Presentation LUT Shape"},{"tag1":"(7FD1,0010)","vr":"LO","value":"GEIIS","tag2":"","desc":"Private Creator Data Element"}]}} \ No newline at end of file diff --git a/data/examples/RX_Thorax/sub-2/rx/sub-2_ses-1_bp-thorax_vp-ap_dx.nii.gz b/data/examples/RX_Thorax/sub-2/rx/sub-2_ses-1_bp-thorax_vp-ap_dx.nii.gz new file mode 100644 index 0000000..f7ac2ba Binary files /dev/null and b/data/examples/RX_Thorax/sub-2/rx/sub-2_ses-1_bp-thorax_vp-ap_dx.nii.gz differ diff --git a/data/examples/RX_Thorax/sub-2/rx/sub-2_ses-1_bp-thorax_vp-ll_dx.json b/data/examples/RX_Thorax/sub-2/rx/sub-2_ses-1_bp-thorax_vp-ll_dx.json new file mode 100644 index 0000000..099a8a8 --- /dev/null +++ b/data/examples/RX_Thorax/sub-2/rx/sub-2_ses-1_bp-thorax_vp-ll_dx.json @@ -0,0 +1 @@ +{"ResultSet":{"Result":[{"tag1":"(0002,0001)","vr":"OB","value":"00\\01","tag2":"","desc":"File Meta Information Version"},{"tag1":"(0002,0002)","vr":"UI","value":"1.2.840.10008.5.1.4.1.1.1.1","tag2":"","desc":"Media Storage SOP Class UID"},{"tag1":"(0002,0003)","vr":"UI","value":"1.3.46.670589.30.36.0.1.72567767433727.1508740832189.2","tag2":"","desc":"Media Storage SOP Instance UID"},{"tag1":"(0002,0010)","vr":"UI","value":"1.2.840.10008.1.2.1","tag2":"","desc":"Transfer Syntax UID"},{"tag1":"(0002,0012)","vr":"UI","value":"1.2.40.0.13.1.1","tag2":"","desc":"Implementation Class UID"},{"tag1":"(0002,0013)","vr":"SH","value":"dcm4che-2.0","tag2":"","desc":"Implementation Version Name"},{"tag1":"(0002,0016)","vr":"AE","value":"CTP","tag2":"","desc":"Source Application Entity Title"},{"tag1":"(0008,0005)","vr":"CS","value":"ISO_IR 100","tag2":"","desc":"Specific Character Set"},{"tag1":"(0008,0008)","vr":"CS","value":"ORIGINAL\\PRIMARY\\","tag2":"","desc":"Image Type"},{"tag1":"(0008,0016)","vr":"UI","value":"1.2.840.10008.5.1.4.1.1.1.1","tag2":"","desc":"SOP Class UID"},{"tag1":"(0008,0018)","vr":"UI","value":"1.3.46.670589.30.36.0.1.72567767433727.1508740832189.2","tag2":"","desc":"SOP Instance UID"},{"tag1":"(0008,0020)","vr":"DA","value":"20171023","tag2":"","desc":"Study Date"},{"tag1":"(0008,0021)","vr":"DA","value":"20171023","tag2":"","desc":"Series Date"},{"tag1":"(0008,0022)","vr":"DA","value":"20171023","tag2":"","desc":"Acquisition Date"},{"tag1":"(0008,0023)","vr":"DA","value":"20171023","tag2":"","desc":"Content Date"},{"tag1":"(0008,0030)","vr":"TM","value":"083836.209000","tag2":"","desc":"Study Time"},{"tag1":"(0008,0031)","vr":"TM","value":"083839.000000","tag2":"","desc":"Series Time"},{"tag1":"(0008,0032)","vr":"TM","value":"083916","tag2":"","desc":"Acquisition Time"},{"tag1":"(0008,0033)","vr":"TM","value":"083916","tag2":"","desc":"Content Time"},{"tag1":"(0008,0050)","vr":"SH","value":"","tag2":"","desc":"Accession Number"},{"tag1":"(0008,0060)","vr":"CS","value":"DX","tag2":"","desc":"Modality"},{"tag1":"(0008,0068)","vr":"CS","value":"FOR PRESENTATION","tag2":"","desc":"Presentation Intent Type"},{"tag1":"(0008,0070)","vr":"LO","value":"Philips Medical Systems","tag2":"","desc":"Manufacturer"},{"tag1":"(0008,0090)","vr":"PN","value":"","tag2":"","desc":"Referring Physician’s Name"},{"tag1":"(0008,1010)","vr":"SH","value":"SJDIDI01","tag2":"","desc":"Station Name"},{"tag1":"(0008,1030)","vr":"LO","value":"padchest_ds17","tag2":"","desc":"Study Description"},{"tag1":"(0008,1032)","vr":"SQ","value":"","tag2":"(0008,1032)","desc":"Procedure Code Sequence"},{"tag1":"(0008,1032)","vr":"SH","value":"3061010101001040","tag2":"(0008,0100)","desc":"Code Value"},{"tag1":"(0008,1032)","vr":"SH","value":"CCG_CSTemp","tag2":"(0008,0102)","desc":"Coding Scheme Designator"},{"tag1":"(0008,1032)","vr":"LO","value":"RX TORAX PA Y LAT","tag2":"(0008,0104)","desc":"Code Meaning"},{"tag1":"(0008,103E)","vr":"LO","value":"Trax","tag2":"","desc":"Series Description"},{"tag1":"(0008,1090)","vr":"LO","value":"DigitalDiagnost","tag2":"","desc":"Manufacturer’s Model Name"},{"tag1":"(0008,1110)","vr":"SQ","value":"","tag2":"(0008,1110)","desc":"Referenced Study Sequence"},{"tag1":"(0008,1110)","vr":"UI","value":"1.2.840.100008.3.1.2.3.1","tag2":"(0008,1150)","desc":"Referenced SOP Class UID"},{"tag1":"(0008,1110)","vr":"UI","value":"1.2.840.113619.2.182.10808617219229.1508740222.1172960","tag2":"(0008,1155)","desc":"Referenced SOP Instance UID"},{"tag1":"(0008,1111)","vr":"SQ","value":"","tag2":"(0008,1111)","desc":"Referenced Performed Procedure Step Sequence"},{"tag1":"(0008,1111)","vr":"UI","value":"1.2.840.10008.3.1.2.3.3","tag2":"(0008,1150)","desc":"Referenced SOP Class UID"},{"tag1":"(0008,1111)","vr":"UI","value":"1.3.46.670589.30.36.0.1.72567767433727.1508740652038.1","tag2":"(0008,1155)","desc":"Referenced SOP Instance UID"},{"tag1":"(0008,3010)","vr":"UI","value":"1.3.46.670589.30.36.0.1.72567767433727.1508740752489.1","tag2":"","desc":"Irradiation Event UID"},{"tag1":"(0009,0010)","vr":"LO","value":"GEIIS","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(0010,0010)","vr":"PN","value":"100008301845755693600822040133468866003","tag2":"","desc":"Patient’s Name"},{"tag1":"(0010,0020)","vr":"LO","value":"117677712752528732526839762067921423608","tag2":"","desc":"Patient ID"},{"tag1":"(0010,0030)","vr":"DA","value":"19631102","tag2":"","desc":"Patient’s Birth Date"},{"tag1":"(0010,0040)","vr":"CS","value":"F","tag2":"","desc":"Patient’s Sex"},{"tag1":"(0010,1010)","vr":"AS","value":"053Y","tag2":"","desc":"Patient’s Age"},{"tag1":"(0010,1020)","vr":"DS","value":"0","tag2":"","desc":"Patient’s Size"},{"tag1":"(0010,1030)","vr":"DS","value":"0","tag2":"","desc":"Patient’s Weight"},{"tag1":"(0010,2000)","vr":"LO","value":"","tag2":"","desc":"Medical Alerts"},{"tag1":"(0010,2110)","vr":"LO","value":"","tag2":"","desc":"Allergies"},{"tag1":"(0010,2160)","vr":"SH","value":"","tag2":"","desc":"Ethnic Group"},{"tag1":"(0010,21B0)","vr":"LT","value":"","tag2":"","desc":"Additional Patient History"},{"tag1":"(0010,21C0)","vr":"US","value":"4","tag2":"","desc":"Pregnancy Status"},{"tag1":"(0018,0015)","vr":"CS","value":"CHEST","tag2":"","desc":"Body Part Examined"},{"tag1":"(0018,0060)","vr":"DS","value":"125","tag2":"","desc":"KVP"},{"tag1":"(0018,1000)","vr":"LO","value":"72567767433727","tag2":"","desc":"Device Serial Number"},{"tag1":"(0018,1020)","vr":"LO","value":"4.1.3.2","tag2":"","desc":"Software Version(s)"},{"tag1":"(0018,1030)","vr":"LO","value":"Trax","tag2":"","desc":"Protocol Name"},{"tag1":"(0018,1050)","vr":"DS","value":"0.148","tag2":"","desc":"Spatial Resolution"},{"tag1":"(0018,1110)","vr":"DS","value":"1807","tag2":"","desc":"Distance Source to Detector"},{"tag1":"(0018,1111)","vr":"DS","value":"1753","tag2":"","desc":"Distance Source to Patient"},{"tag1":"(0018,1114)","vr":"DS","value":"0.99394939493971","tag2":"","desc":"Estimated Radiographic Magnification Factor"},{"tag1":"(0018,1150)","vr":"IS","value":"5","tag2":"","desc":"Exposure Time"},{"tag1":"(0018,1152)","vr":"IS","value":"1","tag2":"","desc":"Exposure"},{"tag1":"(0018,1153)","vr":"IS","value":"1400","tag2":"","desc":"Exposure in µAs"},{"tag1":"(0018,115E)","vr":"DS","value":"0.59","tag2":"","desc":"Image and Fluoroscopy Area Dose Product"},{"tag1":"(0018,1164)","vr":"DS","value":"0.148\\0.148","tag2":"","desc":"Imager Pixel Spacing"},{"tag1":"(0018,1166)","vr":"CS","value":"IN","tag2":"","desc":"Grid"},{"tag1":"(0018,1400)","vr":"LO","value":"","tag2":"","desc":"Acquisition Device Processing Description"},{"tag1":"(0018,1405)","vr":"IS","value":"391","tag2":"","desc":"Relative X-Ray Exposure"},{"tag1":"(0018,1411)","vr":"DS","value":"391","tag2":"","desc":"Exposure Index"},{"tag1":"(0018,1508)","vr":"CS","value":"NONE","tag2":"","desc":"Positioner Type"},{"tag1":"(0018,1600)","vr":"CS","value":"POLYGONAL","tag2":"","desc":"Shutter Shape"},{"tag1":"(0018,1620)","vr":"IS","value":"103\\2064\\128\\0\\2829\\0\\2829\\2064","tag2":"","desc":"Vertices of the Polygonal Shutter"},{"tag1":"(0018,1700)","vr":"CS","value":"RECTANGULAR","tag2":"","desc":"Collimator Shape"},{"tag1":"(0018,1702)","vr":"IS","value":"0","tag2":"","desc":"Collimator Left Vertical Edge"},{"tag1":"(0018,1704)","vr":"IS","value":"2389","tag2":"","desc":"Collimator Right Vertical Edge"},{"tag1":"(0018,1706)","vr":"IS","value":"0","tag2":"","desc":"Collimator Upper Horizontal Edge"},{"tag1":"(0018,1708)","vr":"IS","value":"2829","tag2":"","desc":"Collimator Lower Horizontal Edge"},{"tag1":"(0018,5101)","vr":"CS","value":"LL","tag2":"","desc":"View Position"},{"tag1":"(0018,7001)","vr":"DS","value":"31.3","tag2":"","desc":"Detector Temperature"},{"tag1":"(0018,7004)","vr":"CS","value":"SCINTILLATOR","tag2":"","desc":"Detector Type"},{"tag1":"(0018,7008)","vr":"LT","value":"SingleShot1s","tag2":"","desc":"Detector Mode"},{"tag1":"(0018,700A)","vr":"SH","value":"SN1546U4","tag2":"","desc":"Detector ID"},{"tag1":"(0018,700C)","vr":"DA","value":"20171018","tag2":"","desc":"Date of Last Detector Calibration"},{"tag1":"(0018,700E)","vr":"TM","value":"082323","tag2":"","desc":"Time of Last Detector Calibration"},{"tag1":"(0018,7012)","vr":"DS","value":"36403.63","tag2":"","desc":"Detector Time Since Last Exposure"},{"tag1":"(0018,702A)","vr":"LO","value":"TRIXELL","tag2":"","desc":"Detector Manufacturer Name"},{"tag1":"(0018,702B)","vr":"LO","value":"PIXIUM4343RC","tag2":"","desc":"Detector Manufacturer’s Model Name"},{"tag1":"(0018,7030)","vr":"DS","value":"0\\0","tag2":"","desc":"Field of View Origin"},{"tag1":"(0018,7032)","vr":"DS","value":"0","tag2":"","desc":"Field of View Rotation"},{"tag1":"(0018,7034)","vr":"CS","value":"YES","tag2":"","desc":"Field of View Horizontal Flip"},{"tag1":"(0018,7050)","vr":"CS","value":"COPPER\\ALUMINIUM","tag2":"","desc":"Filter Material"},{"tag1":"(0018,7062)","vr":"LT","value":"4","tag2":"","desc":"Exposure Control Mode Description"},{"tag1":"(0018,8150)","vr":"DS","value":"5000","tag2":"","desc":"Exposure Time in µS"},{"tag1":"(0020,000D)","vr":"UI","value":"1.2.840.113619.2.182.10808617219229.1508740222.1172960","tag2":"","desc":"Study Instance UID"},{"tag1":"(0020,000E)","vr":"UI","value":"1.3.46.670589.30.36.0.1.72567767433727.1508740832187.1","tag2":"","desc":"Series Instance UID"},{"tag1":"(0020,0010)","vr":"SH","value":"","tag2":"","desc":"Study ID"},{"tag1":"(0020,0011)","vr":"IS","value":"1","tag2":"","desc":"Series Number"},{"tag1":"(0020,0013)","vr":"IS","value":"2","tag2":"","desc":"Instance Number"},{"tag1":"(0020,0020)","vr":"CS","value":"A\\F","tag2":"","desc":"Patient Orientation"},{"tag1":"(0020,0062)","vr":"CS","value":"","tag2":"","desc":"Image Laterality"},{"tag1":"(0028,0002)","vr":"US","value":"1","tag2":"","desc":"Samples per Pixel"},{"tag1":"(0028,0004)","vr":"CS","value":"MONOCHROME2","tag2":"","desc":"Photometric Interpretation"},{"tag1":"(0028,0010)","vr":"US","value":"2830","tag2":"","desc":"Rows"},{"tag1":"(0028,0011)","vr":"US","value":"2390","tag2":"","desc":"Columns"},{"tag1":"(0028,0030)","vr":"DS","value":"0.1489009407858\\0.1489009407858","tag2":"","desc":"Pixel Spacing"},{"tag1":"(0028,0100)","vr":"US","value":"16","tag2":"","desc":"Bits Allocated"},{"tag1":"(0028,0101)","vr":"US","value":"12","tag2":"","desc":"Bits Stored"},{"tag1":"(0028,0102)","vr":"US","value":"11","tag2":"","desc":"High Bit"},{"tag1":"(0028,0103)","vr":"US","value":"0","tag2":"","desc":"Pixel Representation"},{"tag1":"(0028,0300)","vr":"CS","value":"NO","tag2":"","desc":"Quality Control Image"},{"tag1":"(0028,0301)","vr":"CS","value":"NO","tag2":"","desc":"Burned In Annotation"},{"tag1":"(0028,0303)","vr":"CS","value":"","tag2":"","desc":"Longitudinal Temporal Information Modified"},{"tag1":"(0028,1040)","vr":"CS","value":"LOG","tag2":"","desc":"Pixel Intensity Relationship"},{"tag1":"(0028,1041)","vr":"SS","value":"-1","tag2":"","desc":"Pixel Intensity Relationship Sign"},{"tag1":"(0028,1050)","vr":"DS","value":"2047.5","tag2":"","desc":"Window Center"},{"tag1":"(0028,1051)","vr":"DS","value":"4095","tag2":"","desc":"Window Width"},{"tag1":"(0028,1052)","vr":"DS","value":"0","tag2":"","desc":"Rescale Intercept"},{"tag1":"(0028,1053)","vr":"DS","value":"1","tag2":"","desc":"Rescale Slope"},{"tag1":"(0028,1054)","vr":"LO","value":"US","tag2":"","desc":"Rescale Type"},{"tag1":"(0028,2110)","vr":"CS","value":"00","tag2":"","desc":"Lossy Image Compression"},{"tag1":"(0032,1060)","vr":"LO","value":"","tag2":"","desc":"Requested Procedure Description"},{"tag1":"(0032,1064)","vr":"SQ","value":"","tag2":"(0032,1064)","desc":"Requested Procedure Code Sequence"},{"tag1":"(0032,1064)","vr":"SH","value":"3061010101001040","tag2":"(0008,0100)","desc":"Code Value"},{"tag1":"(0032,1064)","vr":"SH","value":"CCG_CSTemp","tag2":"(0008,0102)","desc":"Coding Scheme Designator"},{"tag1":"(0032,1064)","vr":"LO","value":"RX T�RAX, PA Y LAT","tag2":"(0008,0104)","desc":"Code Meaning"},{"tag1":"(0040,0241)","vr":"AE","value":"SJDIDI01","tag2":"","desc":"Performed Station AE Title"},{"tag1":"(0040,0244)","vr":"DA","value":"20171023","tag2":"","desc":"Performed Procedure Step Start Date"},{"tag1":"(0040,0245)","vr":"TM","value":"083836.209000","tag2":"","desc":"Performed Procedure Step Start Time"},{"tag1":"(0040,0250)","vr":"DA","value":"20171023","tag2":"","desc":"Performed Procedure Step End Date"},{"tag1":"(0040,0251)","vr":"TM","value":"084032.059000","tag2":"","desc":"Performed Procedure Step End Time"},{"tag1":"(0040,0252)","vr":"CS","value":"","tag2":"","desc":"Performed Procedure Step Status"},{"tag1":"(0040,0254)","vr":"LO","value":"","tag2":"","desc":"Performed Procedure Step Description"},{"tag1":"(0040,0301)","vr":"US","value":"2","tag2":"","desc":"Total Number of Exposures"},{"tag1":"(0040,0302)","vr":"US","value":"0","tag2":"","desc":"Entrance Dose"},{"tag1":"(0040,1002)","vr":"LO","value":"","tag2":"","desc":"Reason for the Requested Procedure"},{"tag1":"(0040,1003)","vr":"SH","value":"","tag2":"","desc":"Requested Procedure Priority"},{"tag1":"(0040,1400)","vr":"LT","value":"","tag2":"","desc":"Requested Procedure Comments"},{"tag1":"(0040,2001)","vr":"LO","value":"","tag2":"","desc":"Reason for the Imaging Service Request"},{"tag1":"(0040,2004)","vr":"DA","value":"","tag2":"","desc":"Issue Date of Imaging Service Request"},{"tag1":"(0040,2017)","vr":"LO","value":"","tag2":"","desc":"Filler Order Number / Imaging Service Request"},{"tag1":"(0040,2400)","vr":"LT","value":"","tag2":"","desc":"Imaging Service Request Comments"},{"tag1":"(0040,8302)","vr":"DS","value":"0.077","tag2":"","desc":"Entrance Dose in mGy"},{"tag1":"(0903,0010)","vr":"LO","value":"GEIIS PACS","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(0905,0010)","vr":"LO","value":"GEIIS","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(2001,0010)","vr":"LO","value":"Philips Imaging DD 001","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(2001,0011)","vr":"LO","value":"Philips Imaging DD 002","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(2001,0090)","vr":"LO","value":"Philips Imaging DD 129","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(200B,0010)","vr":"LO","value":"Philips RAD Imaging DD 001","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(200B,0070)","vr":"LO","value":"Philips RAD Imaging DD 097","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(200B,0072)","vr":"LO","value":"Philips RAD Imaging DD 099","tag2":"","desc":"Private Creator Data Element"},{"tag1":"(2050,0020)","vr":"CS","value":"IDENTITY","tag2":"","desc":"Presentation LUT Shape"},{"tag1":"(7FD1,0010)","vr":"LO","value":"GEIIS","tag2":"","desc":"Private Creator Data Element"}]}} \ No newline at end of file diff --git a/data/examples/RX_Thorax/sub-2/rx/sub-2_ses-1_bp-thorax_vp-ll_dx.nii.gz b/data/examples/RX_Thorax/sub-2/rx/sub-2_ses-1_bp-thorax_vp-ll_dx.nii.gz new file mode 100644 index 0000000..ad49be4 Binary files /dev/null and b/data/examples/RX_Thorax/sub-2/rx/sub-2_ses-1_bp-thorax_vp-ll_dx.nii.gz differ diff --git a/data/examples/RX_Thorax/sub-2/sub-2_ses-1_scans.tsv b/data/examples/RX_Thorax/sub-2/sub-2_ses-1_scans.tsv new file mode 100644 index 0000000..b58ced0 --- /dev/null +++ b/data/examples/RX_Thorax/sub-2/sub-2_ses-1_scans.tsv @@ -0,0 +1,3 @@ +filename Manufacturer (0008,0070) Series Description (0008,103E) Manufacturer’s Model Name (0008,1090) Patient ID (0010,0020) Patient’s Sex (0010,0040) Patient’s Age (0010,1010) Patient’s Weight (0010,1030) Scanning Sequence (0018,0020) Sequence Variant (0018,0021) Scan Options (0018,0022) MR Acquisition Type (0018,0023) Slice Thickness (0018,0050) Repetition Time (0018,0080) Echo Time (0018,0081) (0018,0082) Imaging Frequency (0018,0084) Magnetic Field Strength (0018,0087) Manufacturer’s Model Name (0008,1090) Spacing Between Slices (0018,0088) Echo Train Length (0018,0091) Percent Sampling (0018,0093) Pixel Bandwidth (0018,0095) Flip Angle (0018,1314) Patient Position (0018,5100) Image Position (Patient) (0020,0032) Image Orientation (Patient) (0020,0037) Position Reference Indicator (0020,1040) Slice Location (0020,1041) Rows (0028,0010) Columns (0028,0011) Pixel Spacing (0028,0030) Bits Allocated (0028,0100) Number of Averages (0018,0083) Echo Number(s) (0018,0086) (0018,9461) +dx/sub-1_ses-2_bp-thorax_vp_ap_dx.nii.gz GE MEDICAL SYSTEMS Thorax AP OPTIMA 332424083962373450045181767823697702475 F 057Y 80 GR SS\SP\SK FAST_GEMS\EDR_GEMS\PFF 3D 1 6.816 1.984 None 63.867408 1.5 OPTIMA MR360 0.5 1 100 244.141 12 HFS -139.453\-147.422\39.1247 1\-0\0\-0\1\0 39.12474823 256 256 1.0938\1.0938 16 2 1 None +dx/sub-1_ses-2_bp-thorax_vp_lat_dx.nii.gz GE MEDICAL SYSTEMS Thorax LAT OPTIMA 332424083962373450045181767823697702475 F 057Y 80 GR SS\SP\SK FAST_GEMS\EDR_GEMS\PFF 3D 1 6.816 1.984 None 63.867408 1.5 OPTIMA MR360 0.5 1 100 244.141 12 HFS -139.453\-147.422\39.1247 1\-0\0\-0\1\0 39.12474823 256 256 1.0938\1.0938 16 2 1 None \ No newline at end of file diff --git a/images/MIDS_directory.png b/images/MIDS_directory.png new file mode 100644 index 0000000..f515076 Binary files /dev/null and b/images/MIDS_directory.png differ diff --git a/images/dicom2bids.png b/images/dicom2bids.png new file mode 100644 index 0000000..598a8f4 Binary files /dev/null and b/images/dicom2bids.png differ diff --git a/images/logo_CEIB.png b/images/logo_CEIB.png new file mode 100644 index 0000000..96db60a Binary files /dev/null and b/images/logo_CEIB.png differ diff --git a/images/logotipo-fisabio_tauv.png b/images/logotipo-fisabio_tauv.png new file mode 100644 index 0000000..2c965b6 Binary files /dev/null and b/images/logotipo-fisabio_tauv.png differ diff --git a/images/xnat_directory.png b/images/xnat_directory.png new file mode 100644 index 0000000..968d52b Binary files /dev/null and b/images/xnat_directory.png differ diff --git a/xnat2mids/__init__.py b/xnat2mids/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/xnat2mids/__main__.py b/xnat2mids/__main__.py new file mode 100644 index 0000000..99d28eb --- /dev/null +++ b/xnat2mids/__main__.py @@ -0,0 +1,236 @@ +#!/usr/bin/env python #iniciaize enviroment +# -*- coding: utf-8 -*-. +u""" +Subdirección General de Sistemas de Información para la Salud + +Centro de Excelencia e Innovación Tecnológica de Bioimagen de la Conselleria de Sanitat + +http://ceib.san.gva.es/ + +María de la Iglesia Vayá -> delaiglesia_mar@gva.es or miglesia@cipf.es + +Jose Manuel Saborit Torres -> jmsaborit@cipf.es + +Jhon Jairo Saenz Gamboa ->jsaenz@cipf.es + +Joaquim Ángel Montell Serrano -> jamontell@cipf.es + +--- + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License version 3 as published by +the Free Software Foundation. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . + +--- + +Prerequisites + +Python --version >= 3.8 + +Description: + This application allow the user to download one project on XNAT and + transform this project in MIDS format + + There are 2 functions in this code: + download one project from xnat application: + arguments: + Prefix -w --web PAGE_WEB 1) The URL page where XNAT is. + Prefix -p --project [PROJECTS] 2) The project name to download + Prefix -i --input PATH 3) the directory where the files + will be downloaded + Prefix -u --user [USER] 4) The username to login in XNAT + If not write a username, It + loggin as guest. + + Convert the xnat directories of the project in MIDS format: + arguments: + Prefix -i --input PATH 1) the directory where the files will + be downloaded + Prefix -o --output PATH 2) Directory where the MIDS model + is applied. +""" +############################################################################### +# Imports +############################################################################### + +import os +import argparse +from pathlib import Path +# serialize model to json + +from xnat2mids.xnat.xnat_session import XnatSession +from xnat2mids.xnat.xnat_session import list_directory_xnat +#import mids_conversion +from xnat2mids.xnat.variables import types_files_xnat +from xnat2mids.xnat.variables import format_message +from xnat2mids.xnat.variables import reset_terminal +from xnat2mids.xnat.variables import dict_paths +from xnat2mids.xnat.variables import dict_uris +from xnat2mids.mids_conversion import create_directory_mids_v1 +from xnat2mids.mids_conversion import create_tsvs + + +############################################################################### +# Functions +############################################################################### + + +def main(): + """ + This Fuction is de main programme + """ + # Control of arguments of programme + parser = argparse.ArgumentParser( + formatter_class=argparse.RawDescriptionHelpFormatter, description=""" + This sorfware allows the user to Download one project into XNAT platform + and convert the XNAT images directory in MIDS directory. + + The aplication execution needs Python --version >= 3.5. + + there are 2 functions in this code: + + Download temporary projects from xnat application: + + arguments: + + Prefix -w --web PAGE_WEB 1) The URL page where XNAT is. + + + Prefix -u --user [USER] 2) The username to login in XNAT + If not write a username, It logins + as guest. + + + Prefix -i --input INPUT 4) The directory where the + files will be downloaded. + + + Prefix -t --types [sdnbr] 5) Download types of MRI images + included in xnat + - d = dicom + dicom metadata in + folder NIFTI + - n = nifti or png if image is + one slide (2D) + roi + - b = BIDS (only in CENTRAL XNAT) + - r = Structural report + default = nr + + + + Prefix --overwrite 5) Overwrite download files + + + Convert the xnat directories of the project in MIDS format: + + arguments: + + + Prefix -i --input INPUT 1) The directory where the files + will be downloaded. + + + Prefix -o --output OUTPUT 2) Directory where the MIDS model + is applied. + + Prefix -bp --body-part 3) Specify which part of the body are + in the dataset(A clear dataset with + only one part are needed) + """ + ) + parser.add_argument('-w', '--web', type=str, default=None, + help='The URL page where XNAT is.') + parser.add_argument('-u', '--user', type=str, default=None, + help="""The username to login in XNAT + If not write a username, It logins + as guest.""") + parser.add_argument('-i ', '--input', type=str, + help="""the directory where the files will + be downloaded.""") + # parser.add_argument('-o ', '--output', type=str, + # help='Directory where the MIDS model is applied.') + # parser.add_argument('-p ', '--projects', nargs='*', default=None, type=str, + # help="""The project name to download, if the project is + # omitted,the aplication show all projects in xnat + # to choice.""") + parser.add_argument('-v ', '--verbose', default=False, action='store_true', + help="""Active Verbose""") + parser.add_argument('-bp', '--body-part', dest="body_part", type=str, + help="""Specify which part of the body are + in the dataset(REQUIRED if tag body part not exist in dicom images)""") + parser.add_argument('--overwrite', default=False, action='store_true', + help=""" Overwrite download files""") + # parser.add_argument('-t', '--types', type=str, default="nr", nargs=1, + # help="""Download types of MRI images + # included in xnat + # - s = snapshoot + # - d = dicom + dicom metadata in folder NIFTI + # - n = nifti or png if image is one slide (2D) + # - r = Structural report + # - m = Roi segmentation (Mask) + # default = nr""") + # save the arguments in varaibles + args = parser.parse_args() + print(reset_terminal, end="", flush=True) + print(args) + page = args.web + user = args.user + xnat_data_path = Path(args.input) + mids_data_path = Path(args.input) + #project_list = args.projects + verbose = args.verbose + body_part = args.body_part + #types = args.types[0] + overwrite = args.overwrite + + # Comprobation if Xnat dowload can be execute + if xnat_data_path and page: + xnat_data_path.mkdir(exist_ok=True) + with XnatSession(page, user) as xnat_session: + xnat_session.download_projects( + xnat_data_path, + with_department=True, + bool_list_resources=[True for char in types_files_xnat], + overwrite=overwrite, + verbose=verbose + ) + # conditions to move xnat project to MIDS project + if xnat_data_path and mids_data_path: + # if project_list is None, the projects in the folder xnat must be + # chosen + + project_paths = [dirs for dirs in xnat_data_path.iterdir()] + project_names = [path_.name for path_ in project_paths] + project_list = list_directory_xnat(project_names) + mids_data_path.mkdir(exist_ok=True) + # for each project choice + for xnat_project in project_list: + xnat_data_path = xnat_data_path.joinpath(xnat_project,"sourcedata") + if not xnat_data_path.exists(): + raise FileNotFoundError(f'No folder exists at the location specified in {xnat_data_path}') + mids_data_path = mids_data_path.joinpath(xnat_project) + print(f"{xnat_data_path}") + print(f"{mids_data_path}") + + print("MIDS are generating...") + create_directory_mids_v1( + xnat_data_path, + mids_data_path, + body_part + ) + + print("participats tsv are generating...") + create_tsvs(xnat_data_path, mids_data_path, body_part) + + # print("scan tsv are generating...") + # MIDS_funtions.create_scans_tsv( + # os.path.join(mids_data_path, xnat_project) + # ) + # + # print("sessions tsv are generating...") + # MIDS_funtions.create_sessions_tsv( + # os.path.join(xnat_data_path, xnat_project), + # mids_data_path + # ) + +if __name__ == "__main__": + main() diff --git a/xnat2mids/conversion/dcm2niix.sh b/xnat2mids/conversion/dcm2niix.sh new file mode 100644 index 0000000..65eb7aa --- /dev/null +++ b/xnat2mids/conversion/dcm2niix.sh @@ -0,0 +1,3 @@ +#!/bin/bash +#-i y -m y -ba n -f %j_%p -z y +dcm2niix $3 -o $1 $2 diff --git a/xnat2mids/conversion/dicom_converters.py b/xnat2mids/conversion/dicom_converters.py new file mode 100644 index 0000000..92c019f --- /dev/null +++ b/xnat2mids/conversion/dicom_converters.py @@ -0,0 +1,87 @@ +import subprocess +import SimpleITK as sitk +import pydicom +import json +import os +import pydicom +import nibabel as nib +from nibabel.nicom.dicomreaders import read_mosaic_dir +# def sitk_dicom2mifti(dicom_path): +# reader = sitk.ImageSeriesReader() +# dicom_names = reader.GetGDCMSeriesFileNames(dicom_path.parent) +# reader.SetFileNames(dicom_names) +# image = reader.Execute() +# +# # Added a call to PermuteAxes to change the axes of the data +# image = sitk.PermuteAxes(image, [2, 1, 0]) +# +# sitk.WriteImage(image, 'nifti.nii.gz') +# +# def dicom2nii(dicom_path): +# #settings.disable_validate_slice_increment() +# print(dicom_path.parent) +# nifti_path = dicom_path.parent.parent.parent.joinpath("LOCAL_NIFTI", "files") +# nifti_path.mkdir(parents=True, exist_ok=True) +# #dicom2nifti.convert_directory(dicom_path.parent, nifti_path, compression=True, reorient_nifti=True) +# array_nifty = dicom2nifti.convert_dicom.dicom_series_to_nifti(str(dicom_path.parent),str(nifti_path), reorient_nifti=True) +# #save_dicom_metadata( +# # dicom_path, nifti_path.parent.joinpath(nifti_path.name.split(".")[0] + ".json") +# #) +# return array_nifty + + +def dicom2niix(folder_json, str_options): + folder_nifti = folder_json.parent.parent.joinpath("LOCAL_NIFTI", "files") + folder_nifti.mkdir(parents=True, exist_ok=True) + print(f"dcm2niix {str_options} -g y -b y -o {folder_nifti} {folder_json}") + subprocess.call( + f"dcm2niix {str_options} -g y -b y -o {folder_nifti} {folder_json}", + shell=True, + stdout=subprocess.DEVNULL, + stderr=subprocess.STDOUT + ) + if len(list(folder_nifti.iterdir())) == 0: + # folder_nifti.parent.unlink(missing_ok=True) + return folder_nifti + + add_dicom_metadata(folder_json, folder_nifti) + return folder_nifti + + +def dicom2png(folder_json, str_options): + + dcm_files = list(folder_json.rglob("*dcm")) + for dcm_file in dcm_files: + folder_png = folder_json.parent.parent.joinpath("LOCAL_PNG", "files", dcm_file.stem+".png") + folder_png.parent.mkdir(parents=True, exist_ok=True) + sitk_img = sitk.ReadImage(dcm_file) + sitk.WriteImage(sitk_img, folder_png) + subprocess.call( + f"dcm2niix {str_options} -g y -b o -o {folder_png.parent} {dcm_files[0].parent}", + shell=True, + stdout=subprocess.DEVNULL, + stderr=subprocess.STDOUT + ) + add_dicom_metadata(dcm_files[0].parent, folder_png.parent) + return folder_png.parent + + +def add_dicom_metadata( + folder_json, folder_nifti, list_tags = [(0x0008,0x1030), (0x0008,0x0060), (0x0020,0x0020), (0x0020,0x0060), (0x0020,0x1002), (0x0028,0x0002), (0x0028,0x0004), (0x0028, 0x0010), (0x0028, 0x0011), (0x0028, 0x1050), (0x0028, 0x1051), (0x0018,0x5100), (0x0018,0x1040), (0x0018,0x0091), (0x0018,0x0025),(0x0018,0x1060),(0x0018,0x1315),(0x0028,0x0004) ] +): + json_filepath = list(folder_nifti.glob("*.json"))[0] + with json_filepath.open("r") as file_json: + dict_json = json.loads(file_json.read()) + dicom_dir = pydicom.filereader.dcmread(str(list(folder_json.glob("*.dcm"))[0]), stop_before_pixels=True) + extract_values = { + dicom_dir.get(key).name.replace(" ", ""):( + str(dicom_dir.get(key).value) if not dicom_dir.get(key).is_empty else "NaN" + ) + for key in list_tags if dicom_dir.get(key) + } + actualized_dict_json = dict(dict_json, **extract_values) + string_json = json.dumps(actualized_dict_json, default=lambda o: o.__dict__, + sort_keys=True) + with json_filepath.open('w') as dicom_file: + dicom_file.write(string_json) + diff --git a/xnat2mids/conversion/io_json.py b/xnat2mids/conversion/io_json.py new file mode 100644 index 0000000..f2fff08 --- /dev/null +++ b/xnat2mids/conversion/io_json.py @@ -0,0 +1,64 @@ +# -*- coding: utf-8 -*- + +############################################################################### +# Imports +############################################################################### +import json + + +############################################################################### +# Functions +############################################################################### + +""" +This function allows the user to save one tag dicom in an archive json +""" + + +def add_tag_dicom(tag, description, value, json_file_path): + json_file = load_json(json_file_path) + for i in range(len(json_file["ResultSet"]["Result"])): + if json_file["ResultSet"]["Result"][i]["tag1"] == tag: + json_file["ResultSet"]["Result"][i]["value"] = value + break + else: + json_file["ResultSet"]["Result"].append({"tag1":tag, "tag2":"", "desc":description, "value":value}) + save_json(json_file, json_file_path) + + +""" +This function allow the user to obtain one tag dicom from an archive json + + +Return a dict of the tag dicom +""" + +def get_tag_dicom(dict_json, json_file_path): + return {tag:dict_json.get(tag, {"Value":["n/a"]}) for tag in tags} + + + + +""" +This function allow the user store one object in an archive json +""" +def save_json(subject, path): + string_json = json.dumps(subject, default=lambda o: o.__dict__, + sort_keys=True) + try: + f = open(path, "w") + except IOError: + f = open(path, "a") + f.write(string_json) + f.close() + + +""" +This function allow the user obtain one object from an archive json + +Return the struct dict json +""" +def load_json(path): + with path.open('r') as file_: + json_ = json.load(file_) + return json_ diff --git a/xnat2mids/mids_conversion.py b/xnat2mids/mids_conversion.py new file mode 100644 index 0000000..a4fa8d7 --- /dev/null +++ b/xnat2mids/mids_conversion.py @@ -0,0 +1,235 @@ +import re + +from collections import defaultdict +from datetime import datetime + +import pandas + +from xnat2mids.conversion.io_json import load_json +from xnat2mids.procedures.magnetic_resonance_procedures import ProceduresMR +from xnat2mids.procedures.light_procedures import LightProcedure +from xnat2mids.protocols.scans_tagger import Tagger +from xnat2mids.conversion.dicom_converters import dicom2niix +from xnat2mids.conversion.dicom_converters import dicom2png +from tqdm import tqdm + + +adquisition_date_pattern = r"(?P\d+)-(?P\d+)-(?P\d+)T(?P\d+):(?P\d+):(?P\d+).(?P\d+)" +subses_pattern = r"[A-z]+(?P\d*)?(_S)(?P\d+)/[A-z]+\-?[A-z]*(?P\d*)?(_E)(?P\d+)" +aquisition_date_pattern_comp = re.compile(adquisition_date_pattern) +dict_keys = { + 'Modality': '00080060', + 'SeriesDescription': '0008103E', + 'ProtocolName': '00181030', + 'ComplexImage Component Attribute': '00089208', + "ImageType" :'00080008', + #"difusion Directionality": '' +} + +dict_mr_keys = { + 'Manufacturer': '00080070', + 'ScanningSequence': '00180020', + 'SequenceVariant': '00180021', + 'ScanOptions': '00180022', + 'AngioFlag': '00180025', + 'MagneticFieldStrength': '00180087', + 'RepetitionTime': '00180080', + 'InversionTime': '00180082', + 'FlipAngle': '00181314', + 'EchoTime': '00180081', + 'SliceThickness': '00180050', +} + +BIOFACE_PROTOCOL_NAMES = [ + '3D-T2-FLAIR SAG', + '3D-T2-FLAIR SAG NUEVO-1', + 'AAhead_scout', + 'ADVANCED_ASL', + 'AXIAL T2 TSE FS', + 'AX_T2_STAR', + 'DTIep2d_diff_mddw_48dir_p3_AP', # + 'DTIep2d_diff_mddw_4b0_PA', # + 'EPAD-3D-SWI', + 'EPAD-B0-RevPE', # PA + 'EPAD-SE-fMRI', + 'EPAD-SE-fMRI-RevPE', + 'EPAD-SingleShell-DTI48', # AP + 'EPAD-rsfMRI (Eyes Open)', + 'MPRAGE_GRAPPA2', # T1 mprage + 'asl_3d_tra_iso_3.0_highres', + 'pd+t2_tse_tra_p2_3mm', + 't1_mprage_sag_p2_iso', # t1 + 't2_space_dark-fluid_sag_p2_iso', # flair + 't2_swi_tra_p2_384_2mm' +] + +BIOFACE_PROTOCOL_NAMES_DESCARTED = [ + #'DTIep2d_diff_mddw_48dir_p3_AP', + #'DTIep2d_diff_mddw_4b0_PA', + 'EPAD-B0-RevPE', + 'EPAD-SingleShell-DTI48', + 'EPAD-3D-SWI', + 'EPAD-SE-fMRI', + 'EPAD-rsfMRI (Eyes Open)', + 'EPAD-SE-fMRI-RevPE', + 'AAhead_scout', + 'ADVANCED_ASL', + 'MPRAGE_GRAPPA2', + '3D-T2-FLAIR SAG', + '3D-T2-FLAIR SAG NUEVO-1' + +] +LUMBAR_PROTOCOLS_ACEPTED = { + 't2_tse_sag_384': 556, + 't2_tse_tra_384': 534, + 't1_tse_sag_320': 523, + 't1_tse_tra': 518, +} + +options_dcm2niix = "-w 0 -i n -m y -ba n -f %x_%s -z y" + +def create_directory_mids_v1(xnat_data_path, mids_data_path, body_part): + print(xnat_data_path) + print(mids_data_path) + procedure_class_mr = ProceduresMR() + procedure_class_light = LightProcedure() + for subject_xnat_path in tqdm(xnat_data_path.glob('*/')): + if "_S" not in subject_xnat_path.name:continue + num_sessions = len(list(subject_xnat_path.glob('*/'))) + procedure_class_mr.reset_indexes() + procedure_class_light.reset_indexes() + for sessions_xnat_path in subject_xnat_path.glob('*/'): + if "_E" not in sessions_xnat_path.name: continue + + + + findings = re.search(subses_pattern, str(sessions_xnat_path), re.X) + #print('subject,', findings.group('prefix_sub'), findings.group('suffix_sub')) + #print('session,', findings.group('prefix_ses'), findings.group('suffix_ses')) + subject_name = f"sub-{findings.group('prefix_sub')}S{findings.group('suffix_sub')}" + session_name = f"ses-{findings.group('prefix_ses')}S{findings.group('suffix_ses')}" + + mids_session_path = mids_data_path.joinpath(subject_name, session_name) + xml_session_rois = list(sessions_xnat_path.rglob('*.xml')) + #print(f"1: {mids_session_path=}") + tagger = Tagger() + tagger.load_table_protocol( + './xnat2mids/protocols/protocol_RM_brain.tsv' + ) + if not sessions_xnat_path.joinpath("scans").exists(): continue + for scans_path in sessions_xnat_path.joinpath("scans").iterdir(): + #if "LOCAL_" not in str(scans_path): + + num_jsons = len(list(scans_path.joinpath("resources").rglob("*.dcm"))) # + + + if num_jsons ==0: + continue + if num_jsons>0: + path_dicoms= list(scans_path.joinpath("resources").rglob("*.dcm"))[0].parent + folder_conversion = dicom2niix(path_dicoms, options_dcm2niix) #.joinpath("resources") + else: + continue + # path_dicoms= list(scans_path.joinpath("resources").rglob("*.dcm"))[0].parent + # folder_conversion = dicom2png(path_dicoms, options_dcm2niix) #.joinpath("resources") + + print("---------", len(list(folder_conversion.iterdir()))) + if len(list(folder_conversion.iterdir())) == 0: continue + + dict_json = load_json(folder_conversion.joinpath(list(folder_conversion.glob("*.json"))[0])) + + + modality = dict_json.get("Modality", "n/a") + study_description = dict_json.get("SeriesDescription", "n/a") + Protocol_name = dict_json.get("ProtocolName", "n/a") + image_type = dict_json.get("ImageType", "n/a") + acquisition_date_time = dict_json.get("AcquisitionDateTime", "") + body_part = dict_json.get("BodyPartExamined", body_part) + acquisition_date_time_check = aquisition_date_pattern_comp.search(acquisition_date_time) + time_values = list(int (x) for x in acquisition_date_time_check.groups()) + acquisition_date_time_correct = f"\ +{time_values[0]:04d}-\ +{time_values[1]:02d}-\ +{time_values[2]:02d}T\ +{time_values[3]:02d}:\ +{time_values[4]:02d}:\ +{time_values[5]:02d}.\ +{time_values[6]:06d}\ +" + # print() + # print(modality, study_description, ProtocolName, image_type) + print(f"{study_description=}") + print(f"{Protocol_name=}") + if modality == "MR": + # via BIDS protocols + #if study_description in LUMBAR_PROTOCOLS_ACEPTED: + + + json_adquisitions = { + f'{k}': dict_json.get(k, -1) for k in dict_mr_keys.keys() + } + + protocol, acq, task, ce, rec, dir_, part, folder_BIDS = tagger.classification_by_min_max(json_adquisitions) + print(protocol, acq, task, ce, rec, dir_, part, folder_BIDS) + continue + procedure_class_mr.control_sequences( + folder_conversion, mids_session_path, session_name, protocol, acq, dir_, folder_BIDS, body_part + ) + + if modality == "OP": + laterality = dict_json.get("Laterality") + acq = "" if "ORIGINAL" in image_type else "opacitysubstract" + # print(laterality, acq) + procedure_class_light.control_image(folder_conversion, mids_session_path.joinpath("mim-light"), session_name, "op", acq, laterality, acquisition_date_time_correct) + procedure_class_mr.copy_sessions(subject_name) + procedure_class_light.copy_sessions(subject_name) + + +participants_header = ['participant', 'modalities', 'body_parts', 'patient_birthday', 'age', 'gender'] +participants_keys = ['Modality', 'BodyPartExamined', 'PatientBirthDate', 'PatientSex', 'AcquisitionDateTime'] +session_header = ['session', 'acquisition_date_Time',] +def create_tsvs(xnat_data_path, mids_data_path, body_part_aux): + """ + This function allows the user to create a table in format ".tsv" + whit a information of subject + """ + + list_information= [] + for subject_path in mids_data_path.glob('*/'): + if not subject_path.match("sub-*"): continue + subject = subject_path.parts[-1] + for session_path in subject_path.glob('*/'): + if not session_path.match("ses-*"): continue + session = session_path.parts[-1] + modalities = [] + body_parts = [] + patient_birthday = None + patient_ages = list([]) + patient_sex = None + adquisition_date_time = None + for json_pathfile in subject_path.glob('**/*.json'): + json_file = load_json(json_pathfile) + print(json_file) + modalities.append(json_file[participants_keys[0]]) + try: + body_parts.append(json_file[participants_keys[1]].lower()) + except KeyError as e: + body_parts.append(body_part_aux.lower()) + patient_birthday = datetime.fromisoformat(json_file[participants_keys[2]]) + patient_sex = json_file[participants_keys[3]] + adquisition_date_time = datetime.fromisoformat(json_file[participants_keys[4]].split('T')[0]) + patient_ages.append(int((adquisition_date_time - patient_birthday).days / (365.25))) + patient_ages = sorted(list(set(patient_ages))) + modalities = sorted(list(set(modalities))) + body_parts = sorted(list(set(body_parts))) + list_information.append({ + key:value + for key, value in zip( + participants_header, + [subject, modalities, body_parts, str(patient_birthday.date()), patient_ages, patient_sex] + ) + }) + print(list_information) + pandas.DataFrame.from_dict(list_information).to_csv( + mids_data_path.joinpath("participants.tsv"), sep="\t", index=False + ) diff --git a/xnat2mids/procedures/__init__.py b/xnat2mids/procedures/__init__.py new file mode 100644 index 0000000..e115fe8 --- /dev/null +++ b/xnat2mids/procedures/__init__.py @@ -0,0 +1,40 @@ + +from abc import ABC, abstractmethod + + +class Procedures(ABC): + def __int__(self): + self.view_positions_2d = ['pa', 'll', 'lateral', 'ap', None] + self.view_positions_3d = ['ax', 'sag', 'cor', None] + + @abstractmethod + def reset_indexes(self): + pass + + @staticmethod + def get_mids_path(mids_path, department_id, subject_id, session_id): + return mids_path.pathjoin(department_id, subject_id, session_id) + + @staticmethod + def get_name( + subject_id, + session_id, + acq_index, + run_index, + len_nifti_files, + body_part, + view_position, + scan, + ext + ): + return "".join([ + subject_id, + (("_" + session_id) if session_id else ""), + ("_acq-" + str(acq_index) if len_nifti_files > 1 else ""), + "_run-" + run_index, + (("_bp-" + body_part) if body_part != "head" else "") + (("_vp-" + view_position) if view_position and body_part != "head" else ""), + "_", + scan, + ext + ]) diff --git a/xnat2mids/procedures/electrical_activity_procedures.py b/xnat2mids/procedures/electrical_activity_procedures.py new file mode 100644 index 0000000..e69de29 diff --git a/xnat2mids/procedures/general_radiology_procedure.py b/xnat2mids/procedures/general_radiology_procedure.py new file mode 100644 index 0000000..b08a9f5 --- /dev/null +++ b/xnat2mids/procedures/general_radiology_procedure.py @@ -0,0 +1,71 @@ +from shutil import copyfile +from pathlib import Path +from xnat2mids.procedures import Procedures + + +class GeneralRadiologyProcedures(Procedures): + def __init__(self): + self.view_positions_2d = ['pa', 'll', 'lateral', 'ap', None] + self.view_positions_3d = ['ax', 'sag', 'cor', None] + self.reset_indexes() + + def reset_indexes(self): + self.dict_indexes = { + "cr": {k: 1 for k in self.view_positions_2d}, + "dx": {k: 1 for k in self.view_positions_2d}, + "ct": {k: 1 for k in self.view_positions_3d}, + # not defined yet + "bmd": {None: 1}, + "xa": {None: 1}, + "io": {None: 1}, + "mg": {None: 1}, + "vf": {None: 1}, + "rf": {None: 1}, + "rtimage": {None: 1}, + "rtplan": {None: 1}, + "rtrecord": {None: 1}, + "rtdose": {None: 1}, + "df": {None: 1}, + "rg": {None: 1}, + "ds": {None: 1}, + } + + def procedure( + self, department_id, subject_id, session_id, body_part, + view_position, dicom_modality): + """ + Function that copies the elements to the CR images of + the mids. + """ + nifti_files = sorted([str(i) for i in Path('/'.join(str(json_path).split('/')[:-4])).glob("**/*.png")]) + len_nifti_files = len(nifti_files) + new_path_mids = self.get_mids_path(mids_path=department_id) + + os.makedirs(new_path_mids) + for num, nifti_file in enumerate(nifti_files): + nii_name =self.get_name( + subject_id=subject_id, + session_id=session_id, + acq_index=acq_index, + run_index=str(self.dict_indexes[scan][view_position]), + len_nifti_files=len_nifti_files, + body_part=body_part, + view_position=view_position, + scan=dicom_modality, + ext=".nii.gz" if dicom_modality=="cr" else ".png" + ) + # copy the nifti file in the new path + copyfile(nifti_file, str(new_path_mids.joinpath(nii_name)) + + json_name = self.get_name( + subject_id=subject_id, + session_id=session_id, + acq_index=acq_index, + run_index=str(self.dict_indexes[scan][iop]), + len_nifti_files=len_nifti_files, + body_part=body_part, + view_position=view_position, + scan="cr", + ext=".json" + ) + copyfile(str(dicom_json), str(new_path_mids.joinpath(json_name))) \ No newline at end of file diff --git a/xnat2mids/procedures/light_procedures.py b/xnat2mids/procedures/light_procedures.py new file mode 100644 index 0000000..86486fb --- /dev/null +++ b/xnat2mids/procedures/light_procedures.py @@ -0,0 +1,79 @@ +import pandas +import numpy +import json +import shutil +from datetime import datetime +from xnat2mids.procedures import Procedures +class LightProcedure(Procedures): + def __init__(self): + self.reset_indexes() + + def reset_indexes(self): + self.run_dict = {} + + def control_image(self, folder_conversion, mids_session_path, session_name, protocol, rec, laterality, acquisition_date_time): + png_files = sorted([i for i in folder_conversion.glob("*.png")]) + nifti_files = sorted([i for i in folder_conversion.glob("*.nii*")]) + + len_files = len(png_files) + len(nifti_files) + if not len_files: return + + key = json.dumps([session_name, rec, laterality, protocol]) + value = self.run_dict.get(key, []) + value.append({ + "run":[*png_files, *nifti_files], + "adquisition_time":datetime.fromisoformat(acquisition_date_time), + "folder_mids": mids_session_path}) + self.run_dict[key]=value + + + def copy_sessions(self, subject_name): + for key, runs_list in self.run_dict.items(): + df_aux = pandas.DataFrame.from_dict(runs_list) + df_aux.sort_values(by="adquisition_time", inplace = True) + df_aux.index = numpy.arange(1, len(df_aux) + 1) + print(len(df_aux)) + activate_run = True if len(df_aux) > 1 else False + print(f"{activate_run=}") + for index, row in df_aux.iterrows(): + activate_acq_partioned = True if len(row['run']) > 1 else False + for acq, file_ in enumerate(sorted(row['run'])): + + dest_file_name = self.calculate_name( + subject_name=subject_name, + key=key, + num_run=index, + num_part=acq, + activate_run=activate_run, + activate_acq_partioned=activate_acq_partioned + ) + print("origen:", file_) + print("destino:", row["folder_mids"].joinpath(str(dest_file_name) + "".join(file_.suffix))) + + row["folder_mids"].mkdir(parents=True, exist_ok=True) + shutil.copyfile(file_, row["folder_mids"].joinpath(str(dest_file_name) + "".join(file_.suffix))) + other_files = [f for f in file_.parent.iterdir() if file_.suffix not in str(f) and not f.is_dir()] + for other_file in other_files: + print("origen:", other_file) + print("destino:", row["folder_mids"].joinpath(str(dest_file_name) + "".join(other_file.suffixes))) + shutil.copyfile(str(other_file), row["folder_mids"].joinpath(str(dest_file_name) + "".join(other_file.suffixes))) + + def calculate_name(self, subject_name, key, num_run, num_part, activate_run, activate_acq_partioned): + key_list = json.loads(key) + # print(num_part, activate_acq_partioned) + rec = f"{key_list[1] if key_list[1] else ''}" + chunk = f"{num_part if activate_acq_partioned else ''}" + run = f"{num_run if activate_run else ''}" + print(f"{run=}") + # print(f"{key=}") + return "_".join([ + part for part in [ + subject_name, + key_list[0], + f"acq-{key_list[2]}", + f"rec-{rec}", + f'run-{run}', + (f'chunk-{chunk}') if activate_acq_partioned else '', + key_list[3] + ] if part.split('-')[-1] != '' + ]) diff --git a/xnat2mids/procedures/magnetic_resonance_procedures.py b/xnat2mids/procedures/magnetic_resonance_procedures.py new file mode 100644 index 0000000..de9d360 --- /dev/null +++ b/xnat2mids/procedures/magnetic_resonance_procedures.py @@ -0,0 +1,120 @@ +import shutil +from shutil import copyfile + +import nibabel as nib +from xnat2mids.conversion.dicom_converters import dicom2niix + +body_part_bids = ['head','brain'] + +class ProceduresMR: + def __init__(self): + self.reset_indexes() + + def reset_indexes(self): + """Reset all values in dictionary of the atribute "dict_indexes".""" + + self.run_dict = {} + + + def control_sequences( + self, folder_nifti, mids_session_path, session_name, protocol, acq, dir_, folder_BIDS, body_part + ): + + folder_image_mids = mids_session_path.joinpath( + "" if body_part.lower() in body_part_bids else "mim-mr", + folder_BIDS + ) + print(f'{folder_image_mids=}') + folder_image_mids.mkdir(parents=True, exist_ok=True) + + + + self.control_image(folder_nifti, folder_image_mids, session_name, protocol, acq, dir_, body_part) + + def control_image(self, nifti_path, folder_image_mids, session_name, protocol, acq, dir_, body_part): + + """ + + """ + + + # Search all nifti files in the old folder and sort them + nifti_files = sorted([i for i in nifti_path.glob("*.nii.gz")]) + + len_nifti_files = len(nifti_files) + if len_nifti_files == 0: return + + # This is a counter for several nifties in one adquisition + + protocol_label = f'{protocol}' + acq_label = f'{acq}' if acq else '' + bp_label = f"{body_part}" + vp_label = [ + ( + f"{self.get_plane_nib(nifti_file)}" + if body_part.lower() in body_part_bids + else f"{self.get_plane_nib(nifti_file)}" + ) + for nifti_file in nifti_files + ] + key = str([session_name, acq_label, dir_, bp_label, vp_label, protocol_label]) + value = self.run_dict.get(key, {"runs":[], "folder_mids": None}) + value['runs'].append(nifti_files) + value['folder_mids'] = folder_image_mids + self.run_dict[key] = value + + def copy_sessions(self, subject_name): + for key_str, runs in self.run_dict.items(): + keys = eval(key_str) + print("-"*79) + print(keys, runs) + print("-" * 79) + + activate_run = True if len(runs["runs"]) > 1 else False + for num_run, run in enumerate(runs["runs"],1): + + activate_nifti_parted = True if len(run) > 1 else False + for num_part, partition in enumerate(run,1): + + dest_file_name = self.calculate_name( + subject_name, keys, num_run, num_part, activate_run, activate_nifti_parted + ) + + print("origen:", partition) + print("destino:", runs["folder_mids"].joinpath(str(dest_file_name) + "".join(partition.suffixes))) + shutil.copyfile(partition, runs["folder_mids"].joinpath(str(dest_file_name) + "".join(partition.suffixes))) + other_files = [f for f in partition.parent.iterdir() if "".join(partition.suffixes) not in str(f)] + for other_file in other_files: + print("origen:", other_file) + print("destino:", runs["folder_mids"].joinpath(str(dest_file_name) + "".join(other_file.suffixes))) + shutil.copyfile(str(other_file), runs["folder_mids"].joinpath(str(dest_file_name) + "".join(other_file.suffixes))) + + def get_plane_nib(self, nifti): + """ + Calculate the type of plane with the tag image orientation patient + in dicom metadata. + """ + + img = nib.load(nifti) + plane = nib.aff2axcodes(img.affine)[2] + return "ax" if plane in ["S", "I"] else "sag" if plane in ["R", "L"] else "cor" + + def calculate_name(self, subject_name, keys, num_run, num_part, activate_run, activate_acq_partioned): + print(num_part, activate_acq_partioned) + acq = f"{keys[1] if keys[1] else ''}" + chunk = f"{num_part if activate_acq_partioned else ''}" + print(f"{keys=}") + return "_".join([ + part for part in [ + subject_name, + keys[0], + f'acq-{acq}' if acq else '', + f'dir-{keys[2]}' if keys[2] else '', + f'run-{num_run}' if activate_run else '', + (f'chunk-{chunk}') if activate_acq_partioned else '', + '' if keys[3].lower() in body_part_bids else f'bp-{keys[3]}', + f'desc-{keys[4][num_part-1]}' if keys[3].lower() in body_part_bids else f'vp-{keys[4][num_part-1]}', + keys[5] + ] if part != '' + ]) + diff --git a/xnat2mids/procedures/nuclear_medicine_procedures.py b/xnat2mids/procedures/nuclear_medicine_procedures.py new file mode 100644 index 0000000..bbc03aa --- /dev/null +++ b/xnat2mids/procedures/nuclear_medicine_procedures.py @@ -0,0 +1 @@ +magnetic_resonance_procedures.py \ No newline at end of file diff --git a/xnat2mids/procedures/ultrasound_procedures.py b/xnat2mids/procedures/ultrasound_procedures.py new file mode 100644 index 0000000..bbc03aa --- /dev/null +++ b/xnat2mids/procedures/ultrasound_procedures.py @@ -0,0 +1 @@ +magnetic_resonance_procedures.py \ No newline at end of file diff --git a/xnat2mids/protocols/protocol_RM_brain.tsv b/xnat2mids/protocols/protocol_RM_brain.tsv new file mode 100644 index 0000000..70f6ec4 --- /dev/null +++ b/xnat2mids/protocols/protocol_RM_brain.tsv @@ -0,0 +1,35 @@ + Protocol acq task rec ce dir part folder Manufacturer ManufacturersModelName ScanningSequence SequenceVariant ScanOptions SequenceName ImageType AngioFlag MagneticFieldStrength RepetitionTime InversionTime FlipAngle EchoTime NumberOfAverages RawImage DerivedVendorReportedEchoSpacing EffectiveEchoSpacing TotalReadoutTime +1 FLAIR anat "[""Siemens""]" MAGNETOM Vida "[""SE"", ""SE\\IR""]" "[""SP\\SK"", ""SK\\SP\\MP""]" "[""PFP\\PFF\\CG\\RG\\FS\\PER"", ""PFP\\PFF\\FS\\PER"", ""PFP\\CG\\RG\\FS\\PER""]" [“*spcir_284ns”] "[[""ORIGINAL"", ""PRIMARY"", ""M"", ""NORM"", ""DIS3D"", ""DIS2D"", ""MFSPLIT""], [""ORIGINAL"", ""PRIMARY"", ""M"", ""NONE""], [""ORIGINAL"", ""PRIMARY"", ""M"", ""NORM"", ""DIS2D"", ""MFSPLIT""]]" N [3.0] [5.0] [1.8, 1.65] [120.0] [0.393] [-1] [-1] [-1] [-1] +2 T2w swi mag anat "[""Siemens""]" MAGNETOM Vida "[""GR""]" "[""SK"", ""SP""]" "[""CG\\RG\\PER"", ""PER""]" [“*swi3d1r”] "[[""ORIGINAL"", ""PRIMARY"", ""M"", ""NORM"", ""DIS2D"", ""FM"", ""FIL"", ""MFSPLIT""], [""ORIGINAL"", ""PRIMARY"", ""M"", ""NORM"", ""DIS2D"", ""MFSPLIT""], [""ORIGINAL"", ""PRIMARY"", ""T2"", ""STAR"", ""NONE""], [""ORIGINAL"", ""PRIMARY"", ""M"", ""NORM"", ""DIS2D"", ""MFSPLIT""], [""ORIGINAL"", ""PRIMARY"", ""M"", ""SWI"", ""DIS2D"", ""MFSPLIT""], [""ORIGINAL"", ""PRIMARY"", ""M"", ""SWI"", ""NORM"", ""DIS2D"", ""MFSPLIT""], [""ORIGINAL"", ""PRIMARY"", ""SWI"", ""NONE""]]" N [3.0] [0.028] [-1] [15.0] [0.02] [-1] [-1] [-1] [-1] +3 T2w swi phase anat "[""Siemens""]" MAGNETOM Vida "[""GR""]" "[""SK"", ""SP""]" "[""CG\\RG\\PER"", ""PER""]" [“*swi3d1r”] "[[""ORIGINAL"", ""PRIMARY"", ""P"", ""DIS2D"", ""MFSPLIT"", ""PHASE""], [""ORIGINAL"", ""PRIMARY"", ""T2"", ""STAR"", ""NONE"", ""PHASE""]]" N [3.0] [0.028] [-1] [15.0] [0.02] [-1] [-1] [-1] [-1] +4 T2w anat "[""Siemens""]" MAGNETOM Vida "[""SE""]" "[""SP\\SK""]" "[""CG\\RG\\FS\\PER""]" [“*qtse2d1_15”] "[[""ORIGINAL"", ""PRIMARY"", ""M"", ""NORM"", ""DIS2D"", ""MFSPLIT""]]" N [3.0] [4.0] [-1] [150.0] [0.078] [-1] [-1] [-1] [-1] +5 T1w mprage anat "[""Siemens""]" MAGNETOM Vida "[""GR"", ""RM"", ""GR\\IR""]" "[""SK"", ""MTC\\SS\\OSP"", ""SK\\SP\\MP""]" "[""PFP\\CG\\RG\\PER"", ""PFP\\PER"", ""CG\\RG\\FS\\PER"", ""PFP\\CG\\RG\\FS\\PER"", ""PFP\\RG\\FS"", ""CG\\RG\\PER""]" [“*tfl3d1_16ns”] "[[""ORIGINAL"", ""PRIMARY"", ""M"", ""NONE""], [""ORIGINAL"", ""PRIMARY"", ""M"", ""NORM"", ""DIS2D"", ""MFSPLIT""], [""ORIGINAL"", ""PRIMARY"", ""M"", ""NORM"", ""DIS3D"", ""DIS2D"", ""MFSPLIT""]]" N [3.0] [2,2, 2,3] [0.968, 0.900] [8.0, 9.0] [0.00223, 0.00293] [-1] [-1] [-1] [-1] +6 PDT2 anat "[""Siemens""]" MAGNETOM Vida "[""SE""]" "[""SP\\SK"", ""SK\\SP""]" "[""CG\\RG\\PER"", ""PER""]" [“*tse2d2_5”] "[[""ORIGINAL"", ""PRIMARY"", ""M"", ""NONE""], [""ORIGINAL"", ""PRIMARY"", ""M"", ""NORM"", ""DIS2D"", ""MFSPLIT""]]" N [3.0] [0.0175, 0.01875, 0.0225, 4.78] [-1] [146.0, 142.0, 145.0, 131.0, 137.0, 138.0, 124.0, 135.0, 141.0, 143.0] [0.009] [-1] [-1] [-1] [-1] +7 T1w ahead anat "[""Siemens""]" MAGNETOM Vida "[""GR"", ""EP""]" "[""FS\\PER"", ""CG\\RG\\FS\\PER""]" "[""FS\\PER"", ""CG\\RG\\FS\\PER""]" [“*fl3d1_ns”] [[“ORIGINAL”, “PRIMARY”, “M”, “NORM”, “DIS3D”, “DIS2D”, “MFSPLIT”], [“ORIGINAL”, “PRIMARY”, “M”, “NONE”], [“DERIVED”, “PRIMARY”, “MPR”, “NORM”, “DIS3D”, “DIS2D”, “MFSPLIT”], [“DERIVED”, “PRIMARY”, “MPR”, “RESAMPLED”]] N [3.0] [0.00315] [8.0] [8.0] [0.00137] [-1] [-1] [-1] [-1] +8 asl perf "[""Siemens""]" MAGNETOM Vida "[""GR"", ""EP""]" "[""SK"", ""SK\\OSP""]" "[""FS\\PER"", ""CG\\RG\\FS\\PER""]" [“*tgse3d1_10080”, “*tgse3d1_15120”, “*tgse3d1_3968”] "[[""ORIGINAL"", ""PRIMARY"", ""ASL"", ""NONE"", ""NORM"", ""DIS3D"", ""DIS2D"", ""MFSPLIT""], [""ORIGINAL"", ""PRIMARY"", ""ASL"", ""NONE""]]" N [3.0] [16.0, 36.8, 55.2, 4.6] [-1] [180.0, 160.0] [0.017,0.0219] [-1] [-1] [-1] [-1] +9 dwi AP dwi "[""Siemens""]" MAGNETOM Vida "[""GR\\EP"", “EP”]" "[""SK"", ""SK\\SP""]" "[""CG\\RG\\FS\\PER"", ""FS\\PER""]" [“*ep_b0”] "[[""ORIGINAL"", ""PRIMARY"", ""DIFFUSION"", ""NONE"", ""ND"", ""NORM"", ""MFSPLIT""], [""ORIGINAL"", ""PRIMARY"", ""DIFFUSION"", ""NONE""]]" N [3.0] [8.9] [-1] [90.0] [0.078] [-1] [0.00096] [0.00032] [0.03552] +10 dwi b0 PA dwi "[""Siemens""]" MAGNETOM Vida "[""GR\\EP"", “EP”]" "[""SK"", ""SK\\SP""]" "[""CG\\RG\\FS\\PER"", ""FS\\PER""]" [“*ep_b0”] "[[""ORIGINAL"", ""PRIMARY"", ""DIFFUSION"", ""NONE"", ""ND"", ""NORM"", ""MFSPLIT""], [""ORIGINAL"", ""PRIMARY"", ""DIFFUSION"", ""NONE""]]" N [3.0] [8.9] [-1] [90.0] [0.078] [2] FALSE [0.00072] [0.00024] [0.02664] +11 dwi tracew AP dwi "[""Siemens""]" MAGNETOM Vida "[""GR\\EP"", “EP”]" "[""SK"", ""SK\\SP""]" "[""CG\\RG\\FS\\PER"", ""FS\\PER""]" [“*ep_b1000t”] [[“DERIVED”, “PRIMARY”, “DIFFUSION”, “TRACEW”, “ND”, “NORM”, “MFSPLIT”],[“DERIVED”, “PRIMARY”, “DIFFUSION”, “TRACEW”]] N [3.0] [8.9] [-1] [90.0] [0.078] [-1] [0.00096] [0.00032] [0.03552] +12 dwi FA AP dwi "[""Siemens""]" MAGNETOM Vida "[""GR\\EP"", “EP”]" "[""SK"", ""SK\\SP""]" "[""CG\\RG\\FS\\PER"", ""FS\\PER""]" [“*ep_b0_1000”] [[“DERIVED”, “PRIMARY”, “DIFFUSION”, “FA”, “ND”, “NORM”, “MFSPLIT”],[“DERIVED”, “PRIMARY”, “DIFFUSION”, “FA”]] N [3.0] [8.9] [-1] [90.0] [0.078] [-1] [0.00096] [0.00032] [0.03552] +13 dwi tensorb0 AP dwi "[""Siemens""]" MAGNETOM Vida "[""GR\\EP"", “EP”]" "[""SK"", ""SK\\SP""]" "[""CG\\RG\\FS\\PER"", ""FS\\PER""]" [“*ep_b0_1000”] [[“DERIVED”, “PRIMARY”, “DIFFUSION”, “TENSOR”, “B0”, “ND”, “NORM”, “MFSPLIT”],[“DERIVED”, “PRIMARY”, “DIFFUSION”, “TENSOR”, “B0”]] N [3.0] [8.9] [-1] [90.0] [0.078] [-1] [0.00096] [0.00032] [0.03552] +14 dwi adc AP dwi "[""Siemens""]" MAGNETOM Vida "[""GR\\EP"", “EP”]" "[""SK"", ""SK\\SP""]" "[""CG\\RG\\FS\\PER"", ""FS\\PER""]" [“*ep_b0_1000”] [[“DERIVED”, “PRIMARY”, “DIFFUSION”, “ADC”, “ND”, “NORM”, “MFSPLIT”],[“DERIVED”, “PRIMARY”, “DIFFUSION”, “ADC”]] N [3.0] [8.9] [-1] [90.0] [0.078] [-1] [0.00096] [0.00032] [0.03552] +15 T2starw anat "[""Siemens""]" MAGNETOM Vida "[""GR""]" "[""SK""]" "[""CG\\RG\\PER""]" [“*fl2d1r”] [[“ORIGINAL”, “PRIMARY”, “M”, “NORM”, “DIS2D”, “MFSPLIT”]] N [3.0] [0.64] [-1] [20.0] [0.02] [-1] [-1] [-1] [-1] +16 T2w swi anat "[""Siemens""]" MAGNETOM Vida "[""GR""]" "[""SK"", ""SP""]" "[""CG\\RG\\PER"", ""PER""]" [“*swi3d1r”] [[“ORIGINAL”, “PRIMARY”, “M”, “SWI”, “NORM”, “DIS2D”, “MFSPLIT”], [“ORIGINAL”, “PRIMARY”, “SWI”, “NONE”], [“ORIGINAL”, “PRIMARY”, “M”, “SWI”, “DIS2D”, “MFSPLIT”]] N [3.0] [0.028] [-1] [15.0] [0.02] [-1] [-1] [-1] [-1] +17 T2w mIP anat "[""Siemens""]" MAGNETOM Vida "[""GR""]" "[""SK"", ""SP""]" "[""CG\\RG\\PER"", ""PER""]" [“*swi3d1r”] [[“DERIVED”, “PRIMARY”, “MNIP”, “NORM”, “DIS2D”, “MFSPLIT”], [“DERIVED”, “PRIMARY”, “MNIP”, “ND”, “NORM”, “MFSPLIT”], [“DERIVED”, “PRIMARY”, “SWI”, “MINIMUM”], [“DERIVED”, “PRIMARY”, “MNIP”, “DIS2D”, “MFSPLIT”]] N [3.0] [0.028] [-1] [15.0] [0.02] [-1] [-1] [-1] [-1] +12 dwi coilFA AP dwi "[""Siemens""]" MAGNETOM Vida "[""GR\\EP"", “EP”]" "[""SK"", ""SK\\SP""]" "[""CG\\RG\\FS\\PER"", ""FS\\PER""]" [“*ep_b0_1000”] [[“DERIVED”, “PRIMARY”, “DIFFUSION”, “FA”, “ND”, “NORM”, “MFSPLIT”],[“DERIVED”, “PRIMARY”, “DIFFUSION”, “FA”]] N [3.0] [8.9] [-1] [90.0] [0.078] [-1] [0.00096] [0.00032] [0.03552] +13 bold rest func "[""Siemens""]" MAGNETOM Vida "[""GR\\EP""]" "[""SK""]" "[""CG\\RG\\FS\\PER""]" [“*epfid2d1_64”] [[“ORIGINAL”, “PRIMARY”, “M”, “ND”, “NORM”, “MFSPLIT”]] [] [4.0] [-1] [80.0] [0.06] [-1] [0.00072] [0.00036] [0.02268] +14 bold openeyes rest func "[""Siemens""]" MAGNETOM Vida "[""GR\\EP""]" "[""SK""]" "[""CG\\RG\\FS\\PER""]" [“*epfid2d1_64”] [[“ORIGINAL”, “PRIMARY”, “M”, “ND”, “NORM”, “MFSPLIT”]] [] [2.46] [-1] [80.0] [0.03] [-1] [0.00072] [0.00036] [0.02268] +15 T1w anat "[""Philips""]" [“Ingenia Elition X”, “Achieva”] "[""GR""]" [“MP”] [“FC”] [“”] [[“ORIGINAL”, “PRIMARY”, “M”, “FFE”, “M”, “FFE”], [“ORIGINAL”, “SECONDARY”, “M”, “FFE”, “M”, “FFE”]] N [3.0] [0.0125593, 0.0128999] [-1] [8.0] [0.007056, 0.007216] [-1] FALSE [-1] [-1] [-1] +16 T1w mprage anat "[""Siemens""]" "[""Aera"", ""IMPAX Volume Viewing 3.0""]" "[""GR\\IR""]" "[""SK\\SP\\MP\\OSP""]" "[""IR""]" "[""*tfl3d1_16ns""]" "[[""ORIGINAL"", ""PRIMARY"", ""M"", ""ND"", ""NORM"", ""FM3"", ""2"", ""FIL""], [""DERIVED"", ""SECONDARY"", ""MPR"", ""CSA MPR"", ""CSAPARALLEL"", ""M"", ""ND"", ""NORM"", ""FM3"", ""2"", ""FIL""], [""DERIVED"", ""SECONDARY"", ""CLINAPPS"", ""VV"", ""MPR""], [""DERIVED"", ""SECONDARY"", ""CLINAPPS"", ""OTHER""]]" N [1.5] [2.2, 2.2] [-1] [8.0, 8.0] [0.00266, 0.00266] [-1] [-1] [-1] [-1] +17 FLAIR anat "[""Siemens""]" "[""Aera"", ""IMPAX Volume Viewing 3.0""]" "[""SE\\IR"", ""GR""]" "[""SK\\SP\\MP\\OSP"", ""SP""]" "[""IR\\PFP\\FS"", “”]" "[""*spcir_242ns"", ""*fl2d1r""]" "[[""ORIGINAL"", ""PRIMARY"", ""M"", ""ND"", ""NORM"", ""FM3"", ""2"", ""FIL""], [""DERIVED"", ""SECONDARY"", ""CLINAPPS"", ""VV"", ""MPR""], [""DERIVED"", ""SECONDARY"", ""CLINAPPS"", ""OTHER""]]" N [1.5] [0.8, 5.0] [-1] [20.0, 120.0] [0.025, 0.334] [-1] [-1] [-1] [-1] +18 PDT2 tse anat "[""Siemens""]" "[""Aera"", ""IMPAX Volume Viewing 3.0""]" "[""SE""]" "[""SK\\SP\\OSP""]" [“”] "[""*tse2d2_5""]" "[[""ORIGINAL"", ""PRIMARY"", ""M"", ""ND"", ""NORM"", ""FM3"", ""2"", ""FIL""]]" N [1.5] [0.0175, 0.02625] [-1] [149.0, 150.0] [0.011, 0.011] [-1] [-1] [-1] [-1] +19 T1w ahead anat "[""Siemens""]" "[""Aera"", ""IMPAX Volume Viewing 3.0""]" "[""GR""]" "[""SP""]" "[""PFP""]" "[""*fl3d1_ns""]" "[[""ORIGINAL"", ""PRIMARY"", ""M"", ""ND"", ""NORM""]]" N [1.5] [0.00452, 0.00452] [-1] [8.0, 8.0] [0.00238, 0.00238] [-1] [-1] [-1] [-1] +20 dwi AP dwi "[""Siemens""]" "[""Aera"", ""IMPAX Volume Viewing 3.0""]" [“”] [“”] [“”] [“”] N [] [] [] [] [] [] [] [] [] +21 dwi b0 PA dwi "[""Siemens""]" "[""Aera"", ""IMPAX Volume Viewing 3.0""]" [“”] [“”] [“”] [“”] N [] [] [] [] [] [] [] [] [] +22 dwi tracew AP dwi "[""Siemens""]" "[""Aera"", ""IMPAX Volume Viewing 3.0""]" "[""EP""]" "[""SK\\SP""]" "[""PFP\\FS""]" "[""*ep_b1000t"", ""*ep_b0""]" "[[""DERIVED"", ""PRIMARY"", ""DIFFUSION"", ""TRACEW"", ""ND""]]" N [1.5] [3.2, 18.9006] [90.0, 90.0] [0.089, 0.089] [-1] FALSE [0.000960003, 0.000979931] [0.000480001, 0.000489965] [0.0609602, 0.187657] +23 dwi FA AP dwi "[""Siemens""]" "[""Aera"", ""IMPAX Volume Viewing 3.0""]" "[""EP""]" "[""SK\\SP""]" "[""PFP\\FS""]" "[""*ep_b0_1000""]" "[[""DERIVED"", ""PRIMARY"", ""DIFFUSION"", ""FA"", ""ND""]]" N [1.5] [] [90.0, 90.0] [0.085, 0.085] [-1] FALSE [0.000960003, 0.000960003] [0.000480001, 0.000480001] [0.0609602, 0.0609602] +24 dwi tensorb0 AP dwi "[""Siemens""]" "[""Aera"", ""IMPAX Volume Viewing 3.0""]" "[""EP""]" "[""SK\\SP""]" "[""PFP\\FS""]" "[""*ep_calc_b1500""]" "[[""DERIVED"", ""PRIMARY"", ""DIFFUSION"", ""CALC"", ""BVALUE"", ""TRACEW"", ""ND""]]" N [1.5] [6.3, 6.3] [90.0, 90.0] [0.089, 0.089] [-1] FALSE [0.000979931, 0.000979931] [0.000489965, 0.000489965] [0.187657, 0.187657] +25 dwi adc AP dwi "[""Siemens""]" "[""Aera"", ""IMPAX Volume Viewing 3.0""]" "[""EP""]" "[""SK\\SP""]" "[""PFP\\FS""]" "[""*ep_b0_1000""]" "[[""DERIVED"", ""PRIMARY"", ""DIFFUSION"", ""ADC"", ""ND""]]" N [1.5] [3.2, 6.3] [90.0, 90.0] [0.085, 0.089] [-1] FALSE [0.000960003, 0.000979931] [0.000480001, 0.000489965] [0.0609602, 0.187657] +26 dwi coilFA AP dwi "[""Siemens""]" "[""Aera"", ""IMPAX Volume Viewing 3.0""]" [“”] [“”] [“”] [“”] [“”] [“”] [] [] [] [] [] [-1] FALSE [0.000960003, 0.000960003] [0.000480001, 0.000480001] [0.0609602, 0.0609602] +27 dwi moco AP dwi "[""Siemens""]" "[""Aera"", ""IMPAX Volume Viewing 3.0""]" "[""EP""]" "[""SK""]" "[""PFP\\FS""]" "[""*epfid2d1_64""]" "[[""ORIGINAL"", ""PRIMARY"", ""FMRI"", ""NONE"", ""ND"", ""MOSAIC""]]" N [1.5] [4.0, 4.0] [90.0, 90.0] [0.05, 0.05] [-1] [0.000489996, 0.000489996] [0.000244998, 0.000244998] [0.0154349, 0.0154349] +28 dwi mddw AP dwi "[""Siemens""]" "[""Aera"", ""IMPAX Volume Viewing 3.0""]" "[""EP""]" "[""SK""]" "[""FS""]" "[""*ep_b0""]" "[[""ORIGINAL"", ""PRIMARY"", ""DIFFUSION"", ""NONE"", ""ND"", ""MOSAIC""]]" N [1.5] [3.2, 3.2] [90.0, 90.0] [0.085, 0.085] [-1] [0.000960003, 0.000960003] [0.000480001, 0.000480001] [0.0609602, 0.0609602] diff --git a/xnat2mids/protocols/protocol_RM_brain_old.tsv b/xnat2mids/protocols/protocol_RM_brain_old.tsv new file mode 100644 index 0000000..09ab6e8 --- /dev/null +++ b/xnat2mids/protocols/protocol_RM_brain_old.tsv @@ -0,0 +1,10 @@ + Protocol acq dir folder Manufacturer ScanningSequence SequenceVariant ScanOptions AngioFlag MagneticFieldStrength RepetitionTime InversionTime FlipAngle EchoTime SliceThickness +1 FLAIR anat [Siemens] [SE, SE\IR] [SP\SK, SK\SP\MP] [PFP\PFF\CG\RG\FS\PER, PFP\PFF\FS\PER, PFP\CG\RG\FS\PER] N [3.0] [5.0] [1.8, 1.65] [120.0] [0.393] [1.0] +2 T2w swi anat [Siemens] [GR] [SK, SP] [CG\RG\PER, PER] N [3.0] [0.028] [-1] [15.0] [0.02] [2.0] +3 T2w anat [Siemens] [SE] [SP\SK] [CG\RG\FS\PER] N [3.0] [4.0] [-1] [150.0] [0.078] [3.0] +4 T1w mprage anat [Siemens] [GR, RM, GR\IR] [SK, MTC\SS\OSP, SK\SP\MP] [PFP\CG\RG\PER, PFP\PER, CG\RG\FS\PER, PFP\CG\RG\FS\PER, PFP\RG\FS, CG\RG\PER] N [3.0] [2,2, 2,3] [0.968, 0.900] [8.0, 9.0] [0.00223, 0.00293] [1.2] +5 PDT2 anat [Siemens] [SE] [SP\SK, SK\SP] [CG\RG\PER, PER] N [3.0] [0.0175, 0.01875, 0.0225, 4.78] [-1] [146.0, 142.0, 145.0, 131.0, 137.0, 138.0, 124.0, 135.0, 141.0, 143.0] [0.009] [3.0] +6 T1w ahead anat [Siemens] [GR, EP] [FS\PER, CG\RG\FS\PER] [FS\PER, CG\RG\FS\PER] N [3.0] [0.00315] [8.0] [8.0] [0.00137] [1.6] +7 asl perf [Siemens] [GR, EP] [SK, SK\OSP] [FS\PER, CG\RG\FS\PER] N [3.0] [16.0, 36.8, 55.2, 4.6] [-1] [180.0, 160.0] [0.017,0.0219] [3.0, 4.5] +8 dwi AP dwi [Siemens] [GR\EP] [SK] [CG\RG\FS\PER] N [3.0] [8.9] [-1] [90.0] [0.078] [2.0] +9 dwi PA dwi [Siemens] [GR\EP] [SK] [CG\RG\FS\PER, FS\PER] N [3.0] [8.9] [-1] [90.0] [0.078] [2.0] diff --git a/xnat2mids/protocols/protocol_RM_brain_old_old.tsv b/xnat2mids/protocols/protocol_RM_brain_old_old.tsv new file mode 100644 index 0000000..f9df568 --- /dev/null +++ b/xnat2mids/protocols/protocol_RM_brain_old_old.tsv @@ -0,0 +1,22 @@ + Protocol acq task rec ce dir part folder Manufacturer ManufacturersModelName ScanningSequence SequenceVariant ScanOptions SequenceName ImageType AngioFlag MagneticFieldStrength RepetitionTime InversionTime FlipAngle EchoTime NumberOfAverages RawImage DerivedVendorReportedEchoSpacing EffectiveEchoSpacing TotalReadoutTime +1 FLAIR anat "[""Siemens""]" MAGNETOM Vida "[""SE"", ""SE\\IR""]" "[""SP\\SK"", ""SK\\SP\\MP""]" "[""PFP\\PFF\\CG\\RG\\FS\\PER"", ""PFP\\PFF\\FS\\PER"", ""PFP\\CG\\RG\\FS\\PER""]" [“*spcir_284ns”] "[[""ORIGINAL"", ""PRIMARY"", ""M"", ""NORM"", ""DIS3D"", ""DIS2D"", ""MFSPLIT""], [""ORIGINAL"", ""PRIMARY"", ""M"", ""NONE""], [""ORIGINAL"", ""PRIMARY"", ""M"", ""NORM"", ""DIS2D"", ""MFSPLIT""]]" N [3.0] [5.0] [1.8, 1.65] [120.0] [0.393] [-1] [-1] [-1] [-1] +2 T2w swi mag anat "[""Siemens""]" MAGNETOM Vida "[""GR""]" "[""SK"", ""SP""]" "[""CG\\RG\\PER"", ""PER""]" [“*swi3d1r”] "[[""ORIGINAL"", ""PRIMARY"", ""M"", ""NORM"", ""DIS2D"", ""FM"", ""FIL"", ""MFSPLIT""], [""ORIGINAL"", ""PRIMARY"", ""M"", ""NORM"", ""DIS2D"", ""MFSPLIT""], [""ORIGINAL"", ""PRIMARY"", ""T2"", ""STAR"", ""NONE""], [""ORIGINAL"", ""PRIMARY"", ""M"", ""NORM"", ""DIS2D"", ""MFSPLIT""], [""ORIGINAL"", ""PRIMARY"", ""M"", ""SWI"", ""DIS2D"", ""MFSPLIT""], [""ORIGINAL"", ""PRIMARY"", ""M"", ""SWI"", ""NORM"", ""DIS2D"", ""MFSPLIT""], [""ORIGINAL"", ""PRIMARY"", ""SWI"", ""NONE""]]" N [3.0] [0.028] [-1] [15.0] [0.02] [-1] [-1] [-1] [-1] +3 T2w swi phase anat "[""Siemens""]" MAGNETOM Vida "[""GR""]" "[""SK"", ""SP""]" "[""CG\\RG\\PER"", ""PER""]" [“*swi3d1r”] "[[""ORIGINAL"", ""PRIMARY"", ""P"", ""DIS2D"", ""MFSPLIT"", ""PHASE""], [""ORIGINAL"", ""PRIMARY"", ""T2"", ""STAR"", ""NONE"", ""PHASE""]]" N [3.0] [0.028] [-1] [15.0] [0.02] [-1] [-1] [-1] [-1] +4 T2w anat "[""Siemens""]" MAGNETOM Vida "[""SE""]" "[""SP\\SK""]" "[""CG\\RG\\FS\\PER""]" [“*qtse2d1_15”] "[[""ORIGINAL"", ""PRIMARY"", ""M"", ""NORM"", ""DIS2D"", ""MFSPLIT""]]" N [3.0] [4.0] [-1] [150.0] [0.078] [-1] [-1] [-1] [-1] +5 T1w mprage anat "[""Siemens""]" MAGNETOM Vida "[""GR"", ""RM"", ""GR\\IR""]" "[""SK"", ""MTC\\SS\\OSP"", ""SK\\SP\\MP""]" "[""PFP\\CG\\RG\\PER"", ""PFP\\PER"", ""CG\\RG\\FS\\PER"", ""PFP\\CG\\RG\\FS\\PER"", ""PFP\\RG\\FS"", ""CG\\RG\\PER""]" [“*tfl3d1_16ns”] "[[""ORIGINAL"", ""PRIMARY"", ""M"", ""NONE""], [""ORIGINAL"", ""PRIMARY"", ""M"", ""NORM"", ""DIS2D"", ""MFSPLIT""], [""ORIGINAL"", ""PRIMARY"", ""M"", ""NORM"", ""DIS3D"", ""DIS2D"", ""MFSPLIT""]]" N [3.0] [2,2, 2,3] [0.968, 0.900] [8.0, 9.0] [0.00223, 0.00293] [-1] [-1] [-1] [-1] +6 PDT2 anat "[""Siemens""]" MAGNETOM Vida "[""SE""]" "[""SP\\SK"", ""SK\\SP""]" "[""CG\\RG\\PER"", ""PER""]" [“*tse2d2_5”] "[[""ORIGINAL"", ""PRIMARY"", ""M"", ""NONE""], [""ORIGINAL"", ""PRIMARY"", ""M"", ""NORM"", ""DIS2D"", ""MFSPLIT""]]" N [3.0] [0.0175, 0.01875, 0.0225, 4.78] [-1] [146.0, 142.0, 145.0, 131.0, 137.0, 138.0, 124.0, 135.0, 141.0, 143.0] [0.009] [-1] [-1] [-1] [-1] +7 T1w ahead anat "[""Siemens""]" MAGNETOM Vida "[""GR"", ""EP""]" "[""FS\\PER"", ""CG\\RG\\FS\\PER""]" "[""FS\\PER"", ""CG\\RG\\FS\\PER""]" [“*fl3d1_ns”] [[“ORIGINAL”, “PRIMARY”, “M”, “NORM”, “DIS3D”, “DIS2D”, “MFSPLIT”], [“ORIGINAL”, “PRIMARY”, “M”, “NONE”], [“DERIVED”, “PRIMARY”, “MPR”, “NORM”, “DIS3D”, “DIS2D”, “MFSPLIT”], [“DERIVED”, “PRIMARY”, “MPR”, “RESAMPLED”]] N [3.0] [0.00315] [8.0] [8.0] [0.00137] [-1] [-1] [-1] [-1] +8 asl perf "[""Siemens""]" MAGNETOM Vida "[""GR"", ""EP""]" "[""SK"", ""SK\\OSP""]" "[""FS\\PER"", ""CG\\RG\\FS\\PER""]" [“*tgse3d1_10080”, “*tgse3d1_15120”, “*tgse3d1_3968”] "[[""ORIGINAL"", ""PRIMARY"", ""ASL"", ""NONE"", ""NORM"", ""DIS3D"", ""DIS2D"", ""MFSPLIT""], [""ORIGINAL"", ""PRIMARY"", ""ASL"", ""NONE""]]" N [3.0] [16.0, 36.8, 55.2, 4.6] [-1] [180.0, 160.0] [0.017,0.0219] [-1] [-1] [-1] [-1] +9 dwi AP dwi "[""Siemens""]" MAGNETOM Vida "[""GR\\EP"", “EP”]" "[""SK"", ""SK\\SP""]" "[""CG\\RG\\FS\\PER"", ""FS\\PER""]" [“*ep_b0”] "[[""ORIGINAL"", ""PRIMARY"", ""DIFFUSION"", ""NONE"", ""ND"", ""NORM"", ""MFSPLIT""], [""ORIGINAL"", ""PRIMARY"", ""DIFFUSION"", ""NONE""]]" N [3.0] [8.9] [-1] [90.0] [0.078] [-1] [0.00096] [0.00032] [0.03552] +10 dwi b0 PA dwi "[""Siemens""]" MAGNETOM Vida "[""GR\\EP"", “EP”]" "[""SK"", ""SK\\SP""]" "[""CG\\RG\\FS\\PER"", ""FS\\PER""]" [“*ep_b0”] "[[""ORIGINAL"", ""PRIMARY"", ""DIFFUSION"", ""NONE"", ""ND"", ""NORM"", ""MFSPLIT""], [""ORIGINAL"", ""PRIMARY"", ""DIFFUSION"", ""NONE""]]" N [3.0] [8.9] [-1] [90.0] [0.078] [2] FALSE [0.00072] [0.00024] [0.02664] +11 dwi tracew AP dwi "[""Siemens""]" MAGNETOM Vida "[""GR\\EP"", “EP”]" "[""SK"", ""SK\\SP""]" "[""CG\\RG\\FS\\PER"", ""FS\\PER""]" [“*ep_b1000t”] [[“DERIVED”, “PRIMARY”, “DIFFUSION”, “TRACEW”, “ND”, “NORM”, “MFSPLIT”],[“DERIVED”, “PRIMARY”, “DIFFUSION”, “TRACEW”]] N [3.0] [8.9] [-1] [90.0] [0.078] [-1] [0.00096] [0.00032] [0.03552] +12 dwi FA AP dwi "[""Siemens""]" MAGNETOM Vida "[""GR\\EP"", “EP”]" "[""SK"", ""SK\\SP""]" "[""CG\\RG\\FS\\PER"", ""FS\\PER""]" [“*ep_b0_1000”] [[“DERIVED”, “PRIMARY”, “DIFFUSION”, “FA”, “ND”, “NORM”, “MFSPLIT”],[“DERIVED”, “PRIMARY”, “DIFFUSION”, “FA”]] N [3.0] [8.9] [-1] [90.0] [0.078] [-1] [0.00096] [0.00032] [0.03552] +13 dwi tensorb0 AP dwi "[""Siemens""]" MAGNETOM Vida "[""GR\\EP"", “EP”]" "[""SK"", ""SK\\SP""]" "[""CG\\RG\\FS\\PER"", ""FS\\PER""]" [“*ep_b0_1000”] [[“DERIVED”, “PRIMARY”, “DIFFUSION”, “TENSOR”, “B0”, “ND”, “NORM”, “MFSPLIT”],[“DERIVED”, “PRIMARY”, “DIFFUSION”, “TENSOR”, “B0”]] N [3.0] [8.9] [-1] [90.0] [0.078] [-1] [0.00096] [0.00032] [0.03552] +14 dwi adc AP dwi "[""Siemens""]" MAGNETOM Vida "[""GR\\EP"", “EP”]" "[""SK"", ""SK\\SP""]" "[""CG\\RG\\FS\\PER"", ""FS\\PER""]" [“*ep_b0_1000”] [[“DERIVED”, “PRIMARY”, “DIFFUSION”, “ADC”, “ND”, “NORM”, “MFSPLIT”],[“DERIVED”, “PRIMARY”, “DIFFUSION”, “ADC”]] N [3.0] [8.9] [-1] [90.0] [0.078] [-1] [0.00096] [0.00032] [0.03552] +15 T2starw anat "[""Siemens""]" MAGNETOM Vida "[""GR""]" "[""SK""]" "[""CG\\RG\\PER""]" [“*fl2d1r”] [[“ORIGINAL”, “PRIMARY”, “M”, “NORM”, “DIS2D”, “MFSPLIT”]] N [3.0] [0.64] [-1] [20.0] [0.02] [-1] [-1] [-1] [-1] +16 T2w swi anat "[""Siemens""]" MAGNETOM Vida "[""GR""]" "[""SK"", ""SP""]" "[""CG\\RG\\PER"", ""PER""]" [“*swi3d1r”] [[“ORIGINAL”, “PRIMARY”, “M”, “SWI”, “NORM”, “DIS2D”, “MFSPLIT”], [“ORIGINAL”, “PRIMARY”, “SWI”, “NONE”], [“ORIGINAL”, “PRIMARY”, “M”, “SWI”, “DIS2D”, “MFSPLIT”]] N [3.0] [0.028] [-1] [15.0] [0.02] [-1] [-1] [-1] [-1] +17 T2w mIP anat "[""Siemens""]" MAGNETOM Vida "[""GR""]" "[""SK"", ""SP""]" "[""CG\\RG\\PER"", ""PER""]" [“*swi3d1r”] [[“DERIVED”, “PRIMARY”, “MNIP”, “NORM”, “DIS2D”, “MFSPLIT”], [“DERIVED”, “PRIMARY”, “MNIP”, “ND”, “NORM”, “MFSPLIT”], [“DERIVED”, “PRIMARY”, “SWI”, “MINIMUM”], [“DERIVED”, “PRIMARY”, “MNIP”, “DIS2D”, “MFSPLIT”]] N [3.0] [0.028] [-1] [15.0] [0.02] [-1] [-1] [-1] [-1] +12 dwi coilFA AP dwi "[""Siemens""]" MAGNETOM Vida "[""GR\\EP"", “EP”]" "[""SK"", ""SK\\SP""]" "[""CG\\RG\\FS\\PER"", ""FS\\PER""]" [“*ep_b0_1000”] [[“DERIVED”, “PRIMARY”, “DIFFUSION”, “FA”, “ND”, “NORM”, “MFSPLIT”],[“DERIVED”, “PRIMARY”, “DIFFUSION”, “FA”]] N [3.0] [8.9] [-1] [90.0] [0.078] [-1] [0.00096] [0.00032] [0.03552] +13 bold rest func "[""Siemens""]" MAGNETOM Vida "[""GR\\EP""]" "[""SK""]" "[""CG\\RG\\FS\\PER""]" [“*epfid2d1_64”] [[“ORIGINAL”, “PRIMARY”, “M”, “ND”, “NORM”, “MFSPLIT”]] [4.0] [-1] [80.0] [0.06] [-1] [0.00072] [0.00036] [0.02268] +14 bold openeyes rest func "[""Siemens""]" MAGNETOM Vida "[""GR\\EP""]" "[""SK""]" "[""CG\\RG\\FS\\PER""]" [“*epfid2d1_64”] [[“ORIGINAL”, “PRIMARY”, “M”, “ND”, “NORM”, “MFSPLIT”]] [2.46] [-1] [80.0] [0.03] [-1] [0.00072] [0.00036] [0.02268] +15 T1w anat "[""Philips""]" [“Ingenia Elition X”, “Achieva”] "[""GR""]" [“MP”] [“FC”] [“”] [[“ORIGINAL”, “PRIMARY”, “M”, “FFE”, “M”, “FFE”], [“ORIGINAL”, “SECONDARY”, “M”, “FFE”, “M”, “FFE”]] N [3.0] [0.0125593, 0.0128999] [-1] [8.0] [0.007056, 0.007216] [-1] FALSE [-1] [-1] [-1] diff --git a/xnat2mids/protocols/protocol_RM_spine_siemens.tsv b/xnat2mids/protocols/protocol_RM_spine_siemens.tsv new file mode 100644 index 0000000..8892cd6 --- /dev/null +++ b/xnat2mids/protocols/protocol_RM_spine_siemens.tsv @@ -0,0 +1,3 @@ + Protocol acq task ce rec dir part folder Manufacturer ManufacturersModelName ScanningSequence SequenceVariant ScanOptions SequenceName ImageType AngioFlag MagneticFieldStrength RepetitionTime InversionTime FlipAngle EchoTime NumberOfAverages RawImage DerivedVendorReportedEchoSpacing EffectiveEchoSpacing TotalReadoutTime +1 T1w tse anat "[""Siemens""]" [“MAGNETOM_ESSENZA”] "[""SE"", ""GR""]" "[""SK\\SP\\OSP"", ""SP\\OSP""]" "[""SAT1"", ""SAT1\\FS""]" [“*tse2d1_3”, “*fl2d1”, “*tseR2d1rr17”] "[[""ORIGINAL"", ""PRIMARY"", ""M"", ""NORM"", ""DIS2D"", ""FM3"", ""2"", ""FIL""], [""ORIGINAL"", ""PRIMARY"", ""M"", ""NORM"", ""DIS2D"", ""FM2"", ""2"", ""FIL""]]" N [1.5] [0.33, 0.953] [-1] [20.0, 150.0] [0.0092, 0.012] [2.0,3.0] [-1] [-1] [-1] [-1] +2 T2w tse anat "[""Siemens""]" [“MAGNETOM_ESSENZA”] "[""SE"", ""GR"", “SE\\IR”]" "[""SK\\SP\\OSP"", ""SP\\OSP"", “SK\\SP\\MP\\OSP”]" "[""SAT1"", ""SAT1\\FS"", “SAT2”,”SAT2\\FS”,”IR\\SAT1\\FS”, “FS”,””]" "[""*tseR2d1_13"", ""*fl2d1"", ""*tse2d1_14"", ""*tir2d1_9"", ""*tseR2d1_15"", ""*tse2d1_15"", ""*tse2d1_3"", ""*tseR2d1rr18"", ""*tseR2d1rr17"", ""*tse2d1rs9"", ""*tseR2d1rs13""]" "[[""ORIGINAL"", ""PRIMARY"", ""M"", ""NORM"", ""DIS2D"", ""FM3"", ""2"", ""FIL""], [""DERIVED"", ""SECONDARY"", ""POSDISP"", ""M"", ""NORM"", ""DIS2D"", ""CSA"" ""RESAMPLED""], [""DERIVED"", ""SECONDARY"", ""POSDISP"", ""M"", ""NORM"", ""DIS2D"", ""FM3"", ""2"", ""FIL"", ""CSA"" ""RESAMPLED""], [""DERIVED"", ""SECONDARY"", ""POSDISP"", ""M"", ""NORM"", ""DIS2D""], [""ORIGINAL"", ""PRIMARY"", ""M"", ""NORM"", ""DIS2D""], [""ORIGINAL"", ""PRIMARY"", ""M"", ""NORM"", ""DIS2D"", ""FM2"", ""2"", ""FIL""], [""DERIVED"", ""SECONDARY"", ""POSDISP"", ""M"", ""NORM"", ""DIS2D"", ""FM3"", ""2"", ""FIL""], [""ORIGINAL"", ""PRIMARY"", ""M"", ""NORM"", ""DIS2D"", ""FM"", ""FIL""], [""DERIVED"", ""SECONDARY"", ""POSDISP"", ""M"", ""NORM"", ""DIS2D"", ""FM2"", ""2"", ""FIL""], [""DERIVED"", ""SECONDARY"", ""POSDISP"", ""M"", ""NORM"", ""DIS2D"", ""FM2"", ""2"", ""FIL"", ""CSA"" ""RESAMPLED""]]" [1.7, 4.7] [-1] [20.0, 150.0] [0.086, 0.096] [2.0,3.0] [-1] [-1] [-1] [-1] diff --git a/xnat2mids/protocols/scans_tagger.py b/xnat2mids/protocols/scans_tagger.py new file mode 100644 index 0000000..1d41850 --- /dev/null +++ b/xnat2mids/protocols/scans_tagger.py @@ -0,0 +1,72 @@ +import pandas as pd +import numpy as np +import json +pd.set_option('display.max_columns', None) + +class Tagger: + # scan group + # SE = Spin Echo =====>>>> 'SE' + # IR = Inversion Recovery =====>>>> 'IR' 'IR\\SE' 'SE\\IR' + # GR = Gradient Recalled =====>>>> 'GR' + # EP = Echo Planar =====>>>> 'EP' 'EP\\SE' 'EP\\SE\\EP' 'EP\\S' + # RM = Research Mode =====>>>> 'RM' + + def __init__(self): + + self.ScanSeq = [['SE'], ['IR', 'IR\\SE', 'SE\\IR'], ['GR', 'GR\\IR', 'IR\\GR', 'EP\\GR'], + ['EP', 'EP\\SE', 'EP\\SE\\EP', 'EP\\S', 'EP\\G', 'EP\\IR'], ['RM']] + + def load_table_protocol(self, protocol_table_path): + self.table_protocols = pd.read_csv(protocol_table_path, sep='\t', index_col=False) + + def classification_by_min_max(self, dict_atrubutes): + + # targetScan = pd.DataFrame.from_dict([dict_atrubutes]) + # Verify to which scan group corresponds + scaning_sequence = dict_atrubutes["ScanningSequence"] + sequence_variant = dict_atrubutes["SequenceVariant"] + scan_options = dict_atrubutes["ScanOptions"] + #sequence_name = dict_atrubutes["SequenceName"] + #image_type = dict_atrubutes["ImageType"] + print(f"{scaning_sequence=:}") + print(f"{sequence_variant=:}") + print(f"{scan_options=:}") + #scaning_sequence = scaning_sequence if type(scaning_sequence) is str else "\\".join(scaning_sequence) + for l in list(self.table_protocols["ScanningSequence"]): + for s in json.loads(l): + print(s,scaning_sequence, s == scaning_sequence) + table_protocol_SS = self.table_protocols[[ + any([True for s in json.loads(l) if s == scaning_sequence]) + for l in list(self.table_protocols["ScanningSequence"]) + ]] + + table_protocol_SS_SV = table_protocol_SS[[ + any([True for s in json.loads(l) if s == sequence_variant]) + for l in list(table_protocol_SS["SequenceVariant"]) + ]] + table_protocol_SS_SV = table_protocol_SS_SV + print("#"*40, "table_protocol_SS", "#"*40) + print(table_protocol_SS) + print("#" * 40, "table_protocol_SS_VS", "#" * 40) + print(table_protocol_SS_SV[["Protocol", "acq"]]) + # print(f"{dict_atrubutes=}") + matrix = [] + # print(list(dict_atrubutes.keys())[-5:]) + adquisition_param_keys = list(dict_atrubutes.keys())[-5:-1] + for p in adquisition_param_keys: + distance = [] + # print("p_value", dict_atrubutes[p], type(dict_atrubutes[p])) + + p_value = float(dict_atrubutes[p]) # if dict_atrubutes[p] !="nan" else -1 + for list_values in table_protocol_SS_SV[p]: + + min_ = np.amin(eval(list_values)) + max_ = np.amax(eval(list_values)) + if p_value >= min_ and p_value <= max_: + distance.append(np.sum([0., 0.])) + else: + distance.append(np.sum([abs(p_value - min_), abs(p_value - max_)])) + matrix.append(distance) + + pos_table_protocol = np.argmin(np.array(matrix).sum(axis=0)) + return table_protocol_SS_SV.iloc[pos_table_protocol][["Protocol", "acq", "task", "ce", "rec", "dir", "part", "folder"]].fillna('') diff --git a/xnat2mids/requirements.txt b/xnat2mids/requirements.txt new file mode 100644 index 0000000..8e4d1da --- /dev/null +++ b/xnat2mids/requirements.txt @@ -0,0 +1,62 @@ +absl-py==1.0.0 +astunparse==1.6.3 +async-timeout==4.0.2 +beautifulsoup4==4.11.1 +bs4==0.0.1 +cachetools==5.1.0 +certifi==2021.10.8 +chardet==4.0.0 +charset-normalizer==2.0.12 +Deprecated==1.2.13 +flatbuffers==2.0 +gast==0.5.3 +google-auth==2.6.6 +google-auth-oauthlib==0.4.6 +google-pasta==0.2.0 +grpcio==1.46.1 +h5py==3.6.0 +idna==3.3 +imageio==2.19.1 +keras==2.8.0 +Keras-Preprocessing==1.1.2 +libclang==14.0.1 +lxml==4.8.0 +Markdown==3.3.7 +networkx==2.8 +nibabel==3.2.2 +npyscreen==4.10.5 +numpy==1.22.3 +oauthlib==3.2.0 +opt-einsum==3.3.0 +packaging==21.3 +pandas==1.4.2 +Pillow==9.1.0 +progressbar2==4.0.0 +protobuf==3.20.1 +pyasn1==0.4.8 +pyasn1-modules==0.2.8 +pydicom==2.3.0 +pyparsing==3.0.8 +python-dateutil==2.8.2 +python-utils==3.1.0 +pytz==2022.1 +PyWavelets==1.3.0 +redis==4.3.0 +requests==2.27.1 +requests-oauthlib==1.3.1 +rsa==4.8 +scikit-image==0.19.2 +scipy==1.8.0 +six==1.16.0 +soupsieve==2.3.2.post1 +tensorboard==2.8.0 +tensorboard-data-server==0.6.1 +tensorboard-plugin-wit==1.8.1 +tensorflow==2.8.0 +tensorflow-io-gcs-filesystem==0.25.0 +termcolor==1.1.0 +tf-estimator-nightly==2.8.0.dev2021122109 +typing-extensions==4.2.0 +urllib3==1.26.9 +Werkzeug==2.1.2 +wrapt==1.14.1 diff --git a/xnat2mids/xnat.py b/xnat2mids/xnat.py new file mode 100644 index 0000000..4877cd7 --- /dev/null +++ b/xnat2mids/xnat.py @@ -0,0 +1,920 @@ +import csv +import getpass +import json +import os +import re +import sys +import time +import traceback +from io import StringIO +from shutil import copyfile + +import progressbar +import pydicom +from xnat import requests +from xnat.xnat.variables import dict_paths +from xnat.xnat.variables import dict_uris +from xnat.xnat.variables import format_message +from xnat.xnat.variables import reset_terminal + + +############################################################################### +# Functions +############################################################################### +def list_directory_xnat(project_list): + project_list.sort() + loop = True + project_names = [path_.split(os.sep)[-1] for path_ in project_list] + while loop: + for i, project_item in enumerate(project_names): + if not i % 5: + print(("")) + string = str(i + 1) + ") " + project_item + print("{0:20s}".format(string), end=" ", flush=True) + answer = input("\nChoose the project: ") + answer = str(answer) + answer_list = [] + answer_list_aux = answer.split(' ') + + for ans in answer_list_aux: + if ans.isdigit(): + ans = int(ans) - 1 + if ans >= len(project_names): + print("the number " + ans + " is not corrected, try again", flush=True) + break + else: + answer_list.append(project_names[ans]) + else: + if not (any([ans in path_ for path_ in project_names])): + if ans == "exit": + exit(1) + else: + print("the project " + ans + + " is not corrected, try again") + break + else: + answer_list.append(ans) + else: + loop = False + + return answer_list + + +def try_to_request(interface, web, level_verbose=15, level_tab=15): + # Function that allows a persistent get request to a web page + + # variable that counts connection attempt + intents = 1 + while True: + try: + req = interface.get(web) + if req.status_code != 504: + break + except requests.exceptions.ConnectionError as e: + + print( + format_message( + level_verbose, + level_tab, + "Intents to download information = {}".format(intents) + ) + ) + time.sleep(60) + except requests.exceptions.HTTPError: + print( + format_message( + level_verbose, + level_tab, + "Intents to download information = {}".format(intents) + ) + ) + time.sleep(60) + return req + + +class Xnat_Session(): + + def __init__(self, url_xnat, user=None, password=None): + self.url_xnat = url_xnat + self.user = user + self.password = password + self.level_verbose = 0 + self.level_tab = 0 + + def __enter__(self): + self.connect() + return self + + def __exit__(self, exc_type, exc_val, exc_tb): + self.exit() + + def connect(self): + self.interface = requests.Session() + if self.user and self.password: + self.interface.auth = (self.user, self.password) + else: + if not self.user: + self.user = input("username: ") + self.password = getpass.getpass("Password: ") + self.interface.auth = (self.user, self.password) + + def exit(self): + self.interface.close() + + def get_projects(self, verbose): + output = StringIO() + if verbose: print(self.url_xnat + dict_uris["projects"], flush=True) + output.write( + try_to_request( + self.interface, self.url_xnat + + dict_uris["projects"], + self.level_verbose, + self.level_tab + ).text + ) + output.seek(0) + print(str(output)) + reader = csv.DictReader(output) + self.dict_projects = dict() + for row in reader: + self.dict_projects[row["ID"]] = Project(self.url_xnat, self.interface, self.level_verbose + 5, + self.level_tab + 5, **row) + output.close() + + def show_list_of_project(self, verbose): + """ + This functions allows the user to visualize al projects in xnat aplication + NOT IN USE, NEXT UPLOAD + """ + project_list = [key for key, _ in self.dict_projects.items()] + answer_list = list_directory_xnat(project_list) + + # project_list.sort() + # loop = True + # while loop: + # for i, project_item in enumerate(project_list): + # if not i % 5: + # print(("")) + # string = str(i + 1) + ") " + project_item + # print("{0:20s}".format(string), end=" ", flush=True) + # answer = input("\nChoose the project: ") + # answer = str(answer) + # answer_list = [] + # answer_list_aux = answer.split(' ') + # for ans in answer_list_aux: + # if ans.isdigit(): + # ans = int(ans) - 1 + # if ans >= len(project_list): + # print("the number " + ans + " is not corrected, try again", flush=True) + # break + # else: + # answer_list.append(project_list[ans]) + # else: + # if not (ans in project_list): + # if ans == "exit": + # exit(1) + # else: + # print("the proyect " + ans + # + " is not corrected, try again") + # break + # else: + # answer_list.append(ans) + # else: + # loop = False + if verbose: print("list of projects to download: {}".format(", ".join(answer_list)), flush=True) + return answer_list + + def download_projects(self, + path_download, + with_department=True, + project_list=None, + bool_list_resources=[False, False, True, False, False, False], + overwrite=False, + verbose=False): + self.get_projects(verbose) + if project_list is None: + project_list = self.show_list_of_project(verbose) + # clear console + print(reset_terminal, end="", flush=True) + print(format_message(self.level_verbose, self.level_tab, "Projects:"), end="", flush=True) + print(format_message(self.level_verbose + 3, self.level_tab, "Subject:"), end="", flush=True) + # move the cursor + bar_project = progressbar.ProgressBar(maxval=len(project_list), prefix="\033[2;0H").start() + bar_project.update(1) + bar_project.update(0) + + for iter, key in enumerate(project_list): + self.dict_projects[key].download( + os.path.join(path_download, ""), + with_department=with_department, + bool_list_resources=bool_list_resources, + overwrite=overwrite, + verbose=verbose + ) + bar_project.update(iter + 1) + bar_project.finish() + print("\033[12:0", end="", flush=True) + + +class Project(dict): + def __init__(self, url_xnat, interface, level_verbose, level_tab, **kwargs): + super().__init__(**kwargs) + self.url_xnat = url_xnat + self.interface = interface + self.level_verbose = level_verbose + self.level_tab = level_tab + + def get_list_subjects(self, verbose): + output = StringIO() + + if verbose: + print(format_message(self.level_verbose, self.level_tab, "Project: {}".format(self["ID"])), flush=True) + output.write(try_to_request(self.interface, self.url_xnat + + dict_uris["subjects"](self["ID"]) + ).text) + output.seek(0) + reader = csv.DictReader(output) + self.dict_subjects = dict() + for row in reader: + row["project"] = self + self.dict_subjects[row["ID"]] = Subject(self.level_verbose + 1, self.level_tab + 1, **row) + output.close() + + def download( + self, + path_download, + with_department=True, + project_list=None, + bool_list_resources=[False, False, True, False, False, False], + overwrite=False, + verbose=False + ): + if with_department: path_download = os.path.join(path_download, self["ID"], "") + # print("\033[5;0H\u001b[0K", end="",flush=True) + self.get_list_subjects(verbose) + # move the cursor + # print("\033[4;0H", end="",flush=True) + bar_subject = progressbar.ProgressBar( + maxval=len(self.dict_subjects), + prefix=format_message(self.level_verbose - 1, 0, "") + ).start() + for iter, subject_obj in enumerate(self.dict_subjects.values()): + subject_obj.download( + path_download, bool_list_resources, + overwrite=overwrite, verbose=verbose + ) + print(format_message(self.level_verbose - 1, 0, "")) + bar_subject.update(iter + 1) + print(format_message(self.level_verbose - 1, 0, "")) + bar_subject.finish() + + +class Subject(dict): + def __init__(self, level_verbose, level_tab, **kwargs): + super().__init__(**kwargs) + self.level_verbose = level_verbose + self.level_tab = level_tab + + def get_list_experiments(self, verbose): + + output = StringIO() + if verbose: print(format_message(self.level_verbose, self.level_tab, f"Subject: {self['ID']}"), flush=True) + output.write( + try_to_request( + self["project"].interface, + self["project"].url_xnat + + dict_uris["experiments"](self["project"]["ID"], self["ID"]) + ).text + ) + output.seek(0) + reader = csv.DictReader(output) + self.dict_sessions = dict() + for row in reader: + self.dict_sessions[row["label"]] = Session(self, self.level_verbose + 1, self.level_tab + 1, **row) + output.close() + + def download(self, path_download, + bool_list_resources=[False, False, True, False, False, False], + overwrite=False, + verbose=False + ): + print("\033[6;0H\u001b[0K", end="", flush=True) + self.get_list_experiments(verbose) + # move the cursor + for session_obj in self.dict_sessions.values(): + session_obj.download( + path_download, bool_list_resources, + overwrite=overwrite, verbose=verbose + ) + + print(format_message(self.level_verbose, self.level_tab, "\u001b[0K"), end="", flush=True) + + +class Resource(dict): + pass + + +class Session(dict): + def __init__(self, subject, level_verbose, level_tab, **kwargs): + super().__init__(**kwargs) + self["subject"] = subject + self.level_verbose = level_verbose + self.level_tab = level_tab + + def get_list_scans(self, verbose): + output = StringIO() + if verbose: print( + format_message(self.level_verbose, self.level_tab, f"Session: {self['ID']}"), flush=True) + output.write( + try_to_request( + self["subject"]["project"].interface, + self["subject"]["project"].url_xnat + + dict_uris["scans"]( + self["subject"]["project"]["ID"], + self["subject"]["ID"], + self["ID"]) + ).text + ) + output.seek(0) + reader = csv.DictReader(output) + self.dict_scans = dict() + for row in reader: + # print(format_message(16, 5, "")) + # print(row) + # If the "xsiType" key of the session is not equal to + # "xnat: mrSessionData", this may not work in this point. + try: + self.dict_scans[row["ID"]] = scan(self, self.level_verbose + 1, self.level_tab + 1, **row) + + except KeyError: + continue + output.close() + + def get_list_resources(self, path_download, overwrite=False, verbose=False): + output = StringIO() + if verbose: print( + format_message(self.level_verbose, self.level_tab, f"Session: {self['ID']}"), flush=True) + output.write( + try_to_request( + self["subject"]["project"].interface, + self["subject"]["project"].url_xnat + + dict_uris["scans"]( + self["subject"]["project"]["ID"], + self["subject"]["ID"], + self["ID"]) + ).text + ) + output.seek(0) + reader = csv.DictReader(output) + self.dict_scans = dict() + for row in reader: + # print(format_message(16, 5, "")) + # print(row) + # If the "xsiType" key of the session is not equal to + # "xnat: mrSessionData", this may not work in this point. + try: + self.dict_scans[row["ID"]] = Resource(self, self.level_verbose + 1, self.level_tab + 1, **row) + + except KeyError: + continue + output.close() + + # def get_list_struct_report( + # self, path_download, bool_list_resources, overwrite=False, verbose=False + # ): + # output = StringIO() + # output.write( + # try_to_request( + # self["subject"]["project"].interface, + # self["subject"]["project"].url_xnat + # + dict_uris["struct_reports"]( + # self["subject"]["project"]["ID"], + # self["subject"]["ID"], + # self["ID"]) + # ).text + # ) + # output.seek(0) + # reader = csv.DictReader(output) + # + # if verbose: + # print(format_message(self.level_verbose, self.level_tab, f"Session SR: {self['ID']}"), flush=True) + # for row in reader: + # # id_session=re.search(r'\d+', row["Name"]).group(0) + # try: + # id_session = re.search(r'sr.*', row["Name"]).group(0) + # except KeyError as e: + # print("\033[20;0H\u001b[0K", end="", flush=True) + # print(row) + # print(self["subject"]["project"]["ID"], + # self["subject"]["ID"], + # self["ID"]) + # return + # self.download_struct_report( + # path_download, row["Name"], overwrite=overwrite, verbose=verbose + # ) + # output.close() + # + # def download_struct_report(self, path_download, filename, overwrite=False, verbose=False): + # + # complet_path = ( + # os.path.join( + # path_download, + # dict_path["path_sr"]( + # self["subject"]["ID"], + # self["ID"] + # ) + # ) + # ) + # sr_path = os.path.join(complet_path, filename) + # if not overwrite and os.path.exists(sr_path): + # print("Structural Report exists", flush=True) + # return + # os.makedirs(complet_path, exist_ok=True) + # url_sr = (self["subject"]["project"].url_xnat + # + dict_uri["struct_reports"]( + # self["subject"]["project"]["ID"], + # self["subject"]["ID"], + # self["ID"] + # ).split("?")[0] + os.sep + # + filename + # ) + # # if verbose: print(" Downloading sr file... " + url_sr,flush=True) + # sr = try_to_request( + # self["subject"]["project"].interface, + # url_sr + # ) + # # nifti = self["scan"]["session"]["subject"]["project"].interface.get(url_nifti, allow_redirects=True) + # sr.raise_for_status() + # + # with open(os.path.join(complet_path, filename), 'wb') as sr_file: + # sr_file.write(sr.content) + + def get_list_assessors(self, verbose): + output = StringIO() + if verbose: + print(format_message(self.level_verbose, self.level_tab, f"Assessors: {self['ID']}"), flush=True) + output.write( + try_to_request( + self["subject"]["project"].interface, + self["subject"]["project"].url_xnat + + dict_uris["assessors"]( + self["subject"]["project"]["ID"], + self["subject"]["ID"], + self["ID"] + + ) + ).text + ) + output.seek(0) + reader = csv.DictReader(output) + self.dict_assessors = dict() + for row in reader: + try: + self.dict_assessors[row["ID"]] = assessors(self, self.level_verbose + 1, self.level_tab + 1, **row) + except Exception as e: + print(e) + # sys.exit(2) + continue + output.close() + + def download(self, path_download, + bool_list_resources=[False, False, True, False, False, False], + overwrite=False, + verbose=False + ): + # print("\033[7;0H\u001b[0K", end="",flush=True) + self.get_list_scans(verbose) + for scan_obj in self.dict_scans.values(): + scan_obj.download( + path_download, bool_list_resources=bool_list_resources, + overwrite=overwrite, verbose=verbose + ) + # print("\033[18;0H\u001b[0K", end="",flush=True) + self.get_list_struct_report(path_download, bool_list_resources, overwrite=False, verbose=verbose) + + self.get_list_assessors(verbose) + for resource_obj in self.dict_assessors.values(): + # sys.exit(1) + resource_obj.download( + path_download, + bool_list_resources=bool_list_resources, + overwrite=overwrite, verbose=verbose) + print(format_message(self.level_verbose, self.level_tab, "\u001b[0K"), end="", flush=True) + + +class scan(dict): + def __init__(self, session, level_verbose, level_tab, **kwargs): + super().__init__(**kwargs) + self["session"] = session + self.level_verbose = level_verbose + self.level_tab = level_tab + + def get_list_resources(self, verbose): + output = StringIO() + if verbose: print(format_message(self.level_verbose, self.level_tab, f"scan: {self['ID']}")) + output.write( + try_to_request( + self["session"]["subject"]["project"].interface, + self["session"]["subject"]["project"].url_xnat + + dict_uris["scan_resources"]( + self["session"]["subject"]["project"]["ID"], + self["session"]["subject"]["ID"], + self["session"]["ID"], + self["ID"] + ) + ).text + ) + output.seek(0) + reader = csv.DictReader(output) + self.dict_resources = dict() + for row in reader: + self.dict_resources[row["xnat_abstractresource_id"]] = resources(self, self.level_verbose + 1, + self.level_tab + 1, **row) + output.close() + + def download( + self, path_download, + bool_list_resources=[False, False, True, False, False, False], + overwrite=False, + verbose=False + ): + # print(format_message(13, 4, "entro en scan")) + self.get_list_resources(verbose) + for resource_obj in self.dict_resources.values(): + try: + resource_obj.download( + path_download, + bool_list_resources=bool_list_resources, + overwrite=overwrite, verbose=verbose) + except requests.exceptions.RequestException as e: + complet_path = (path_download + dict_path["path_download"]( + self["session"]["subject"]["ID"], + self["session"]["ID"], + self["ID"], + "NIFTI" + ) + ) + print(e) + # with open(os.path.join(path_download, ".log"), "a") as log: + # log.write( + # "Error: {} in nifti url {}".format( + # e, + # complet_path + # ) + + # ) + # return + print(format_message(self.level_verbose, self.level_tab, "\u001b[0K"), end="", flush=True) + + +class scan_resources(dict): + def __init__(self, scan, level_verbose, level_tab, **kwargs): + super().__init__(**kwargs) + self["scan"] = scan + self.level_verbose = level_verbose + self.level_tab = level_tab + + def get_list_files(self, verbose): + output = StringIO() + if verbose: print(format_message(self.level_verbose, self.level_tab, f"resource: {self['label']}"), + end=" ----> ", + flush=True) + file_text = try_to_request( + self["scan"]["session"]["subject"]["project"].interface, + self["scan"]["session"]["subject"]["project"].url_xnat + + dict_uri["files"]( + self["scan"]["session"]["subject"]["project"]["ID"], + self["scan"]["session"]["subject"]["ID"], + self["scan"]["session"]["ID"], + self["scan"]["ID"], + self["label"] + ) + ) + file_text.raise_for_status() + output.write(file_text.text) + output.seek(0) + reader = csv.DictReader(output) + self.dict_resources = dict() + for row in reader: + self.dict_resources[row["Name"]] = dict(**row) + output.close() + + def download_dicom(self, path_download, filename, overwrite=False, verbose=False): + + complet_path = ( + path_download + dict_path["path_download"]( + self["scan"]["session"]["subject"]["ID"], + self["scan"]["session"]["ID"], + self["scan"]["ID"], + self["label"] + ) + ) + complet_path_metadata = ( + path_download + dict_path["path_download"]( + self["scan"]["session"]["subject"]["ID"], + self["scan"]["session"]["ID"], + self["scan"]["ID"], + "NIFTI" + ) + ) + + dicom_path = os.path.join(complet_path, filename) + dicom_path_metadata = os.path.join(complet_path_metadata, "dicom.json") + if not overwrite and (os.path.exists(dicom_path) and os.path.exists(dicom_path_metadata)): + # if verbose: print("DICOM file already exist") + return dicom_path, dicom_path_metadata + # if not overwrite and os.path.exists(dicom_path): + # if verbose: print(" DICOM metadata file already exist") + # return + if verbose: + pass + # print("Downloading DICOM file...", flush=True, end="") + # print(" Downloading DICOM Metadata file...",flush=True) + + os.makedirs(complet_path, exist_ok=True) + os.makedirs(complet_path_metadata, exist_ok=True) + try: + copyfile(dict_uri["local_files"]( + self["scan"]["session"]["subject"]["project"]["ID"], + self["scan"]["session"]["label"], + self["scan"]["ID"], + self["label"], + filename + + ), dicom_path) + except FileNotFoundError as e: + url_dicom = (self["scan"]["session"]["subject"]["project"].url_xnat + + dict_uri["files"]( + self["scan"]["session"]["subject"]["project"]["ID"], + self["scan"]["session"]["subject"]["ID"], + self["scan"]["session"]["ID"], + self["scan"]["ID"], + self["label"] + ).split("?")[0] + "/" + + filename + ) + + # with open(path_download + "urls_descarga.txt", "a") as f: + # f.write("%s \n %s # %r # %r # %r \n" % ( + # url_dicom, dicom_path, overwrite, verbose, os.path.exists(dicom_path))) + # f.close() + + dicom = try_to_request( + self["scan"]["session"]["subject"]["project"].interface, + url_dicom + ) + # nifti = self["scan"]["session"]["subject"]["project"].interface.get(url_nifti, allow_redirects=True) + dicom.raise_for_status() + + with open(dicom_path, 'wb') as dicom_file: + dicom_file.write(dicom.content) + + return dicom_path, dicom_path_metadata + + def download_nifti(self, path_download, filename, overwrite=False, verbose=False): + complet_path = (path_download + dict_path["path_download"]( + self["scan"]["session"]["subject"]["ID"], + self["scan"]["session"]["ID"], + self["scan"]["ID"], + self["label"] + ) + ) + + nifti_path = os.path.join(complet_path, filename) + if not overwrite and os.path.exists(nifti_path): + if verbose: print("nifti file already exist") + return + if verbose: print("Downloading NIFTI file...", flush=True) + os.makedirs(complet_path, exist_ok=True) + url_nifti = (self["scan"]["session"]["subject"]["project"].url_xnat + + dict_uri["files"]( + self["scan"]["session"]["subject"]["project"]["ID"], + self["scan"]["session"]["subject"]["ID"], + self["scan"]["session"]["ID"], + self["scan"]["ID"], + self["label"] + ).split("?")[0] + "/" + + filename + ) + + # with open(path_download + "urls_descarga.txt", "a") as f: + # f.write( + # "%s \n %s # %r # %r # %r \n" % (url_nifti, nifti_path, overwrite, verbose, os.path.exists(nifti_path))) + # f.close() + nifti = try_to_request( + self["scan"]["session"]["subject"]["project"].interface, + url_nifti + ) + # nifti = self["scan"]["session"]["subject"]["project"].interface.get(url_nifti, allow_redirects=True) + nifti.raise_for_status() + + with open(os.path.join(complet_path, filename), 'wb') as nifti_file: + nifti_file.write(nifti.content) + + def download_bids(self): + pass + + def download_png(self, path_download, filename, overwrite=False, verbose=False): + complet_path = (path_download + dict_path["path_download"]( + self["scan"]["session"]["subject"]["ID"], + self["scan"]["session"]["ID"], + self["scan"]["ID"], + self["label"] + ) + ) + + png_path = os.path.join(complet_path, filename) + if not overwrite and os.path.exists(png_path): + if verbose: print("png file already exist") + return + if verbose: print("Downloading png file...", flush=True) + os.makedirs(complet_path, exist_ok=True) + url_png = (self["scan"]["session"]["subject"]["project"].url_xnat + + dict_uri["files"]( + self["scan"]["session"]["subject"]["project"]["ID"], + self["scan"]["session"]["subject"]["ID"], + self["scan"]["session"]["ID"], + self["scan"]["ID"], + self["label"] + ).split("?")[0] + "/" + + filename + ) + + # with open(path_download + "urls_descarga.txt", "a") as f: + # f.write("%s \n %s # %r # %r # %r \n" % (url_png, png_path, overwrite, verbose, os.path.exists(png_path))) + # f.close() + png = try_to_request( + self["scan"]["session"]["subject"]["project"].interface, + url_png + ) + # png = self["scan"]["session"]["subject"]["project"].interface.get(url_png, allow_redirects=True) + png.raise_for_status() + + with open(os.path.join(complet_path, filename), 'wb') as png_file: + png_file.write(png.content) + + def download( + self, + path_download, + bool_list_resources=[False, False, True, False, False, False], + overwrite=False, + verbose=False + ): + + self.get_list_files(verbose) + is_metadata_saved = False + + for index, file_obj in enumerate(self.dict_resources.values()): + + if self["label"] == "DICOM" and bool_list_resources[1]: + print(format_message(self.level_verbose + 1, self.level_tab + 1, f"{index} of {self['file_count']}"), + end="", + flush=True) + # self.download_dicom(path_download, file_obj["Name"], overwrite=overwrite, verbose=verbose) + + if self["label"] == "SECONDARY" and bool_list_resources[2]: + # self.download_dicom(path_download, file_obj["Name"], overwrite=overwrite, verbose=verbose) + pass + print(format_message(self.level_verbose, self.level_tab, "\u001b[0K"), end="", flush=True) + print(format_message(self.level_verbose + 1, self.level_tab + 1, "\u001b[0K"), end="", flush=True) + + +class assessors(dict): + def __init__(self, session, level_verbose, level_tab, **kwargs): + super().__init__(**kwargs) + self["session"] = session + self.level_verbose = level_verbose + self.level_tab = level_tab + + def get_list_assessors_resources(self, verbose): + output = StringIO() + if verbose: + print(format_message(self.level_verbose, self.level_tab, f"assessor: {self['label']}"), flush=True) + file_text = try_to_request( + self["session"]["subject"]["project"].interface, + self["session"]["subject"]["project"].url_xnat + + dict_uri["assessors_resources"]( + self["session"]["subject"]["project"]["ID"], + self["session"]["subject"]["ID"], + self["session"]["ID"], + self["ID"] + ) + ) + file_text.raise_for_status() + output.write(file_text.text) + output.seek(0) + reader = csv.DictReader(output) + self.dict_resources = dict() + for row in reader: + self.dict_resources[row["xnat_abstractresource_id"]] = assessors_resources( + self, self.level_verbose + 1, self.level_tab + 1, **row + ) + output.close() + + def download( + self, path_download, + bool_list_resources=[False, False, True, False, False, False], + overwrite=False, + verbose=False + ): + + # sys.exit(0) + self.get_list_assessors_resources(verbose) + for resource_obj in self.dict_resources.values(): + + # sys.exit(1) + try: + resource_obj.download( + path_download, + bool_list_resources=bool_list_resources, + overwrite=overwrite, verbose=verbose) + except requests.exceptions.RequestException as e: + print("descarga fallida") + traceback.print_exc() + traceback.print_stack() + sys.exit(1) + print(format_message(self.level_verbose, self.level_tab, "\u001b[0K"), end="", flush=True) + + + def __init__(self, assessors, level_verbose, level_tab, **kwargs): + super().__init__(**kwargs) + self["assessors"] = assessors + self.level_verbose = level_verbose + self.level_tab = level_tab + + def get_list_roi_files(self, verbose): + output = StringIO() + if verbose: + print( + format_message( + self.level_verbose, self.level_tab, f"assessor resources: {self['label']}" + ), end=" ----> ", flush=True + ) + file_text = try_to_request( + self["assessors"]["session"]["subject"]["project"].interface, + self["assessors"]["session"]["subject"]["project"].url_xnat + + dict_uri["roi_files"]( + self["assessors"]["session"]["subject"]["project"]["ID"], + self["assessors"]["session"]["subject"]["ID"], + self["assessors"]["session"]["ID"], + self["assessors"]["ID"], + self["xnat_abstractresource_id"] + ) + ) + file_text.raise_for_status() + output.write(file_text.text) + output.seek(0) + reader = csv.DictReader(output) + self.dict_roi_files = dict() + for row in reader: + self.dict_roi_files[row["Name"]] = dict(**row) + output.close() + + def download_roi_files(self, path_download, filename, overwrite=False, verbose=False): + complet_path = (path_download + dict_path["path_download_roi"]( + self["assessors"]["session"]["subject"]["ID"], + self["assessors"]["session"]["ID"], + self["assessors"]["ID"], + self["xnat_abstractresource_id"] + ) + ) + + roi_path = os.path.join(complet_path, filename) + if not overwrite and os.path.exists(roi_path): + if verbose: print(" roi file already exist") + return + if verbose: print(" Downloading png file...", flush=True) + os.makedirs(complet_path, exist_ok=True) + url_roi = (self["assessors"]["session"]["subject"]["project"].url_xnat + + dict_uri["files"]( + self["assessors"]["session"]["subject"]["project"]["ID"], + self["assessors"]["session"]["subject"]["ID"], + self["assessors"]["session"]["ID"], + self["assessors"]["ID"], + self["xnat_abstractresource_id"] + ).split("?")[0] + "/" + + filename + ) + + roi = try_to_request( + self["assessors"]["session"]["subject"]["project"].interface, + url_roi + ) + + # png = self["scan"]["session"]["subject"]["project"].interface.get(url_png, allow_redirects=True) + roi.raise_for_status() + + with open(os.path.join(complet_path, filename), 'wb') as roi_file: + roi_file.write(roi.content) + + def download( + self, + path_download, + bool_list_resources=[False, False, True, False, False, False], + overwrite=False, + verbose=False + ): + self.get_list_roi_files(verbose) + for file_obj in self.dict_roi_files.values(): + self.download_roi_files(path_download, file_obj["Name"], overwrite=overwrite, verbose=verbose) + print(format_message(self.level_verbose, self.level_tab, "\u001b[0K"), end="", flush=True) diff --git a/xnat2mids/xnat/__init__.py b/xnat2mids/xnat/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/xnat2mids/xnat/assessor.py b/xnat2mids/xnat/assessor.py new file mode 100644 index 0000000..623f43a --- /dev/null +++ b/xnat2mids/xnat/assessor.py @@ -0,0 +1,60 @@ +import csv +from io import StringIO +from xnat2mids.xnat.variables import format_message +from xnat2mids.xnat.variables import dict_uris +from xnat2mids.xnat.request import try_to_request +from xnat2mids.xnat.assessor_resource import AssessorsResources +import requests +class Assessors(dict): + def __init__(self, session, level_verbose, level_tab, **kwargs): + super().__init__(**kwargs) + self["session"] = session + self.level_verbose = level_verbose + self.level_tab = level_tab + + def get_list_assessors_resources(self, verbose): + output = StringIO() + if verbose: + print(format_message(self.level_verbose, self.level_tab, f"assessor: {self['label']}"), flush=True) + file_text = try_to_request( + self["session"]["subject"]["project"].interface, + self["session"]["subject"]["project"].url_xnat + + dict_uris["assessors_resources"]( + self["session"]["subject"]["project"]["ID"], + self["session"]["subject"]["ID"], + self["session"]["ID"], + self["ID"] + ) + ) + file_text.raise_for_status() + output.write(file_text.text) + output.seek(0) + reader = csv.DictReader(output) + self.dict_resources = dict() + for row in reader: + self.dict_resources[row["xnat_abstractresource_id"]] = AssessorsResources( + self, self.level_verbose + 1, self.level_tab + 1, **row + ) + output.close() + + def download( + self, path_download, + bool_list_resources=[False, False, True, False, False, False], + overwrite=False, + verbose=False + ): + + # sys.exit(0) + self.get_list_assessors_resources(verbose) + for resource_obj in self.dict_resources.values(): + + # sys.exit(1) + try: + resource_obj.download( + path_download, + bool_list_resources=bool_list_resources, + overwrite=overwrite, verbose=verbose) + except requests.exceptions.RequestException as e: + print("descarga fallida") + + print(format_message(self.level_verbose, self.level_tab, "\u001b[0K"), end="", flush=True) diff --git a/xnat2mids/xnat/assessor_resource.py b/xnat2mids/xnat/assessor_resource.py new file mode 100644 index 0000000..20ce311 --- /dev/null +++ b/xnat2mids/xnat/assessor_resource.py @@ -0,0 +1,97 @@ + + +import csv +import os +from pathlib import Path +from io import StringIO +from xnat2mids.xnat.variables import format_message +from xnat2mids.xnat.variables import dict_uris +from xnat2mids.xnat.variables import dict_paths +from xnat2mids.xnat.request import try_to_request +from xnat2mids.xnat.convert_xml2image import xml2image + +class AssessorsResources(dict): + def __init__(self, assessors, level_verbose, level_tab, **kwargs): + super().__init__(**kwargs) + self["assessors"] = assessors + self.level_verbose = level_verbose + self.level_tab = level_tab + + def get_list_roi_files(self, verbose): + output = StringIO() + if verbose: + print( + format_message( + self.level_verbose, self.level_tab, f"assessor resources: {self['label']}" + ), end=" ----> ", flush=True + ) + file_text = try_to_request( + self["assessors"]["session"]["subject"]["project"].interface, + self["assessors"]["session"]["subject"]["project"].url_xnat + + dict_uris["assessor_resource_roi_files"]( + self["assessors"]["session"]["subject"]["project"]["ID"], + self["assessors"]["session"]["subject"]["ID"], + self["assessors"]["session"]["ID"], + self["assessors"]["ID"], + self["xnat_abstractresource_id"] + ) + ) + file_text.raise_for_status() + output.write(file_text.text) + output.seek(0) + reader = csv.DictReader(output) + self.dict_roi_files = dict() + for row in reader: + self.dict_roi_files[row["Name"]] = dict(**row) + output.close() + + def download_roi_files(self, path_download, filename, overwrite=False, verbose=False): + complet_path = (path_download + dict_paths["path_download_roi"]( + self["assessors"]["session"]["subject"]["ID"], + self["assessors"]["session"]["ID"], + self["assessors"]["ID"], + self["xnat_abstractresource_id"] + ) + ) + + roi_path = os.path.join(complet_path, filename) + if not overwrite and os.path.exists(roi_path): + if verbose: print(" roi file already exist") + xml2image(Path(roi_path)) + return + if verbose: print(" Downloading png file...", flush=True) + os.makedirs(complet_path, exist_ok=True) + url_roi = (self["assessors"]["session"]["subject"]["project"].url_xnat + + dict_uris["assessor_resource_roi_files"]( + self["assessors"]["session"]["subject"]["project"]["ID"], + self["assessors"]["session"]["subject"]["ID"], + self["assessors"]["session"]["ID"], + self["assessors"]["ID"], + self["xnat_abstractresource_id"] + ).split("?")[0] + "/" + + filename + ) + + roi = try_to_request( + self["assessors"]["session"]["subject"]["project"].interface, + url_roi + ) + + # png = self["scan"]["session"]["subject"]["project"].interface.get(url_png, allow_redirects=True) + roi.raise_for_status() + + with open(roi_path, 'wb') as roi_file: + roi_file.write(roi.content) + #xml2image(Path(roi_path)) + + def download( + self, + path_download, + bool_list_resources=[False, False, True, False, False, False], + overwrite=False, + verbose=False + ): + self.get_list_roi_files(verbose) + for file_obj in self.dict_roi_files.values(): + self.download_roi_files(path_download, file_obj["Name"], overwrite=overwrite, verbose=verbose) + print(format_message(self.level_verbose, self.level_tab, "\u001b[0K"), end="", flush=True) \ No newline at end of file diff --git a/xnat2mids/xnat/convert_xml2image.py b/xnat2mids/xnat/convert_xml2image.py new file mode 100644 index 0000000..03c9d66 --- /dev/null +++ b/xnat2mids/xnat/convert_xml2image.py @@ -0,0 +1,59 @@ +import xml.etree.ElementTree as ET +import pandas as pd +import numpy as np + + + +def xml2image(xml_file): + + tree = ET.parse(str(xml_file)) + root = tree.getroot() + + mki = 0 + values = [] + for imageanotation in root.iter('{gme://caCORE.caCORE/4.4/edu.northwestern.radiology.AIM}ImageAnnotation'): + value = imageanotation[3].attrib['value'] + for markupentity in imageanotation.iter('{gme://caCORE.caCORE/4.4/edu.northwestern.radiology.AIM}MarkupEntity'): + mki+=1 + for _2dspatioancoordinate in markupentity.iter('{gme://caCORE.caCORE/4.4/edu.northwestern.radiology.AIM}TwoDimensionSpatialCoordinate'): + values.append([mki, value, _2dspatioancoordinate[0].attrib['value'], _2dspatioancoordinate[1].attrib['value'], _2dspatioancoordinate[2].attrib['value']]) + + coords = pd.DataFrame.from_records(values, columns=['Mark', 'Type', 'idx', 'x', 'y']) + + masks = [] + eq = list(enumerate(list(set(coords['Type'])), 1)) + eq = {x: i for i, x in eq} + coords['label'] = coords['Type'].map(eq) + n_diff_marks = len(list(set(coords['label']))) + for t_mark in list(set(coords['label'])): + marks = coords[(coords['label'] == t_mark)] + for m_idx in list(set(marks['Mark'])): + mark = marks[marks['Mark'] == m_idx] + print(mark) + poly = [] + poly.append(mark) + # La mascara de fondo tiene que estar en np.uint8 + mask = np.zeros(img.shape, dtype=np.uint8) + # points = np.int32(mark[['x','y']].astype(float).astype("int32").to_numpy()) + test = mark[["x", "y"]].to_numpy() + # Hay que pasar de string a float + test = test.astype(np.float32) + # Despues a int + test = test.astype(np.int32) + # Despues meter el array de numpy en un [], sin el [] no funciona + test = np.array([test], dtype=np.int32) + cv2.fillPoly(mask, test, 255) + mask = np.where(mask == 255, t_mark, mask) + masks.append(mask) + + dest = np.zeros(masks[0].shape + (3,)).astype("uint8") + for mask in masks: + a = np.array([mask, mask, mask]) + + a = np.transpose(a, (1, 2, 0)) + print(a.shape) + dest = cv2.addWeighted(dest, 1, a, 1, 0) + + gray_image = cv2.cvtColor(dest, cv2.COLOR_BGR2GRAY) + np.image.imsave(xml_file.parent.joinpath(xml_file.stem + ".png"), gray_image) + coords.to_csv(xml_file.parent.joinpath(xml_file.stem + ".csv"), sep='\t') \ No newline at end of file diff --git a/xnat2mids/xnat/project.py b/xnat2mids/xnat/project.py new file mode 100644 index 0000000..14577e6 --- /dev/null +++ b/xnat2mids/xnat/project.py @@ -0,0 +1,59 @@ +import csv +import os +import progressbar +from io import StringIO +from xnat2mids.xnat.subject import Subject +from xnat2mids.xnat.variables import format_message +from xnat2mids.xnat.variables import dict_uris +from xnat2mids.xnat.request import try_to_request +class Project(dict): + def __init__(self, url_xnat, interface, level_verbose, level_tab, **kwargs): + super().__init__(**kwargs) + self.url_xnat = url_xnat + self.interface = interface + self.level_verbose = level_verbose + self.level_tab = level_tab + + def get_list_subjects(self, verbose): + output = StringIO() + + if verbose: + print(format_message(self.level_verbose, self.level_tab, "Project: {}".format(self["ID"])), flush=True) + output.write(try_to_request(self.interface, self.url_xnat + + dict_uris["subjects"](self["ID"]) + ).text) + output.seek(0) + reader = csv.DictReader(output) + self.dict_subjects = dict() + for row in reader: + row["project"] = self + self.dict_subjects[row["ID"]] = Subject(self.level_verbose + 1, self.level_tab + 1, **row) + output.close() + + def download( + self, + path_download, + with_department=True, + project_list=None, + bool_list_resources=[False, False, True, False, False, False], + overwrite=False, + verbose=False + ): + path_download = path_download.joinpath(self["ID"], "sourcedata") + # print("\033[5;0H\u001b[0K", end="",flush=True) + self.get_list_subjects(verbose) + # move the cursor + # print("\033[4;0H", end="",flush=True) + bar_subject = progressbar.ProgressBar( + maxval=len(self.dict_subjects), + prefix=format_message(self.level_verbose - 1, 0, "") + ).start() + for iter, subject_obj in enumerate(self.dict_subjects.values()): + subject_obj.download( + path_download, bool_list_resources, + overwrite=overwrite, verbose=verbose + ) + print(format_message(self.level_verbose - 1, 0, "")) + bar_subject.update(iter + 1) + print(format_message(self.level_verbose - 1, 0, "")) + bar_subject.finish() \ No newline at end of file diff --git a/xnat2mids/xnat/request.py b/xnat2mids/xnat/request.py new file mode 100644 index 0000000..a6f02b9 --- /dev/null +++ b/xnat2mids/xnat/request.py @@ -0,0 +1,36 @@ +import time +import requests + +from xnat2mids.xnat.variables import format_message + + +def try_to_request(interface, web, level_verbose=15, level_tab=15): + # Function that allows a persistent get request to a web page + + # variable that counts connection attempt + intents = 1 + while True: + try: + req = interface.get(web) + if req.status_code != 504: + break + except requests.exceptions.ConnectionError as e: + + print( + format_message( + level_verbose, + level_tab, + "Intents to download information = {}".format(intents) + ) + ) + time.sleep(60) + except requests.exceptions.HTTPError: + print( + format_message( + level_verbose, + level_tab, + "Intents to download information = {}".format(intents) + ) + ) + time.sleep(60) + return req diff --git a/xnat2mids/xnat/scan.py b/xnat2mids/xnat/scan.py new file mode 100644 index 0000000..754193c --- /dev/null +++ b/xnat2mids/xnat/scan.py @@ -0,0 +1,62 @@ +import requests +import csv +from io import StringIO +from xnat2mids.xnat.variables import format_message +from xnat2mids.xnat.variables import dict_uris +from xnat2mids.xnat.request import try_to_request +from xnat2mids.xnat.scan_resources import ScanResources + + +class Scan(dict): + def __init__(self, session, level_verbose, level_tab, **kwargs): + super().__init__(**kwargs) + self["session"] = session + self.level_verbose = level_verbose + self.level_tab = level_tab + + def get_list_resources(self, verbose): + output = StringIO() + if verbose: print(format_message(self.level_verbose, self.level_tab, f"scan: {self['ID']}")) + output.write( + try_to_request( + self["session"]["subject"]["project"].interface, + self["session"]["subject"]["project"].url_xnat + + dict_uris["scan_resources"]( + self["session"]["subject"]["project"]["ID"], + self["session"]["subject"]["ID"], + self["session"]["ID"], + self["ID"] + ) + ).text + ) + output.seek(0) + reader = csv.DictReader(output) + self.dict_resources = dict() + for row in reader: + self.dict_resources[row["xnat_abstractresource_id"]] = ScanResources(self, self.level_verbose + 1, self.level_tab + 1, **row) + output.close() + + def download( + self, path_download, + bool_list_resources=[False, False, True, False, False, False], + overwrite=False, + verbose=False + ): + #print(format_message(13, 4, "entro en scan")) + self.get_list_resources(verbose) + for resource_obj in self.dict_resources.values(): + try: + resource_obj.download( + path_download, + bool_list_resources=bool_list_resources, + overwrite=overwrite, verbose=verbose) + except requests.exceptions.RequestException as e: + complet_path = (path_download + dict_path["path_download"]( + self["session"]["subject"]["ID"], + self["session"]["ID"], + self["ID"], + "NIFTI" + ) + ) + print(e) + print(format_message(self.level_verbose, self.level_tab, "\u001b[0K"), end="", flush=True) diff --git a/xnat2mids/xnat/scan_resources.py b/xnat2mids/xnat/scan_resources.py new file mode 100644 index 0000000..ae50cd0 --- /dev/null +++ b/xnat2mids/xnat/scan_resources.py @@ -0,0 +1,213 @@ +import csv +import os +import pydicom +import json +from io import StringIO +from shutil import copyfile + +from xnat2mids.xnat.variables import format_message +from xnat2mids.xnat.variables import dict_uris +from xnat2mids.xnat.variables import dict_paths + +from xnat2mids.xnat.request import try_to_request + + +class ScanResources(dict): + def __init__(self, scan, level_verbose, level_tab, **kwargs): + super().__init__(**kwargs) + self["scan"] = scan + self.level_verbose = level_verbose + self.level_tab = level_tab + + def get_list_files(self, verbose): + output = StringIO() + if verbose: print(format_message(self.level_verbose, self.level_tab, f"resource: {self['label']}"), + end=" ----> ", + flush=True) + file_text = try_to_request( + self["scan"]["session"]["subject"]["project"].interface, + self["scan"]["session"]["subject"]["project"].url_xnat + + dict_uris["scan_resource_files"]( + self["scan"]["session"]["subject"]["project"]["ID"], + self["scan"]["session"]["subject"]["ID"], + self["scan"]["session"]["ID"], + self["scan"]["ID"], + self["label"] + ) + ) + file_text.raise_for_status() + output.write(file_text.text) + output.seek(0) + reader = csv.DictReader(output) + self.dict_resources = dict() + for row in reader: + self.dict_resources[row["Name"]] = dict(**row) + output.close() + + def download_dicom(self, path_download, filename, overwrite=False, verbose=False): + + complet_path = path_download.joinpath( + dict_paths["path_download"]( + self["scan"]["session"]["subject"]["ID"], + self["scan"]["session"]["ID"], + self["scan"]["ID"], + self["label"] + ) + ) + + + dicom_path = os.path.join(complet_path, filename) + dicom_path_metadata = os.path.join(complet_path, "dicom.json") + if not overwrite and (os.path.exists(dicom_path)) and (os.path.exists(dicom_path_metadata)): + # #if verbose: print("DICOM file already exist") + return + + os.makedirs(complet_path, exist_ok=True) + #os.makedirs(complet_path_metadata, exist_ok=True) + + url_dicom = (self["scan"]["session"]["subject"]["project"].url_xnat + + dict_uris["scan_resource_files"]( + self["scan"]["session"]["subject"]["project"]["ID"], + self["scan"]["session"]["subject"]["ID"], + self["scan"]["session"]["ID"], + self["scan"]["ID"], + self["label"] + ).split("?")[0] + "/" + + filename + ) + + dicom = try_to_request( + self["scan"]["session"]["subject"]["project"].interface, + url_dicom + ) + # nifti = self["scan"]["session"]["subject"]["project"].interface.get(url_nifti, allow_redirects=True) + dicom.raise_for_status() + + with open(dicom_path, 'wb') as dicom_file: + dicom_file.write(dicom.content) + + if not self.is_metadata_saved: + self.is_metadata_saved = True + self.store_metadata(dicom_path, dicom_path_metadata.format("DICOM")) + + def download_nifti(self, path_download, filename, overwrite=False, verbose=False): + complet_path = path_download.joinpath(dict_paths["path_download"]( + self["scan"]["session"]["subject"]["ID"], + self["scan"]["session"]["ID"], + self["scan"]["ID"], + self["label"] + )) + + nifti_path = os.path.join(complet_path, filename) + if not overwrite and os.path.exists(nifti_path): + if verbose: print("nifti file already exist") + return + if verbose: print("Downloading NIFTI file...", flush=True) + os.makedirs(complet_path, exist_ok=True) + url_nifti = (self["scan"]["session"]["subject"]["project"].url_xnat + + dict_uris["scan_resource_files"]( + self["scan"]["session"]["subject"]["project"]["ID"], + self["scan"]["session"]["subject"]["ID"], + self["scan"]["session"]["ID"], + self["scan"]["ID"], + self["label"] + ).split("?")[0] + "/" + + filename + ) + + # with open(path_download + "urls_descarga.txt", "a") as f: + # f.write( + # "%s \n %s # %r # %r # %r \n" % (url_nifti, nifti_path, overwrite, verbose, os.path.exists(nifti_path))) + # f.close() + nifti = try_to_request( + self["scan"]["session"]["subject"]["project"].interface, + url_nifti + ) + # nifti = self["scan"]["session"]["subject"]["project"].interface.get(url_nifti, allow_redirects=True) + nifti.raise_for_status() + + with open(os.path.join(complet_path, filename), 'wb') as nifti_file: + nifti_file.write(nifti.content) + + + def download_png(self, path_download, filename, overwrite=False, verbose=False): + complet_path = (path_download + dict_paths["path_download"]( + self["scan"]["session"]["subject"]["ID"], + self["scan"]["session"]["ID"], + self["scan"]["ID"], + self["label"] + ) + ) + + png_path = os.path.join(complet_path, filename) + if not overwrite and os.path.exists(png_path): + if verbose: print("png file already exist") + return + if verbose: print("Downloading png file...", flush=True) + os.makedirs(complet_path, exist_ok=True) + url_png = (self["scan"]["session"]["subject"]["project"].url_xnat + + dict_uris["scan_resource_files"]( + self["scan"]["session"]["subject"]["project"]["ID"], + self["scan"]["session"]["subject"]["ID"], + self["scan"]["session"]["ID"], + self["scan"]["ID"], + self["label"] + ).split("?")[0] + "/" + + filename + ) + + # with open(path_download + "urls_descarga.txt", "a") as f: + # f.write("%s \n %s # %r # %r # %r \n" % (url_png, png_path, overwrite, verbose, os.path.exists(png_path))) + # f.close() + png = try_to_request( + self["scan"]["session"]["subject"]["project"].interface, + url_png + ) + # png = self["scan"]["session"]["subject"]["project"].interface.get(url_png, allow_redirects=True) + png.raise_for_status() + + with open(os.path.join(complet_path, filename), 'wb') as png_file: + png_file.write(png.content) + + def store_metadata(self, dicom_path, dicom_path_metadata): + + dicom = pydicom.dcmread(dicom_path, stop_before_pixels=True) + try: + string_json = dicom.to_json(suppress_invalid_tags=True) + except TypeError as e: + self.is_metadata_saved = False + return + dict_json = json.loads(string_json) + # del dict_json["7FE00010"] + string_json = json.dumps(dict_json, default=lambda o: o.__dict__, + sort_keys=True) + with open(dicom_path_metadata, 'w') as dicom_file: + dicom_file.write(string_json) + + def download( + self, + path_download, + bool_list_resources=[False, False, True, False, False, False], + overwrite=False, + verbose=False + ): + + self.get_list_files(verbose) + self.is_metadata_saved = False + for index, file_obj in enumerate(self.dict_resources.values()): + if self["label"].lower() in ["dicom", "secondary"]: + print(format_message(self.level_verbose + 1, self.level_tab + 1, f"{index} of {self['file_count']}"), + end="", + flush=True) + self.download_dicom( + path_download, file_obj["Name"], overwrite=overwrite, verbose=verbose + ) + + #if self["label"] == "NIFTI": + # self.download_nifti(path_download, file_obj["Name"], overwrite=overwrite, verbose=verbose) + + #if self["label"] == "PNG": + # self.download_png(path_download, file_obj["Name"], overwrite=overwrite, verbose=verbose) + + print(format_message(self.level_verbose, self.level_tab, "\u001b[0K"), end="", flush=True) + print(format_message(self.level_verbose + 1, self.level_tab + 1, "\u001b[0K"), end="", flush=True) diff --git a/xnat2mids/xnat/session.py b/xnat2mids/xnat/session.py new file mode 100644 index 0000000..dd9ae36 --- /dev/null +++ b/xnat2mids/xnat/session.py @@ -0,0 +1,211 @@ + +import csv +from io import StringIO +from xnat2mids.xnat.scan import Scan +from xnat2mids.xnat.session_resource import SessionResource +from xnat2mids.xnat.assessor import Assessors +from xnat2mids.xnat.variables import format_message +from xnat2mids.xnat.variables import dict_uris +from xnat2mids.xnat.request import try_to_request + + +class Session(dict): + def __init__(self, subject, level_verbose, level_tab, **kwargs): + super().__init__(**kwargs) + self["subject"] = subject + self.level_verbose = level_verbose + self.level_tab = level_tab + + def get_list_scans(self, verbose): + output = StringIO() + if verbose: print( + format_message(self.level_verbose, self.level_tab, f"Session: {self['ID']}"), flush=True) + output.write( + try_to_request( + self["subject"]["project"].interface, + self["subject"]["project"].url_xnat + + dict_uris["scans"]( + self["subject"]["project"]["ID"], + self["subject"]["ID"], + self["ID"]) + ).text + ) + output.seek(0) + reader = csv.DictReader(output) + self.dict_scans = dict() + for row in reader: + #print(format_message(16, 5, "")) + #print(row) + # If the "xsiType" key of the session is not equal to + # "xnat: mrSessionData", this may not work in this point. + try: + self.dict_scans[row["ID"]] = Scan(self, self.level_verbose + 1, self.level_tab + 1, **row) + + except KeyError: + continue + output.close() + def get_list_session_resources(self, path_download, overwrite=False, verbose=False): + output = StringIO() + if verbose: print( + format_message(self.level_verbose, self.level_tab, f"Session: {self['ID']}"), flush=True) + u = ( + self["subject"]["project"].url_xnat + + dict_uris["session_resources"]( + self["subject"]["project"]["ID"], + self["subject"]["ID"], + self["ID"] + ) + ) + output.write( + try_to_request( + self["subject"]["project"].interface, + self["subject"]["project"].url_xnat + + dict_uris["session_resources"]( + self["subject"]["project"]["ID"], + self["subject"]["ID"], + self["ID"]) + ).text + ) + output.seek(0) + reader = csv.DictReader(output) + self.dict_resources = dict() + for row in reader: + + try: + self.dict_resources[row["label"]] = SessionResource(self, self.level_verbose + 1, self.level_tab + 1, **row) + + except KeyError: + continue + output.close() + # def get_list_struct_report( + # self, path_download, bool_list_resources, overwrite=False, verbose=False + # ): + # output = StringIO() + # output.write( + # try_to_request( + # self["subject"]["project"].interface, + # self["subject"]["project"].url_xnat + # + dict_uris["struct_reports"]( + # self["subject"]["project"]["ID"], + # self["subject"]["ID"], + # self["ID"]) + # ).text + # ) + # output.seek(0) + # reader = csv.DictReader(output) + # + # if verbose: + # print(format_message(self.level_verbose, self.level_tab, f"Session SR: {self['ID']}"), flush=True) + # for row in reader: + # # id_session=re.search(r'\d+', row["Name"]).group(0) + # try: + # id_session = re.search(r'sr.*', row["Name"]).group(0) + # except KeyError as e: + # print("\033[20;0H\u001b[0K", end="", flush=True) + # print(row) + # print(self["subject"]["project"]["ID"], + # self["subject"]["ID"], + # self["ID"]) + # return + # self.download_struct_report( + # path_download, row["Name"], overwrite=overwrite, verbose=verbose + # ) + # output.close() + # + # def download_struct_report(self, path_download, filename, overwrite=False, verbose=False): + # + # complet_path = ( + # os.path.join( + # path_download, + # dict_path["path_sr"]( + # self["subject"]["ID"], + # self["ID"] + # ) + # ) + # ) + # sr_path = os.path.join(complet_path, filename) + # if not overwrite and os.path.exists(sr_path): + # print("Structural Report exists", flush=True) + # return + # os.makedirs(complet_path, exist_ok=True) + # url_sr = (self["subject"]["project"].url_xnat + # + dict_uri["struct_reports"]( + # self["subject"]["project"]["ID"], + # self["subject"]["ID"], + # self["ID"] + # ).split("?")[0] + os.sep + # + filename + # ) + # # if verbose: print(" Downloading sr file... " + url_sr,flush=True) + # sr = try_to_request( + # self["subject"]["project"].interface, + # url_sr + # ) + # # nifti = self["scan"]["session"]["subject"]["project"].interface.get(url_nifti, allow_redirects=True) + # sr.raise_for_status() + # + # with open(os.path.join(complet_path, filename), 'wb') as sr_file: + # sr_file.write(sr.content) + + def get_list_assessors(self, verbose): + output = StringIO() + if verbose: + print(format_message(self.level_verbose, self.level_tab, f"Assessors: {self['ID']}"), flush=True) + output.write( + try_to_request( + self["subject"]["project"].interface, + self["subject"]["project"].url_xnat + + dict_uris["assessors"]( + self["subject"]["project"]["ID"], + self["subject"]["ID"], + self["ID"] + + ) + ).text + ) + output.seek(0) + reader = csv.DictReader(output) + self.dict_assessors = dict() + for row in reader: + try: + self.dict_assessors[row["ID"]] = Assessors(self, self.level_verbose + 1, self.level_tab + 1, **row) + except Exception as e: + print(e) + # sys.exit(2) + continue + output.close() + + def download(self, path_download, + bool_list_resources=[False, False, True, False, False, False], + overwrite=False, + verbose=False + ): + # print("\033[7;0H\u001b[0K", end="",flush=True) + self.get_list_scans(verbose) + for scan_obj in self.dict_scans.values(): + scan_obj.download( + path_download, bool_list_resources=bool_list_resources, + overwrite=overwrite, verbose=verbose + ) + + # print("\033[18;0H\u001b[0K", end="",flush=True) + #self.get_list_struct_report(path_download, bool_list_resources, overwrite=False, verbose=verbose) + + self.get_list_assessors(verbose) + for resource_obj in self.dict_assessors.values(): + + resource_obj.download( + path_download, + bool_list_resources=bool_list_resources, + overwrite=overwrite, verbose=verbose) + + self.get_list_session_resources(verbose) + for resource_obj in self.dict_resources.values(): + + # resource_obj.download( + # path_download, + # bool_list_resources=bool_list_resources, + # overwrite=overwrite, verbose=verbose) + pass + print(format_message(self.level_verbose, self.level_tab, "\u001b[0K"), end="", flush=True) + diff --git a/xnat2mids/xnat/session_resource.py b/xnat2mids/xnat/session_resource.py new file mode 100644 index 0000000..541feff --- /dev/null +++ b/xnat2mids/xnat/session_resource.py @@ -0,0 +1,118 @@ +import csv +import getpass +import json +import os +import re +import sys +import time +import traceback +from io import StringIO +from shutil import copyfile +import requests +from xnat2mids.xnat.request import try_to_request +from xnat2mids.xnat.variables import types_files_xnat +from xnat2mids.xnat.variables import format_message +from xnat2mids.xnat.variables import reset_terminal +from xnat2mids.xnat.variables import dict_paths +from xnat2mids.xnat.variables import dict_uris + + + + +class SessionResource(dict): + def __init__(self, session, level_verbose, level_tab, **kwargs): + super().__init__(**kwargs) + self["session"] = session + self.level_verbose = level_verbose + self.level_tab = level_tab + + + def get_list_files(self, verbose): + output = StringIO() + if verbose: + print(format_message( + self.level_verbose, self.level_tab, f"Session resource file: {self['label']}"), + end=" ----> ", + flush=True + ) + u = self["session"]["subject"]["project"].url_xnat + dict_uris["session_resource_files"]( + self["session"]["subject"]["project"]["ID"], + self["session"]["subject"]["ID"], + self["session"]["ID"], + self["label"] + ) + output.write( + try_to_request( + self["session"]["subject"]["project"].interface, + self["session"]["subject"]["project"].url_xnat + + dict_uris["session_resource_files"]( + self["session"]["subject"]["project"]["ID"], + self["session"]["subject"]["ID"], + self["session"]["ID"], + self["label"] + ) + ).text + ) + + + output.seek(0) + reader = csv.DictReader(output) + self.dict_resources = dict() + for row in reader: + self.dict_resources[row["Name"]] = dict(**row) + output.close() + + + def download_resource_file(self, path_download, filename, overwrite=False, verbose=False): + complet_path = (path_download + dict_paths["path_resources"]( + self["session"]["subject"]["ID"], + self["session"]["ID"], + self["label"] + ) + ) + + resource_path = os.path.join(complet_path, filename) + if not overwrite and os.path.exists(resource_path): + if verbose: print("resource file already exist") + return + if verbose: print("Downloading resource file...", flush=True) + os.makedirs(complet_path, exist_ok=True) + url_resource = (self["session"]["subject"]["project"].url_xnat + + dict_uris["session_resource_files"]( + self["session"]["subject"]["project"]["ID"], + self["session"]["subject"]["ID"], + self["session"]["ID"], + self["label"] + ).split("?")[0] + "/" + + filename + ) + resource = try_to_request( + self["session"]["subject"]["project"].interface, + url_resource + ) + # png = self["scan"]["session"]["subject"]["project"].interface.get(url_png, allow_redirects=True) + resource.raise_for_status() + + with open(os.path.join(complet_path, filename), 'wb') as png_file: + png_file.write(resource.content) + + def download( + self, + path_download, + bool_list_resources=[False, False, True, False, False, False], + overwrite=False, + verbose=False + ): + + self.get_list_files(verbose) + is_metadata_saved = False + + for index, file_obj in enumerate(self.dict_resources.values()): + self.download_resource_file( + path_download, file_obj["Name"], overwrite=overwrite, verbose=verbose + ) + + print(format_message(self.level_verbose, self.level_tab, "\u001b[0K"), end="", flush=True) + print(format_message(self.level_verbose + 1, self.level_tab + 1, "\u001b[0K"), end="", flush=True) + + diff --git a/xnat2mids/xnat/subject.py b/xnat2mids/xnat/subject.py new file mode 100644 index 0000000..87cd54c --- /dev/null +++ b/xnat2mids/xnat/subject.py @@ -0,0 +1,46 @@ +import csv +from io import StringIO +from xnat2mids.xnat.session import Session +from xnat2mids.xnat.variables import format_message +from xnat2mids.xnat.variables import dict_uris +from xnat2mids.xnat.request import try_to_request + +class Subject(dict): + def __init__(self, level_verbose, level_tab, **kwargs): + super().__init__(**kwargs) + self.level_verbose = level_verbose + self.level_tab = level_tab + + def get_list_experiments(self, verbose): + + output = StringIO() + if verbose: print(format_message(self.level_verbose, self.level_tab, f"Subject: {self['ID']}"), flush=True) + output.write( + try_to_request( + self["project"].interface, + self["project"].url_xnat + + dict_uris["experiments"](self["project"]["ID"], self["ID"]) + ).text + ) + output.seek(0) + reader = csv.DictReader(output) + self.dict_sessions = dict() + for row in reader: + self.dict_sessions[row["label"]] = Session(self, self.level_verbose + 1, self.level_tab + 1, **row) + output.close() + + def download(self, path_download, + bool_list_resources=[False, False, True, False, False, False], + overwrite=False, + verbose=False + ): + print("\033[6;0H\u001b[0K", end="", flush=True) + self.get_list_experiments(verbose) + # move the cursor + for session_obj in self.dict_sessions.values(): + session_obj.download( + path_download, bool_list_resources, + overwrite=overwrite, verbose=verbose + ) + + print(format_message(self.level_verbose, self.level_tab, "\u001b[0K"), end="", flush=True) diff --git a/xnat2mids/xnat/variables.py b/xnat2mids/xnat/variables.py new file mode 100644 index 0000000..d618711 --- /dev/null +++ b/xnat2mids/xnat/variables.py @@ -0,0 +1,55 @@ +types_files_xnat = "sdnbrm" + +reset_terminal = chr(27) + "[2J" + +dict_paths = { + "path_download": lambda s, e, sc, r: "{}/{}/scans/{}/resources/{}/files/".format(s, e, sc, r), + "path_download_roi": lambda s, e, ass, r: "{}/{}/assessors/{}/out/resources/{}/files".format(s, e, ass, r), + "path_resources": lambda s, e, r: "{}/{}/resources/{}/files".format(s, e, r) +} +dict_uris = { + "projects": "data/projects?format=csv", + "subjects": lambda p: "data/projects/{}/subjects?format=csv".format(p), + "experiments": lambda p, s: "data/projects/{}/subjects/{}/experiments?format=csv".format(p, s), + "session_resources": ( + lambda p, s, e: "data/projects/{}/subjects/{}/experiments/{}/resources?format=csv".format(p, s, e) + ), + "session_resource_files": ( + lambda p, s, e, r: "data/projects/{}/subjects/{}/experiments/{}/resources/{}/files?format=csv".format(p, s, e, r) + ), + "assessors": lambda p, s, e: "data/projects/{}/subjects/{}/experiments/{}/assessors?format=csv".format(p, s, e), + "assessors_resources": ( + lambda p, s, e, ass: + "data/projects/{}/subjects/{}/experiments/{}/assessors/{}/out/resources?format=csv".format(p, s, e, ass) + ), + "assessor_resource_roi_files": ( + lambda p, s, e, ass, r: + "data/projects/{}/subjects/{}/experiments/{}/assessors/{}/out/resources/{}/files?format=csv".format( + p, s, e, ass, r + ) + ), + "scans": lambda p, s, e: "data/projects/{}/subjects/{}/experiments/{}/scans?format=csv".format(p, s, e), + "scan_resources": ( + lambda p, s, e, sc: + "data/projects/{}/subjects/{}/experiments/{}/scans/{}/resources?format=csv".format(p, s, e, sc) + ), + "scan_resource_files": ( + lambda p, s, e, sc, r: + "data/projects/{}/subjects/{}/experiments/{}/scans/{}/resources/{}/files?format=csv".format(p, s, e, sc, r) + ) +} + + +# def format_message (line, tab_value, message): +# return "\033[{:d};0H{:s}{:s}".format( +# line, +# " " * tab_value + ("-> " if tab_value > 0 else ""), +# message) + + +#def fformat_message (line, tab_value, message): +# return f"\033[{line};0H{{' ' * tab_value} + ('-> ' if tab_value > 0 else '')}{message}" + +format_message = lambda line, tab_value, message: ( + f"\033[{line};0H{' ' * tab_value + ('-> ' if tab_value > 0 else '')}{message}" +) \ No newline at end of file diff --git a/xnat2mids/xnat/xnat_session.py b/xnat2mids/xnat/xnat_session.py new file mode 100644 index 0000000..584abc5 --- /dev/null +++ b/xnat2mids/xnat/xnat_session.py @@ -0,0 +1,147 @@ +############################################################################### +# Imports +############################################################################### +import csv +import getpass +import os +import progressbar +import requests +from io import StringIO +from xnat2mids.xnat.project import Project +from xnat2mids.xnat.request import try_to_request +from xnat2mids.xnat.variables import format_message +from xnat2mids.xnat.variables import reset_terminal +from xnat2mids.xnat.variables import dict_uris +############################################################################### +# Functions +############################################################################### + + +def list_directory_xnat(project_list): + project_list.sort() + loop = True + project_names = [path_.split(os.sep)[-1] for path_ in project_list] + while loop: + for i, project_item in enumerate(project_names): + if not i % 5: + print(("")) + string = str(i + 1) + ") " + project_item + print("{0:20s}".format(string), end=" ", flush=True) + answer = input("\nChoose the project: ") + answer = str(answer) + answer_list = [] + answer_list_aux = answer.split(' ') + + for ans in answer_list_aux: + if ans.isdigit(): + ans = int(ans) - 1 + if ans >= len(project_names): + print("the number " + ans + " is not corrected, try again", flush=True) + break + else: + answer_list.append(project_names[ans]) + else: + if not (any([ans in path_ for path_ in project_names])): + if ans == "exit": + exit(1) + else: + print("the project " + ans + + " is not corrected, try again") + break + else: + answer_list.append(ans) + else: + loop = False + + return answer_list + +class XnatSession: + + def __init__(self, url_xnat, user=None, password=None): + self.url_xnat = url_xnat + self.user = user + self.password = password + self.level_verbose = 0 + self.level_tab = 0 + + def __enter__(self): + self.connect() + return self + + def __exit__(self, exc_type, exc_val, exc_tb): + self.exit() + + def connect(self): + self.interface = requests.Session() + if self.user and self.password: + self.interface.auth = (self.user, self.password) + else: + if not self.user: + self.user = input("username: ") + self.password = getpass.getpass("Password: ") + self.interface.auth = (self.user, self.password) + + def exit(self): + self.interface.close() + + def get_projects(self, verbose): + output = StringIO() + if verbose: print(self.url_xnat + dict_uris["projects"], flush=True) + output.write( + try_to_request( + self.interface, self.url_xnat + + dict_uris["projects"], + self.level_verbose, + self.level_tab + ).text + ) + output.seek(0) + print(str(output)) + reader = csv.DictReader(output) + self.dict_projects = dict() + for row in reader: + self.dict_projects[row["ID"]] = Project(self.url_xnat, self.interface, self.level_verbose + 5, + self.level_tab + 5, **row) + output.close() + + def show_list_of_project(self, verbose): + """ + This functions allows the user to visualize al projects in xnat aplication + NOT IN USE, NEXT UPLOAD + """ + project_list = [key for key, _ in self.dict_projects.items()] + + answer_list = list_directory_xnat(project_list) + if verbose: print("list of projects to download: {}".format(", ".join(answer_list)), flush=True) + return answer_list + + def download_projects(self, + path_download, + with_department=True, + bool_list_resources=[False, False, True, False, False, False], + overwrite=False, + verbose=False): + self.get_projects(verbose) + + project_list = self.show_list_of_project(verbose) + # clear console + print(reset_terminal, end="", flush=True) + print(format_message(self.level_verbose, self.level_tab, "Projects:"), end="", flush=True) + print(format_message(self.level_verbose + 3, self.level_tab, "Subject:"), end="", flush=True) + # move the cursor + bar_project = progressbar.ProgressBar(maxval=len(project_list), prefix="\033[2;0H").start() + bar_project.update(1) + bar_project.update(0) + + for iter, key in enumerate(project_list): + self.dict_projects[key].download( + path_download, + with_department=with_department, + bool_list_resources=bool_list_resources, + overwrite=overwrite, + verbose=verbose + ) + bar_project.update(iter + 1) + bar_project.finish() + format_message(self.level_verbose, self.level_tab, "") + print(format_message(16, 0, ""), end="", flush=True)