diff --git a/CHANGES.rst b/CHANGES.rst index 2efb357d9..4de64197c 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -1,13 +1,14 @@ -22.0.0 (TBD) -============ +22.0.0 (May 3rd, 2022) +====================== First official release after migrating the repository into the *NiPreps*' organization. A major new feature is the rodent pipeline by Eilidh MacNicol (@eilidhmacnicol). A second major feature is the adoption of the updated carpet plots for BOLD fMRI, contributed by Céline Provins (@celprov). +Virtual memory allocation has been ten-fold cut down, and a complementary resource monitor instrumentation is now available with *MRIQC*. This release updates the Docker image with up-to-date dependencies, updates *MRIQC*'s codebase to the latest *NiTransforms* and includes some minor bugfixes. The code, modules and data related to the MRIQC classifier have been extracted into an -isolated package called *MRIQC-learn*. +isolated package called [*MRIQC-learn*](https://github.com/nipreps/mriqc-learn). Finally, this release also contains a major code style overhaul by Zvi Baratz. The contributor/author crediting system has been adapted to the current draft of the @@ -73,319 +74,321 @@ and @jAchtzehn for their contributions. about *MRIQC*. To do so, please move the author(s) name(s) to the front of the following list: - Zvi Baratz \ :sup:`1`\ ; Christopher J. Markiewicz \ :sup:`2`\ ; Dylan Nielson \ :sup:`3`\ ; Jan Varada \ :sup:`4`\ ; Ross W. Blair \ :sup:`2`\ ; William Triplett \ :sup:`5`\ ; Nikita Beliy \ :sup:`6`\ ; Céline Provins \ :sup:`7`\ ; John A. Lee \ :sup:`8`\ ; Ursula A. Tooley \ :sup:`9`\ ; James D. Kent \ :sup:`10`\ ; Bennet Fauber \ :sup:`11`\ ; Taylor Salo \ :sup:`12`\ ; Mathias Goncalves \ :sup:`2`\ ; Pablo Velasco \ :sup:`13`\ ; Thomas Nichols \ :sup:`14`\ ; Adam Huffman \ :sup:`15`\ ; Joke Durnez \ :sup:`2`\ ; Michael Krause \ :sup:`16`\ ; Satrajit S. Ghosh \ :sup:`17`\ ; Asier Erramuzpe \ :sup:`18`\ ; Benjamin Kay \ :sup:`19`\ ; Daniel Birman \ :sup:`2`\ ; Michael G. Clark \ :sup:`20`\ ; Rafael Garcia-Dias \ :sup:`21`\ ; Sean Marret \ :sup:`4`\ ; Adam G. Thomas \ :sup:`22`\ ; Russell A. Poldrack \ :sup:`2`\ ; Krzysztof J. Gorgolewski \ :sup:`23`\ ; Oscar Esteban \ :sup:`24`\ . + Zvi Baratz \ :sup:`1`\ ; Christopher J. Markiewicz \ :sup:`2`\ ; Eilidh MacNicol \ :sup:`3`\ ; Dylan Nielson \ :sup:`4`\ ; Jan Varada \ :sup:`5`\ ; Ross W. Blair \ :sup:`2`\ ; William Triplett \ :sup:`6`\ ; Nikita Beliy \ :sup:`7`\ ; Céline Provins \ :sup:`8`\ ; John A. Lee \ :sup:`9`\ ; Ursula A. Tooley \ :sup:`10`\ ; James D. Kent \ :sup:`11`\ ; Bennet Fauber \ :sup:`12`\ ; Taylor Salo \ :sup:`13`\ ; Mathias Goncalves \ :sup:`2`\ ; Michael Krause \ :sup:`14`\ ; Pablo Velasco \ :sup:`15`\ ; Thomas Nichols \ :sup:`16`\ ; Adam Huffman \ :sup:`17`\ ; Johannes Achtzehn \ :sup:`18`\ ; Joke Durnez \ :sup:`2`\ ; Satrajit S. Ghosh \ :sup:`19`\ ; Asier Erramuzpe \ :sup:`20`\ ; Benjamin Kay \ :sup:`21`\ ; Daniel Birman \ :sup:`2`\ ; Michael G. Clark \ :sup:`22`\ ; Rafael Garcia-Dias \ :sup:`23`\ ; Sean Marret \ :sup:`5`\ ; Adam G. Thomas \ :sup:`24`\ ; Russell A. Poldrack \ :sup:`2`\ ; Krzysztof J. Gorgolewski \ :sup:`25`\ ; Oscar Esteban \ :sup:`26`\ . Affiliations: - 1. Sagol School of Neuroscience, Tel-Aviv University - 2. Department of Psychology, Stanford University, CA, USA - 3. Section on Clinical and Computational Psychiatry, National Institute of Mental Health, Bethesda, MD, USA - 4. Functional MRI Facility, National Institute of Mental Health, Bethesda, MD, USA - 5. University of Florida: Gainesville, Florida, US - 6. CRC ULiege, Liege, Belgium - 7. Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland - 8. Quansight, Dublin, Ireland - 9. Department of Neuroscience, University of Pennsylvania, PA, USA - 10. Department of Psychology, University of Texas at Austin, TX, USA - 11. University of Michigan, Ann Arbor, USA - 12. Department of Psychology, Florida International University, FL, USA - 13. Center for Brain Imaging, New York University, NY, USA - 14. Oxford Big Data Institute, University of Oxford, Oxford, GB - 15. Department of Physics, Imperial College London, London, UK - 16. Max Planck Institute for Human Development, Berlin, Germany - 17. McGovern Institute for Brain Research, MIT, MA, USA; and Department of Otolaryngology, Harvard Medical School, MA, USA - 18. Computational Neuroimaging Lab, BioCruces Health Research Institute - 19. Washington University School of Medicine, St.Louis, MO, USA - 20. National Institutes of Health, USA - 21. Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK - 22. Data Science and Sharing Team, National Institute of Mental Health, Bethesda, MD, USA - 23. Google LLC - 24. Department of Radiology, Lausanne University Hospital and University of Lausanne - + 1. Sagol School of Neuroscience, Tel-Aviv University + 2. Department of Psychology, Stanford University, CA, USA + 3. Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK + 4. Section on Clinical and Computational Psychiatry, National Institute of Mental Health, Bethesda, MD, USA + 5. Functional MRI Facility, National Institute of Mental Health, Bethesda, MD, USA + 6. University of Florida: Gainesville, Florida, US + 7. CRC ULiege, Liege, Belgium + 8. Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland + 9. Quansight, Dublin, Ireland + 10. Department of Neuroscience, University of Pennsylvania, PA, USA + 11. Department of Psychology, University of Texas at Austin, TX, USA + 12. University of Michigan, Ann Arbor, USA + 13. Department of Psychology, Florida International University, FL, USA + 14. Max Planck Institute for Human Development, Berlin, Germany + 15. Center for Brain Imaging, New York University, NY, USA + 16. Oxford Big Data Institute, University of Oxford, Oxford, GB + 17. Department of Physics, Imperial College London, London, UK + 18. Charité Berlin, Berlin, Germany + 19. McGovern Institute for Brain Research, MIT, MA, USA; and Department of Otolaryngology, Harvard Medical School, MA, USA + 20. Computational Neuroimaging Lab, BioCruces Health Research Institute + 21. Washington University School of Medicine, St.Louis, MO, USA + 22. National Institutes of Health, USA + 23. Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK + 24. Data Science and Sharing Team, National Institute of Mental Health, Bethesda, MD, USA + 25. Google LLC + 26. Department of Radiology, Lausanne University Hospital and University of Lausanne + 0.16.1 (January 30, 2021) -========================= +------------------------- Bug-fix release in 0.16.x series. This PR improves BIDS Derivatives compliance, fixes an issue with reading datasets with subjects of the form ``sub-sXYZ``, and improves compatibility with more recent matplotlib. - * FIX: Participant labels starting with ``[sub]`` cannot be used (#890) - * FIX: Change deprecated ``normed`` to ``density`` in parameters to ``hist()`` (#888) - * ENH: Write derivatives metadata (#885) - * ENH: Add ``--pdb`` option to make debugging easier (#884) +* FIX: Participant labels starting with ``[sub]`` cannot be used (#890) +* FIX: Change deprecated ``normed`` to ``density`` in parameters to ``hist()`` (#888) +* ENH: Write derivatives metadata (#885) +* ENH: Add ``--pdb`` option to make debugging easier (#884) 0.16.0 (January 5, 2021) -======================== +------------------------ New feature release in 0.16.x series. This version removes the FSL dependency from the fMRI workflow. - * FIX: Skip version cache on read-only filesystems (#862) - * FIX: Honor ``$OMP_NUM_THREADS`` environment variable (#848) - * RF: Simplify comprehensions, using easy-to-read var names (#875) - * RF: Free the fMRI workflow from FSL (#842) - * CI: Fix up Circle builds (#876) - * CI: Update machine images on Circle (#874) +* FIX: Skip version cache on read-only filesystems (#862) +* FIX: Honor ``$OMP_NUM_THREADS`` environment variable (#848) +* RF: Simplify comprehensions, using easy-to-read var names (#875) +* RF: Free the fMRI workflow from FSL (#842) +* CI: Fix up Circle builds (#876) +* CI: Update machine images on Circle (#874) 0.15.3 (September 18, 2020) -=========================== -A bugfix release to re-enable setting of `--omp-nthreads/--ants-nthreads`. +--------------------------- +A bugfix release to re-enable setting of ``--omp-nthreads/--ants-nthreads``. - * FIX: omp_nthreads typo (#846) +* FIX: ``omp_nthreads`` typo (#846) 0.15.2 (April 6, 2020) -====================== +---------------------- A bugfix release containing mostly maintenance actions and documentation improvements. This version drops Python 3.5. The core of MRIQC has adopted the config-module pattern from fMRIPrep. With thanks to A. Erramuzpe, @justbennet, U. Tooley, and A. Huffman for contributions. - * MAINT: revise style of all files (except for workflows) (#839) - * MAINT: Clear the clutter of warnings (#838) - * RF: Adopt config module pattern from *fMRIPrep* (#837) - * MAINT: Clear the clutter of warnings (#838) - * MAINT: Drop Python 3.5, simplify linting (#833) - * MAINT: Update to latest Ubuntu Xenial tag (#814) - * MAINT: Centralize all requirements and versions on ``setup.cfg`` (#819) - * MAINT: Use recent Python image to build packages in CircleCI (#808) - * DOC: Improve AQI (and other IQMs) and boxplot whiskers descriptions (#816) - * DOC: Refactor how documentation is built on CircleCI (#818) - * DOC: Corrected a couple of typos in ``--help`` text (#809) +* MAINT: revise style of all files (except for workflows) (#839) +* MAINT: Clear the clutter of warnings (#838) +* RF: Adopt config module pattern from *fMRIPrep* (#837) +* MAINT: Clear the clutter of warnings (#838) +* MAINT: Drop Python 3.5, simplify linting (#833) +* MAINT: Update to latest Ubuntu Xenial tag (#814) +* MAINT: Centralize all requirements and versions on ``setup.cfg`` (#819) +* MAINT: Use recent Python image to build packages in CircleCI (#808) +* DOC: Improve AQI (and other IQMs) and boxplot whiskers descriptions (#816) +* DOC: Refactor how documentation is built on CircleCI (#818) +* DOC: Corrected a couple of typos in ``--help`` text (#809) 0.15.1 (July 26, 2019) -====================== +---------------------- A maintenance patch release updating PyBIDS. - * FIX: FileNotFoundError when MELODIC (``--ica``) does not converge (#800) @oesteban - * MAINT: Migrate MRIQC to a ``setup.cfg`` style of installation (#799) @oesteban - * MAINT: Use PyBIDS 0.9.2+ via niworkflows PR (#796) @effigies +* FIX: ``FileNotFoundError`` when MELODIC (``--ica``) does not converge (#800) @oesteban +* MAINT: Migrate MRIQC to a ``setup.cfg`` style of installation (#799) @oesteban +* MAINT: Use PyBIDS 0.9.2+ via niworkflows PR (#796) @effigies 0.15.0 (April 5, 2019) -====================== +---------------------- A long overdue update, pinning updated versions of `TemplateFlow `__ and `Niworkflows `__. With thanks to @garciadias for contributions. - * ENH: Revision of QI2 (#606) @oesteban - * FIX: Set matplotlib backend early (#759) @oesteban - * FIX: Niworkflows pin <0.5 (#766) @oesteban - * DOC: Update BIDS validation link. (#764) @garciadias - * DOC: Add data sharing agreement (#765) @oesteban - * FIX: Catch uncaught exception in WebAPI upload. (#774) @rwblair - * FIX/DOC: Append new line after dashes in ``mriqc_run`` help text (#777) @rwblair - * ENH: Use TemplateFlow and niworkflows-0.8.x (#782) @oesteban - * FIX: Correctly set WebAPI rating endpoint in BOLD reports. (#785) @oesteban - * FIX: Correctly process values of rating widget (#787) @oesteban +* ENH: Revision of QI2 (#606) @oesteban +* FIX: Set matplotlib backend early (#759) @oesteban +* FIX: Niworkflows pin <0.5 (#766) @oesteban +* DOC: Update BIDS validation link. (#764) @garciadias +* DOC: Add data sharing agreement (#765) @oesteban +* FIX: Catch uncaught exception in WebAPI upload. (#774) @rwblair +* FIX/DOC: Append new line after dashes in ``mriqc_run`` help text (#777) @rwblair +* ENH: Use TemplateFlow and niworkflows-0.8.x (#782) @oesteban +* FIX: Correctly set WebAPI rating endpoint in BOLD reports. (#785) @oesteban +* FIX: Correctly process values of rating widget (#787) @oesteban 0.14.2 (August 20, 2018) -======================== +------------------------ - * [FIX] Preempt pandas resolving Path objects (#746) @oesteban - * [FIX] Codacy issues (#745) @oesteban +* [FIX] Preempt pandas resolving ``Path`` objects (#746) @oesteban +* [FIX] Codacy issues (#745) @oesteban 0.14.1 (August 20, 2018) -======================== +------------------------ - * [FIX] Calculate relative path with sessions (#742) @oesteban - * [ENH] Add a toggle button to rating widget (#743) @oesteban +* [FIX] Calculate relative path with sessions (#742) @oesteban +* [ENH] Add a toggle button to rating widget (#743) @oesteban 0.14.0 (August 17, 2018) -======================== +------------------------ - * [ENH] New feedback widget (#740) @oesteban +* [ENH] New feedback widget (#740) @oesteban 0.13.1 (August 16, 2018) -======================== +------------------------ - * [ENH,FIX] Updates to individual reports, fix table after rating (#739) @oesteban +* [ENH,FIX] Updates to individual reports, fix table after rating (#739) @oesteban 0.13.0 (August 15, 2018) -======================== - - * [MAINT] Overdue refactor (#736) @oesteban - * [FIX] Reorganize outputs (closes #396) - * [ENH] Memory usage - lessons learned with FMRIPREP (#703) - * [FIX] Cannot allocate memory (v 0.9.4) (closes #536) - * [FIX] Drop inoperative ``--report-dir`` flag (#550) - * [FIX] Drop misleading WARNING of the group-level execution (#714) - * [FIX] Expand usernames on input paths (#721) - * [MAINT] More robust naming of derivatives (related to #661) - * [FIX] Do not fail with spurious 4th dimension on T1w (#738) @oesteban - * [ENH] Move on to .tsv files (#737) @oesteban +------------------------ + +* [MAINT] Overdue refactor (#736) @oesteban + * [FIX] Reorganize outputs (closes #396) + * [ENH] Memory usage - lessons learned with FMRIPREP (#703) + * [FIX] Cannot allocate memory (v 0.9.4) (closes #536) + * [FIX] Drop inoperative ``--report-dir`` flag (#550) + * [FIX] Drop misleading WARNING of the group-level execution (#714) + * [FIX] Expand usernames on input paths (#721) + * [MAINT] More robust naming of derivatives (related to #661) + +* [FIX] Do not fail with spurious 4th dimension on T1w (#738) @oesteban +* [ENH] Move on to .tsv files (#737) @oesteban 0.12.1 (August 13, 2018) -======================== +------------------------ - * [FIX] BIDSLayout queries (#735) +* [FIX] ``BIDSLayout`` queries (#735) 0.12.0 (August 09, 2018) -======================== +------------------------ - * [FIX] Reduce tSNR memory requirements (#712) - * [DOC] Fix typos in IQM documentation (#725) - * [PIN] Update MRIQC WebAPI version (#734) - * [BUG] Fix missing library in singularity images (#733) - * [PIN] nipype 1.1.0, niworkflows (#726) +* [FIX] Reduce tSNR memory requirements (#712) +* [DOC] Fix typos in IQM documentation (#725) +* [PIN] Update MRIQC WebAPI version (#734) +* [BUG] Fix missing library in singularity images (#733) +* [PIN] nipype 1.1.0, niworkflows (#726) 0.11.0 (June 05, 2018) -====================== +---------------------- - * RF: Resume external nipype dependency (#715) +* RF: Resume external nipype dependency (#715) 0.10.6 (May 29, 2018) -===================== +--------------------- - * [HOTFIX] Bug #659 +* [HOTFIX] Bug #659 0.10.5 (May 28, 2018) -===================== +--------------------- - * [ENH] Report feedback (#659) +* [ENH] Report feedback (#659) 0.10.4 (March 22, 2018) -======================= +----------------------- - * [ENH] Various improvements to reports (#708) - * [MAINT] Style revision (#704) - * [PIN] pybids 0.5 (#700) - * [ENH] Increase FAST memory limits (#702) +* [ENH] Various improvements to reports (#708) +* [MAINT] Style revision (#704) +* [PIN] pybids 0.5 (#700) +* [ENH] Increase FAST memory limits (#702) 0.10.3 (February 26, 2018) -========================== +-------------------------- - * [ENH] Enable T2w metrics uploads (#696) - * [PIN] Updating niworkflows (#698) - * [DOC] Option -o is outdated for classifier (#697) +* [ENH] Enable T2w metrics uploads (#696) +* [PIN] Updating niworkflows (#698) +* [DOC] Option ``-o`` is outdated for classifier (#697) 0.10.2 (February 15, 2018) -========================== +-------------------------- - * [ENH] Add warning about mounting relative paths (#690) - * [FIX] Sanitize inputs (#687) - * [DOC] Fix documentation to use --version instead of -v (#688) +* [ENH] Add warning about mounting relative paths (#690) +* [FIX] Sanitize inputs (#687) +* [DOC] Fix documentation to use ``--version`` instead of ``-v`` (#688) 0.10.1 -====== +------ - * [FIX] Fixed a bug in reading outputs of 3dFWHMx (#678) +* [FIX] Fixed a bug in reading outputs of ``3dFWHMx`` (#678) 0.9.10 -====== +------ - * [FIX] Updated AFNI to 17.3.03. Resolves errors regarding opening display by 3dSkullStrip (#669) +* [FIX] Updated AFNI to 17.3.03. Resolves errors regarding opening display by ``3dSkullStrip`` (#669) 0.9.9 -===== +----- - * [ENH] Update nipype to fix $DISPLAY problem of AFNI's 3dSkullStrip +* [ENH] Update nipype to fix ``$DISPLAY`` problem of AFNI's ``3dSkullStrip`` 0.9.8 -===== - +----- With thanks to Jan Varada (@jvarada) for the session/run filtering. - * [ENH] Report recall in cross-validation (requested by reviewer) (#633) - * [ENH] Hotfixes to 0.9.7 (#635) - * [FIX] Implement filters for session, run and task of BIDS input (#612) +* [ENH] Report recall in cross-validation (requested by reviewer) (#633) +* [ENH] Hotfixes to 0.9.7 (#635) +* [FIX] Implement filters for session, run and task of BIDS input (#612) 0.9.7 -===== - - * [ENH] Clip outliers in FD and SPIKES group plots (#593) - * [ENH] Second revision of the classifier (#555): - * Set matplotlib plugin to `agg` in docker image - * Migrate scalings to sklearn pipelining system - * Add Satra's feature selection for RFC (with thanks to S. Ghosh for his suggestion) - * Make model selection compatible with sklearn `Pipeline` - * Multiclass classification - * Add feature selection filter based on Sites prediction (requires pinning to development sklearn-0.19) - * Add `RobustLeavePGroupsOut`, replace `RobustGridSearchCV` with the standard `GridSearchCV` of sklearn. - * Choice between `RepeatedStratifiedKFold` and `RobustLeavePGroupsOut` in `mriqc_clf` - * Write cross-validation results to an `.npz` file. - * [ENH] First revision of the classifier (#553): - * Add the possibility of changing the scorer function. - * Unifize labels for raters in data tables (to `rater_1`) - * Add the possibility of setting a custom decision threshold - * Write the probabilities in the prediction file - * Revised `mriqc_clf` processing flow - * Revised labels file for ds030. - * Add IQMs for ABIDE and DS030 calculated with MRIQC 0.9.6. - * ANNOUNCEMENT: Dropped support for Python<=3.4 - * WARNING (#596): - We have changed the default number of threads for ANTs. Using parallelism with ANTs - causes numerical instability on the calculated measures. The most sensitive metrics to this - problem are the kurtosis calculations on the intensities of regions and qi_2. +----- + +* [ENH] Clip outliers in FD and SPIKES group plots (#593) +* [ENH] Second revision of the classifier (#555): + * Set matplotlib plugin to `agg` in docker image + * Migrate scalings to sklearn pipelining system + * Add Satra's feature selection for RFC (with thanks to S. Ghosh for his suggestion) + * Make model selection compatible with sklearn `Pipeline` + * Multiclass classification + * Add feature selection filter based on Sites prediction (requires pinning to development sklearn-0.19) + * Add `RobustLeavePGroupsOut`, replace `RobustGridSearchCV` with the standard `GridSearchCV` of sklearn. + * Choice between `RepeatedStratifiedKFold` and `RobustLeavePGroupsOut` in `mriqc_clf` + * Write cross-validation results to an `.npz` file. +* [ENH] First revision of the classifier (#553): + * Add the possibility of changing the scorer function. + * Unifize labels for raters in data tables (to `rater_1`) + * Add the possibility of setting a custom decision threshold + * Write the probabilities in the prediction file + * Revised `mriqc_clf` processing flow + * Revised labels file for ds030. + * Add IQMs for ABIDE and DS030 calculated with MRIQC 0.9.6. +* ANNOUNCEMENT: Dropped support for Python<-3.4 +* WARNING (#596): + We have changed the default number of threads for ANTs. Using parallelism with ANTs + causes numerical instability on the calculated measures. The most sensitive metrics to this + problem are the kurtosis calculations on the intensities of regions and qi_2. 0.9.6 -===== - - * [ENH] Finished setting up `MRIQC Web API `_ - * [ENH] Better error message when --participant_label is set (#542) - * [FIX] Allow --load-classifier option to be empty in mriqc_clf (#544) - * [FIX] Borked bias estimation derived from Conform (#541) - * [ENH] Test against web API 0.3.2 (#540) - * [ENH] Change the default Web API address (#539) - * [ENH] MRIQCWebAPI: hash fields that may have PI (#538) - * [ENH] Added token authorization to MRIQCWebAPI client (#535) - * [FIX] Do not mask and antsAffineInitializer twice (#534) - * [FIX] Datasets where air (hat) mask is empty (#533) - * [ENH] Integration testing for MRIQCWebAPI (#520) - * [ENH] Use AFNI to calculate gcor (#531) - * [ENH] Refactor derivatives (#530) - * [ENH] New bold-IQM: dummy_trs (non-stady state volumes) (#524) - * [FIX] Order of BIDS components in IQMs CSV table (#525) - * [ENH] Improved logging of mriqc_run (#526) +----- + +* [ENH] Finished setting up `MRIQC Web API `_ +* [ENH] Better error message when --participant_label is set (#542) +* [FIX] Allow --load-classifier option to be empty in mriqc_clf (#544) +* [FIX] Borked bias estimation derived from Conform (#541) +* [ENH] Test against web API 0.3.2 (#540) +* [ENH] Change the default Web API address (#539) +* [ENH] MRIQCWebAPI: hash fields that may have PI (#538) +* [ENH] Added token authorization to MRIQCWebAPI client (#535) +* [FIX] Do not mask and antsAffineInitializer twice (#534) +* [FIX] Datasets where air (hat) mask is empty (#533) +* [ENH] Integration testing for MRIQCWebAPI (#520) +* [ENH] Use AFNI to calculate gcor (#531) +* [ENH] Refactor derivatives (#530) +* [ENH] New bold-IQM: dummy_trs (non-stady state volumes) (#524) +* [FIX] Order of BIDS components in IQMs CSV table (#525) +* [ENH] Improved logging of mriqc_run (#526) 0.9.5 -===== +----- - * [ENH] Refactored structural metrics calculation (#513) - * [ENH] Calculate rotation mask (#515) - * [ENH] Intensity harmonization in the anatomical workflow (#510) - * [ENH] Set N4BiasFieldCorrection number of threads (#506) - * [ENH] Convert FWHM in pixel units (#503) - * [ENH] Add MRIQC client for feature crowdsourcing (#464) - * [DOC] Fix functional feature labels in documentation (docs_only) (#507) - * [FIX] New implementation for the rPVE feature (normalization, left-tail values) (#505) - * [ENH] Parse BIDS selectors (run, task, etc.), improve CLI (#504) +* [ENH] Refactored structural metrics calculation (#513) +* [ENH] Calculate rotation mask (#515) +* [ENH] Intensity harmonization in the anatomical workflow (#510) +* [ENH] Set N4BiasFieldCorrection number of threads (#506) +* [ENH] Convert FWHM in pixel units (#503) +* [ENH] Add MRIQC client for feature crowdsourcing (#464) +* [DOC] Fix functional feature labels in documentation (docs_only) (#507) +* [FIX] New implementation for the rPVE feature (normalization, left-tail values) (#505) +* [ENH] Parse BIDS selectors (run, task, etc.), improve CLI (#504) 0.9.4 -===== - - * ANNOUNCEMENT: Dropped Python 2 support - * [ENH] Use versioneer to handle versions (#500) - * [ENH] Speed up spatial normalization (#495) - * [ENH] Resampling of hat mask and TPMs with linear interp (#498) - * [TST] Build documentation in CircleCI (#484) - * [ENH] Use full-resolution T1w images from ABIDE (#486) - * [TST] Parallelize tests (#493) - * [TST] Binding /etc/localtime stopped working in docker 1.9.1 (#492) - * [TST] Downgrade docker to 1.9.1 in circle (build_only) (#491) - * [TST] Check for changes in intermediate nifti files (#485) - * [FIX] Erroneous flag --n_proc in CircleCI (#490) - * [ENH] Add build_only tag to circle builds (#488) - * [ENH] Update Dockerfile (#482) - * [FIX] Ignore --profile flag with Linear plugin (#483) - * [DOC] Deep revision of the documentation (#479) - * [ENH] Minor improvements: SpatialNormalization and segmentation (#472) - * [ENH] Fixed typo for neurodebian install via apt-get (#478) - * [ENH] Updating fs2gif script (#465) - * [ENH] RF: Use niworkflows.interface.SimpleInterface (#468) - * [ENH] Add reproducibility of metrics tracking (#466) +----- + +* ANNOUNCEMENT: Dropped Python 2 support +* [ENH] Use versioneer to handle versions (#500) +* [ENH] Speed up spatial normalization (#495) +* [ENH] Resampling of hat mask and TPMs with linear interp (#498) +* [TST] Build documentation in CircleCI (#484) +* [ENH] Use full-resolution T1w images from ABIDE (#486) +* [TST] Parallelize tests (#493) +* [TST] Binding /etc/localtime stopped working in docker 1.9.1 (#492) +* [TST] Downgrade docker to 1.9.1 in circle (build_only) (#491) +* [TST] Check for changes in intermediate nifti files (#485) +* [FIX] Erroneous flag --n_proc in CircleCI (#490) +* [ENH] Add build_only tag to circle builds (#488) +* [ENH] Update Dockerfile (#482) +* [FIX] Ignore --profile flag with Linear plugin (#483) +* [DOC] Deep revision of the documentation (#479) +* [ENH] Minor improvements: SpatialNormalization and segmentation (#472) +* [ENH] Fixed typo for neurodebian install via apt-get (#478) +* [ENH] Updating fs2gif script (#465) +* [ENH] RF: Use niworkflows.interface.SimpleInterface (#468) +* [ENH] Add reproducibility of metrics tracking (#466) Release 0.9.3 -============= +------------- * [ENH] Reafactor of the Dockerfile to improve transparency, reduce size, and enable injecting code in Singularity (#457) * [ENH] Make more the memory consumption estimates of each processing step more conservative to improve robustness (#456) * [FIX] Minor documentation cleanups (#461) Release 0.9.2 -============= +------------- * [ENH] Optional ICA reports for identifying spatiotemporal artifacts (#412) * [ENH] Add --profile flag (#435) @@ -394,15 +397,14 @@ Release 0.9.2 * [ENH] Make FSL and AFNI motion correction more comparable by using the same scheme for defining the reference image (#444) * [FIX] Temporarily disabling T1w quality classifier until it can be retrained on new measures (#447) - Release 0.9.1 -============= +------------- * [ENH] Add mriqc version and input image hash to IQMs json file (#432) * [FIX] Affine and warp transforms are now applied in the correct order (#431) Release 0.9.0-2 -=============== +--------------- * [ENH] Revise Docker paths (#429) * [FIX] Greedy participant selection (#426) @@ -410,7 +412,7 @@ Release 0.9.0-2 * [FIX] Amends sloppy PR #425 (#428) Release 0.9.0-1 -=============== +--------------- * [FIX] BOLD reports clipped IQMs after spikes_num (#425) * [FIX] Unicode error writing group reports (#424) @@ -430,7 +432,7 @@ Release 0.9.0-1 * [ENH] Add T1w classifier (#389) Release 0.9.0-0 -=============== +--------------- * [FIX] Remove non-repeatable step from pipeline (#369) * [ENH] Improve group level command line, with more informative output when no IQMs are found for a modality (#372) @@ -446,13 +448,13 @@ Release 0.9.0-0 Release 0.8.9 -============= +------------- * [ENH] Added registration svg panel to reports (#297) Release 0.8.8 -============= +------------- * [FIX] Bug translating int16 to uint8 in conform image. * [FIX] Error in ConformImage interface (#297) @@ -481,7 +483,7 @@ Release 0.8.8 * [ENH] Add AFNI's outlier count to carpet plot confound charts (#230) Release 0.8.7 -============= +------------- * [ENH] Anatomical Group reports in html (#227) * [ENH] Add kurtosis to summary statistics (#224) @@ -489,7 +491,7 @@ Release 0.8.7 * [ENH] Anatomical workflow refactor (#219). Release 0.8.6 -============= +------------- * [FIX, CRITICAL] Do not chmod in Docker internal scripts * [FIX] Error creating derivatives folder @@ -501,7 +503,7 @@ Release 0.8.6 * [FIX] QI2 is skipped if background intensity is not appropriate (#147) Release 0.8.5 -============= +------------- * [FIX] Error inverting the T1w-to-MNI warping (#146) * [FIX] TypeError computing DVARS (#145) @@ -519,19 +521,19 @@ Release 0.8.5 and updated options (#115) Release 0.8.4 -============= +------------- * [ENH] PDF reports now use RST templates and jinja2 (#109) * [FIX] Single-session-multiple-run anatomical files were not correctly located (#112) Release 0.8.3 -============= +------------- * [DOC] Added examples of the PDF reports (#107) * [FIX] Fixed problems with Python 3 when generating reports. Release 0.8.2 -============= +------------- * [ENH] Python 3 compatibility (#99) * [ENH] Add JSON settings file for ANTS (#95) @@ -543,31 +545,26 @@ Release 0.8.2 * [AGAVE] Added an agave app description generator (#84) Release 0.3.0 -============= +------------- * [ENH] Updated CircleCI and Docker to use the version 2.1.0 of ANTs compiled by their developers. * [ENH] New anatomical workflows to compute the air mask (#56) -Release 0.2.0 -============= - Release 0.1.0 -============= +------------- * [FIX] #55 * [ENH] Added rotation of output csv files if they exist - Release 0.0.2 -============= +------------- * [ENH] Completed migration from QAP * [ENH] Integration with ReadTheDocs * [ENH] Submission to PyPi - Release 0.0.1 -============= +------------- * Basic mriqc functionality