diff --git a/404.html b/404.html index 9f1e20a..c782266 100644 --- a/404.html +++ b/404.html @@ -1,3 +1,2 @@ -404 Page not found | UQ AIS XNAT

Not found

Oops! This page doesn't exist. Try going back to our home page.

You can learn how to make a 404 page like this in Custom 404 Pages.

- - \ No newline at end of file +404 Page not found | UQ AIS XNAT +

Not found

Oops! This page doesn't exist. Try going back to our home page.

You can learn how to make a 404 page like this in Custom 404 Pages.

\ No newline at end of file diff --git a/_print/docs/user-guides/create-xnat-project/index.html b/_print/docs/user-guides/create-xnat-project/index.html index 763a293..dc63185 100644 --- a/_print/docs/user-guides/create-xnat-project/index.html +++ b/_print/docs/user-guides/create-xnat-project/index.html @@ -1 +1,2 @@ -https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/_print/ \ No newline at end of file +https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/_print/ + \ No newline at end of file diff --git a/_print/docs/user-guides/login-to-xnat/index.html b/_print/docs/user-guides/login-to-xnat/index.html index 2394d31..d9fe04b 100644 --- a/_print/docs/user-guides/login-to-xnat/index.html +++ b/_print/docs/user-guides/login-to-xnat/index.html @@ -1 +1,2 @@ -https://docs.xnat.rcc.uq.edu.au/docs/user-guides/logging-into-xnat/_print/ \ No newline at end of file +https://docs.xnat.rcc.uq.edu.au/docs/user-guides/logging-into-xnat/_print/ + \ No newline at end of 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code{font-size:14px;padding:5px 7px;border-radius:4px;background:rgba(0,0,0,.05);font-family:monospace;font-weight:600;color:#9012fe}.swagger-ui .markdown pre>code,.swagger-ui .renderedMarkdown pre>code{display:block} - -/*# sourceMappingURL=swagger-ui.css.map*/ \ No newline at end of file diff --git a/docs/_print/index.html b/docs/_print/index.html index 24a6e26..659cee8 100644 --- a/docs/_print/index.html +++ b/docs/_print/index.html @@ -1,9 +1,10 @@ -Documentation | UQ AIS XNAT

1 - User Guides

For Researchers and Collaborators

1.1 - Getting Started

Signing up and getting started with UQ-RCC XNAT

1.1.1 - UQ members

For UQ Staff and Students

Signing into XNAT


Step 1

Open https://xnat.rcc.uq.edu.au

Step 2

Login in with the AAF Single sign-on button (shown below).

Follow the AAF login process for your organisation

Step 3

After the AAF sign-in, you should be redirected back to XNAT (Example below)

There will be no projects listed when signing in for the first-time, as your user account would have just been created.

Proceed to to next section for setting up an XNAT project

Creating XNAT project


For UQ users, XNAT uses UQ-RDM HPC collections for storage allocation.
For any general questions about UQ-RDM, please refer to the library guides

Step 1

Before creating an XNAT project, you’ll require a UQ-RDM HPC Collection

  • HPC collections ends with -Q and a 4-digit numerical identifier (e.g. PROJ001-Q0189)
  • Non-HPC collections end with -A (e.g. PROJ001-A0189) or -I (PROJ001-I0189)

To create a new UQ-RDM HPC Collection, proceed with the following

Open https://rdm.uq.edu.au/create-record and sign-in

Fill in the record as per your project details

REQUEST DATA STORAGE when complete

Move on to the next step after the RDM collection is provisioned
You should have an RDM collection name ready (e.g. PROJ001-Q0189)

Step 2

Open a ticket with RCC support

Example below (replace __________ with your details)

Subject: Create XNAT project __________

Hello RCC support -Can we create an XNAT project for RDM collection __________

Step 3

The support ticket will inform you when the project is set up.

  • An XNAT project will be created with the matching name (e.g. PROJ001-Q0189)
  • An xnat directory will be created in the RDM collection for storing the XNAT data files
  • Please do not write or modify anything under the xnat directory

XNAT Project setup typically takes around ~24 hours from ticket submission
An automated email from XNAT will be sent through when project is ready, and your user has been added

1.1.2 - Other AAF members

Other AAF members

This guide is for users from Australian Universities and AAF member organisations, including:

  • QUT, Griffith, CQU, JCU, USQ, USC
  • CSIRO, Australian Universities
  • AAF VHO accounts

Other AAF members usually require UQ AIS XNAT access for:

  • Management of data acquisition from sites such as CAI, HIRF, TRI
  • Collaborating on projects managed on UQ AIS XNAT

Full list of AAF members found here
For all other organisations, use the Non-AAF members guide

Signing into XNAT


Step 1

Open https://xnat.rcc.uq.edu.au

Step 2

Login in with the AAF Single sign-on button (See below).

Follow the AAF login process for your organisation

Step 3

After the AAF sign-in, you should be redirected back to XNAT (Example below)

There will be no projects listed when signing in for the first-time, as your user account would have just been created.

Accessing XNAT Project


If you are Acquiring data at HIRF, CAI or TRI

  • The respective facility will organise the project creation.
  • You will receive a follow up email when access has been granted
  • Contact rcc-support@uq.edu.au if you have not received access within 5 working days

If you are collaborating on an existing XNAT project

  • Contact the project lead to grant you access to the XNAT project

1.1.3 - Non-AAF members

Non-University, non-AAF members and other users

This is for users from non-AAF member organisations, including:

  • QLD Health, TRI, QIMR, QLD Xray

Non-AAF members usually require XNAT access for:

  • Management of data acquisition from sites such as CAI, HIRF, TRI
  • Collaborating on projects managed on UQ-RCC XNAT

XNAT uses AAF for login. QCIF/QRIScloud can provide AAF Virtual Home (VHO) accounts for non-AAF users.

Creating an AAF VHO account


Step 1

Open a ticket with RCC support to request an AAF account

Example below (replace __________ with your details)

Subject: XNAT AAF account for project __________

Hello RCC support -I require an AAF account to access the UQ AIS XNAT service
My details are below
Organisation: __________
Data Acquisition Site: __________

Step 2

AAF’s VHO account will return an email regarding the VHO account registration process

Step 3

After account is provisioned, continue on to the Signing into XNAT guide

Signing into XNAT


Step 1

Open https://xnat.rcc.uq.edu.au

Step 2

Login in with the AAF Single sign-on button (See below).

Select the AAF Virtual Home option (See below) and login with your AAF VHO credentials.

+Documentation | UQ AIS XNAT +

1 - User Guides

For Researchers and Collaborators

1.1 - Getting Started

Signing up and getting started with UQ-RCC XNAT

1.1.1 - UQ members

For UQ Staff and Students

Signing into XNAT


Step 1

Open https://xnat.rcc.uq.edu.au

Step 2

Login in with the AAF Single sign-on button (shown below).

Follow the AAF login process for your organisation

Step 3

After the AAF sign-in, you should be redirected back to XNAT (Example below)

There will be no projects listed when signing in for the first-time, as your user account would have just been created.

Proceed to to next section for setting up an XNAT project

Creating XNAT project


For UQ users, XNAT uses UQ-RDM HPC collections for storage allocation.
For any general questions about UQ-RDM, please refer to the library guides

Step 1

Before creating an XNAT project, you’ll require a UQ-RDM HPC Collection

  • HPC collections ends with -Q and a 4-digit numerical identifier (e.g. PROJ001-Q0189)
  • Non-HPC collections end with -A (e.g. PROJ001-A0189) or -I (PROJ001-I0189)

To create a new UQ-RDM HPC Collection, proceed with the following

Open https://rdm.uq.edu.au/create-record and sign-in

Fill in the record as per your project details

REQUEST DATA STORAGE when complete

Move on to the next step after the RDM collection is provisioned
You should have an RDM collection name ready (e.g. PROJ001-Q0189)

Step 2

Open a ticket with RCC support

Example below (replace __________ with your details)

Subject: Create XNAT project __________

Hello RCC support +Can we create an XNAT project for RDM collection __________

Step 3

The support ticket will inform you when the project is set up.

  • An XNAT project will be created with the matching name (e.g. PROJ001-Q0189)
  • An xnat directory will be created in the RDM collection for storing the XNAT data files
  • Please do not write or modify anything under the xnat directory

XNAT Project setup typically takes around ~24 hours from ticket submission
An automated email from XNAT will be sent through when project is ready, and your user has been added

1.1.2 - Other AAF members

Other AAF members

This guide is for users from Australian Universities and AAF member organisations, including:

  • QUT, Griffith, CQU, JCU, USQ, USC
  • CSIRO, Australian Universities
  • AAF VHO accounts

Other AAF members usually require UQ AIS XNAT access for:

  • Management of data acquisition from sites such as CAI, HIRF, TRI
  • Collaborating on projects managed on UQ AIS XNAT

Full list of AAF members found here
For all other organisations, use the Non-AAF members guide

Signing into XNAT


Step 1

Open https://xnat.rcc.uq.edu.au

Step 2

Login in with the AAF Single sign-on button (See below).

Follow the AAF login process for your organisation

Step 3

After the AAF sign-in, you should be redirected back to XNAT (Example below)

There will be no projects listed when signing in for the first-time, as your user account would have just been created.

Accessing XNAT Project


If you are Acquiring data at HIRF, CAI or TRI

  • The respective facility will organise the project creation.
  • You will receive a follow up email when access has been granted
  • Contact rcc-support@uq.edu.au if you have not received access within 5 working days

If you are collaborating on an existing XNAT project

  • Contact the project lead to grant you access to the XNAT project

1.1.3 - Non-AAF members

Non-University, non-AAF members and other users

This is for users from non-AAF member organisations, including:

  • QLD Health, TRI, QIMR, QLD Xray

Non-AAF members usually require XNAT access for:

  • Management of data acquisition from sites such as CAI, HIRF, TRI
  • Collaborating on projects managed on UQ-RCC XNAT

XNAT uses AAF for login. QCIF/QRIScloud can provide AAF Virtual Home (VHO) accounts for non-AAF users.

Creating an AAF VHO account


Step 1

Open a ticket with RCC support to request an AAF account

Example below (replace __________ with your details)

Subject: XNAT AAF account for project __________

Hello RCC support +I require an AAF account to access the UQ AIS XNAT service
My details are below
Organisation: __________
Data Acquisition Site: __________

Step 2

AAF’s VHO account will return an email regarding the VHO account registration process

Step 3

After account is provisioned, continue on to the Signing into XNAT guide

Signing into XNAT


Step 1

Open https://xnat.rcc.uq.edu.au

Step 2

Login in with the AAF Single sign-on button (See below).

Select the AAF Virtual Home option (See below) and login with your AAF VHO credentials.

-

Step 3

After the AAF sign-in, you should be redirected back to XNAT (Example below)

There will be no projects listed when signing in for the first-time, as your user account would have just been created.

Accessing XNAT Project


If you are Acquiring data at HIRF, CAI or TRI

  • The respective facility will organise the project creation.
  • You will receive a follow up email when access has been granted
  • Contact rcc-support@uq.edu.au if you have not received access within 5 working days

If you are collaborating on an existing XNAT project

  • Contact the project lead to grant you access to the XNAT project

1.1.4 - HIRF users

For users acquiring data at HIRF

Data acquired at HIRF can be sent to the UQ-RCC XNAT repository

To get started, refer to the relevant guide below:

If you have any questions, contact rcc-support@uq.edu.au or HIRFAdministration@health.qld.gov.au

1.2 - Logging into XNAT

Logging into XNAT

AAF

If your organisation is part of the Australian Access Federation (AAF), you can use your AAF credentials to sign up. See here

For more details on the Australian Access Federation, see https://aaf.edu.au

RCC Authenticate

To use this login, you would have received an email from a UQ XNAT administrator with the login information.

1.2.1 - AAF login

Login using Australian Access Federation (AAF)

If your organisation is part of the Australian Access Federation (AAF), you can use your AAF credentials to sign up. Follow the steps below to sign-up/login using AAF.

  1. Open https://xnat.rcc.uq.edu.au
  2. Login in with the AAF Single sign-on button (shown below)

This will take you to your XNAT home page.

1.2.2 - RCC Authenticate

Login using RCC Authenticate

To use this login, you would have received an email from a UQ XNAT administrator with the login information.

  1. Login in with the RCC Authenticate button (shown below)

  1. You’ll be taken to a UQ RCC SERVICES (shown below)

  1. Enter your user name and password to sign in. +

    Step 3

    After the AAF sign-in, you should be redirected back to XNAT (Example below)

    There will be no projects listed when signing in for the first-time, as your user account would have just been created.

    Accessing XNAT Project


    If you are Acquiring data at HIRF, CAI or TRI

    • The respective facility will organise the project creation.
    • You will receive a follow up email when access has been granted
    • Contact rcc-support@uq.edu.au if you have not received access within 5 working days

    If you are collaborating on an existing XNAT project

    • Contact the project lead to grant you access to the XNAT project

1.1.4 - HIRF users

For users acquiring data at HIRF

Data acquired at HIRF can be sent to the UQ-RCC XNAT repository

To get started, refer to the relevant guide below:

If you have any questions, contact rcc-support@uq.edu.au or HIRFAdministration@health.qld.gov.au

1.2 - Logging into XNAT

Logging into XNAT

AAF

If your organisation is part of the Australian Access Federation (AAF), you can use your AAF credentials to sign up. See here

For more details on the Australian Access Federation, see https://aaf.edu.au

RCC Authenticate

To use this login, you would have received an email from a UQ XNAT administrator with the login information.

1.2.1 - AAF login

Login using Australian Access Federation (AAF)

If your organisation is part of the Australian Access Federation (AAF), you can use your AAF credentials to sign up. Follow the steps below to sign-up/login using AAF.

  1. Open https://xnat.rcc.uq.edu.au
  2. Login in with the AAF Single sign-on button (shown below)

This will take you to your XNAT home page.

1.2.2 - RCC Authenticate

Login using RCC Authenticate

To use this login, you would have received an email from a UQ XNAT administrator with the login information.

  1. Login in with the RCC Authenticate button (shown below)

  1. You’ll be taken to a UQ RCC SERVICES (shown below)

  1. Enter your user name and password to sign in. This will take you to your XNAT home page.

1.2.3 - Alias tokens

Alias tokens

AAF is used for logging into the XNAT website itself.

But there are a lot of tools and services that will require a connect to the XNAT server externally

These could include

  • Windows or Mac desktop clients, like XNAT Desktop
  • Command line tools such as xnatpy, pyxnat, xnatutils etc
  • XSYNC

All of these tools and services need a way to authenticating to your XNAT account without AAF.

An alias token is a time-limited, long, randomised username and password used for authenticating from external services, without compromising your AAF account or credentials. They can be generated and revoked easily

We’ll look at how to generate them next

Generating Alias tokens

To access the alias token Click your name on the top right of the website. This will take you to your user profile management page

Then click the “Manage Alias Tokens” option

There, you’ll find the option to “Create an Alias Token”

When you create the alias token, it will appear as a new entry

Alias tokens expire 60 days after creation @@ -18,7 +19,7 @@ Click modify, and then submit for the changes to take effect.

Just note, subject renaming can take a few minutes to take effect

1.3.3 - Sessions

Managing Scan Sessions

Sessions are divided into three types, based on modality information extracted from the DICOM metadata

  • MR
  • CT
  • PET

The following is an example MR session

Editing Sessions

We can edit session details and metadata from the actions panel on the right

Here we can change some of the key properties of the sessions, such as

  • Change session name
  • Move sessions to other projects
  • Move sessions to other subjects
  • Create a new subject, and move session to that subject
  • Fix invalid or blank session names

1.3.3.1 - Scans

Accessing individual Scans

The Scans themselves are listed at the bottom with the relevant series descriptions and other information If you hover over one of them, and click the highlighted view details button. This will open up a more details and an image preview window

Here we can also view View DICOM headers

And see the DICOM headers as shown on the right

1.3.4 - Search

Search across Projects, Subjects and Sessions

You can search across Projects, Subjects or Sessions And Sessions are broken up into MR, PET and CT

For instance, we can fill a couple of fields on the MR Sessions search -You don’t have to specify all the fields

And XNAT will provide a list of results.

1.4 - Managing Data

Managing Data

1.4.1 - Downloading Data

Downloading data from XNAT Projects
  1. Navigate to Scan or Session (See guide on browsing data)
  2. Select Download from controls on top right.
  3. Use the following settings for downloading dataset as zip text

For further information refer to the XNAT official guide on downloading data

1.4.1.1 - Zip Download

Downloading data as Zip using the XNAT UI

The Project, Subject and Sessions page has the option to Download Images from the right hand side menu

+You don’t have to specify all the fields

And XNAT will provide a list of results.

1.4 - Managing Data

Managing Data

1.4.1 - Downloading Data

Downloading data from XNAT Projects
  1. Navigate to Scan or Session (See guide on browsing data)
  2. Select Download from controls on top right.
  3. Use the following settings for downloading dataset as zip text

For further information refer to the XNAT official guide on downloading data

1.4.1.1 - Zip Download

Downloading data as Zip using the XNAT UI

The Project, Subject and Sessions page has the option to Download Images from the right hand side menu

Select Option 2: ZIP download

Filter out the Session and scans from the first two columns and select Submit

1.4.1.2 - Desktop client

Downloading data using the XNAT Desktop client

The XNAT Desktop client is maintained by the XNAT development team. For information see the link below.

XNAT Desktop client
https://www.xnat.org/download/desktop-client/

Install client

Download and install the client for you operating system

Download images

The Project, Subject and Sessions page has the option to Download Images from the right hand side menu

Select Option 1: Download via Desktop Client

Click Download Via App

Select a local destination folder

Download should start, and progress can be monitored

1.4.1.3 - Download Scan

Downloading induvidual Scans using the XNAT UI

Induvidual scans can be downloaded from the Sessions page

Multiple scans can be selected and downloaded using Bulk Actions

1.4.2 - Viewing Images

Viewing Images in the XNAT OHIF Viewer

XNAT OHIF Viewer

AIS XNAT instances come with the XNAT OHIF Image viewer Which is a plugin developed by the Institute for Cancer Research in London

Just note, if your publication uses the OHIF viewer, they have an article for citation. @@ -49,7 +50,7 @@

Once this element is added proxy server settings can be updated in the CTP Launcher GUI
  • Add CTP the anonymiser script
    • Copy CTP/scripts/DicomServiceAnonymizer.script to CTP/scripts/dicom-anonymizer-sender.script
    • Add the PROJECTID parameter to the list of parameters at the start of the file
      • <p t="PROJECTID">my xnat project id</p>
    • Change the PatientComments element 0010,4000 to set XNAT project routing info
      • @always()@append(){Project:@param(@PROJECTID) Subject:@contents([0010,0010]) Session:@contents([0008,0050])}
    • Review/set other parameters at the start of the file
      • PROFILENAME, eg. AIS-Clinical-Site-210604
      • DATEINC, eg. 0
      • PROJECTNAME, SITEID, SITENAME, TRIALNAME, TRIALSPONSOR as required
    • Optional: review script to check anonymisation settings are appropriate
  • Start CTP GUI
    java -jar Launcher.jar
     
  • Click the CTP “Start” button
  • Click the “CTP Home Page” button to open the Web UI
    • If the browser can’t connect, check CTP is not already running, or try changing the Server port
  • Login
    • Top RHS banner should show “Welcome admin”
  • Optional: click “User Manager” to change default usernames/passwords
  • Optional: click “DICOM Anonymizer” to view/edit anonymiser script
  • Unzip DCMTK and MrBrain dicom sample
  • Try sending an dicom to CTP using dcmtk
    cd dcmtk-3.6.5-win64-dynamic/bin
     dcmsend localhost 25055 ../../dicom_viewer_Mrbrain/MRBRAIN.DCM
    -
  • Login to the XNAT server with an admin account to view Prearchive
    • Use “Upload” → “Go to prearchive”
    • DICOM should appear in “Receiving” status, with project id assigned from step 6
      • Optional: non-admin users need to search by subject/etc
    • Use Refresh to check when “Ready” or it disappears from list (as it has been routed to the project)
    • Debugging: use dcm2xml from DCMTK to check anonymised dicom file under CTP/roots/FileAfterAnonymization25055
  • Logout and login with the new XNAT user from step 1
  • Navigate to the project set in step 6
    • You should see the dicom listed as subject “1737775597”
  • Use subject “1737775597” → “MR Session” → “View Images” to view the uploaded image
  • Try a dicom send from the scanner using PC address and port 25055 (check windows firewall settings?)
  • Enable CTP as a Windows Service. Instructions here
  • Further information

    If you need a different commit of CTP-installer

    git clone https://github.com/johnperry/CTP
    +
  • Login to the XNAT server with an admin account to view Prearchive
    • Use “Upload” → “Go to prearchive”
    • DICOM should appear in “Receiving” status, with project id assigned from step 6
      • Optional: non-admin users need to search by subject/etc
    • Use Refresh to check when “Ready” or it disappears from list (as it has been routed to the project)
    • Debugging: use dcm2xml from DCMTK to check anonymised dicom file under CTP/roots/FileAfterAnonymization25055
  • Logout and login with the new XNAT user from step 1
  • Navigate to the project set in step 6
    • You should see the dicom listed as subject “1737775597”
  • Use subject “1737775597” → “MR Session” → “View Images” to view the uploaded image
  • Try a dicom send from the scanner using PC address and port 25055 (check windows firewall settings?)
  • Enable CTP as a Windows Service. Instructions here
  • Further information

    If you need a different commit of CTP-installer

    git clone https://github.com/johnperry/CTP
     cd CTP/products
     git checkout <commit> CTP-Installer.jar
     

    If you need other AIS CTP config files

    git clone https://github.com/Australian-Imaging-Service/configuration.git
    @@ -57,9 +58,9 @@
     

    CTP documentation links:

    MIRC CTP Wiki

    CTP DICOM Anonymizer

    2.1.2 - Proxy Server Settings

    Updating CTP Proxy Server Settings

    If CTP uses a proxy server for internet access, you can update the CTP proxy server settings on Windows as follows

    1. Stop the CTP Windows service

      • If you already have a Services short-cut on the Windows desktop, double-click the short-cut to start Windows Services
      • If not, click the Windows start button, start typing “services” and the Services App icon should appear
        • Click the Services App icon to start Windows Services
      • Locate the CTP service in the list of services, right-click and select Stop from the context menu
    2. Start the CTP Launcher

      • If you already have a CTP Launcher short-cut on the Windows desktop, double-click the short-cut to start the CTP Launcher
      • If not, locate the CTP service in the list of services again, right-click and select Properties from the context menu
        1. Use the Path to executable entry to find the installation folder for CTP. It will be in the form <install folder>\windows\CTP.exe
        2. Open a Windows Command prompt window
          1. Click the Windows Start button, start typing “cmd” and the Command Prompt App icon should appear
          2. Click the Command Prompt App icon to start the Command Prompt
        3. In the Command Prompt window, enter the following commands
        cd <install folder>
         java -jar Launcher.jar
         
    3. Navigate to the CTP Launcher Configuration tab

    4. Use the navigation panel on the left to select Configuration -> Server -> ProxyServer -text

    5. Update the proxy server settings in the right panel as required. You can set an IP address or host name in the proxyIPAddress field

    6. Select File -> Save from the main menu bar to save your changes

    7. Close the CTP Launcher using the Window close button at the top right

    8. Close the Command Prompt window

    9. Re-Start the CTP Windows service using Windows Services

      Locate the CTP service in the list of services, right-click and select Start from the context menu

      text

    Troubleshooting

    • If the CTP Windows service Stop is disabled, try restarting Windows Services as administrator by right-clicking the icon and selecting Run as administrator

    Further information

    2.1.3 - Windows Service

    Enabling CTP as a Windows Service

    The CTP install.bat script uses Apache procrun. Use the following steps to enable CTP as a Windows service, including an update to use a JRE other than system default (leave out step 2 if using the system default JRE)

    1. Install CTP
      java -jar CTP-installer.jar
      +text

    2. Update the proxy server settings in the right panel as required. You can set an IP address or host name in the proxyIPAddress field

    3. Select File -> Save from the main menu bar to save your changes

    4. Close the CTP Launcher using the Window close button at the top right

    5. Close the Command Prompt window

    6. Re-Start the CTP Windows service using Windows Services

      Locate the CTP service in the list of services, right-click and select Start from the context menu

      text

    Troubleshooting

    • If the CTP Windows service Stop is disabled, try restarting Windows Services as administrator by right-clicking the icon and selecting Run as administrator

    Further information

    2.1.3 - Windows Service

    Enabling CTP as a Windows Service

    The CTP install.bat script uses Apache procrun. Use the following steps to enable CTP as a Windows service, including an update to use a JRE other than system default (leave out step 2 if using the system default JRE)

    1. Install CTP
      java -jar CTP-installer.jar
       
    2. To use JRE other than system default, edit <ctp-home>/windows/install.bat. Find the –Jvm=auto, add –JavaHome entry and set both as follows
      --JavaHome="<jre home> " ^
       --Jvm="<jre-home>\bin\server\jvm.dll" ^
       
      • ^ is needed to wrap/continue command line in batch file
      • The jvm.dll location under is the same for JRE 1.7 and 1.8 installs. Confirm this is the case for other JREs/JDKs
    3. Run install.bat as Administrator to create the CTP windows service
      cd <ctp-home>/windows
      @@ -73,6 +74,4 @@
       sudo update-rc.d ctpService defaults 98 02
       

      Start and stop CTP using the following commands

      sudo service ctpService start
       sudo service ctpService stop
      -
    - - \ No newline at end of file + \ No newline at end of file diff --git a/docs/facility-guides/_print/index.html b/docs/facility-guides/_print/index.html index 2d59389..b927f36 100644 --- a/docs/facility-guides/_print/index.html +++ b/docs/facility-guides/_print/index.html @@ -1,8 +1,9 @@ -Facility Guides | UQ AIS XNATFacility Guides | UQ AIS XNAT +

    This is the multi-page printable view of this section. +">

    This is the multi-page printable view of this section. Click here to print.

    Return to the regular view of this page.

    Facility Guides

    For Clinical and Imaging facilities

    1 - Clinical Trials Processor (CTP)

    Clinical trials Processor (CTP)

    1.1 - Installation

    CTP Installation

    Installing CTP on Windows 10

    CTP installation steps

    1. Create a new user for CTP on UQ RCC XNAT (not an AAF/OpenID user) with required project access, without admin access
    2. Download the following files
    3. Install CTP using:
      cd INSTALL_FOLDER (replace with your actual folder)
       java -jar CTP-installer.jar
       
    4. Replace CTP/config.xml with ctp_clinical_site_to_xnat_config.xml
    5. Edit CTP/config.xml
      • Change “xxxx.xxxx” in two “url” tags to “xnat.rcc.uq.edu.au”
      • Change “xxxx” username and password tags to match new user from step 1
      • If CTP internet access is via a proxy server, add the proxy server element to the Server config
        ...
        @@ -17,7 +18,7 @@
         
        Once this element is added proxy server settings can be updated in the CTP Launcher GUI
    6. Add CTP the anonymiser script
      • Copy CTP/scripts/DicomServiceAnonymizer.script to CTP/scripts/dicom-anonymizer-sender.script
      • Add the PROJECTID parameter to the list of parameters at the start of the file
        • <p t="PROJECTID">my xnat project id</p>
      • Change the PatientComments element 0010,4000 to set XNAT project routing info
        • @always()@append(){Project:@param(@PROJECTID) Subject:@contents([0010,0010]) Session:@contents([0008,0050])}
      • Review/set other parameters at the start of the file
        • PROFILENAME, eg. AIS-Clinical-Site-210604
        • DATEINC, eg. 0
        • PROJECTNAME, SITEID, SITENAME, TRIALNAME, TRIALSPONSOR as required
      • Optional: review script to check anonymisation settings are appropriate
    7. Start CTP GUI
      java -jar Launcher.jar
       
    8. Click the CTP “Start” button
    9. Click the “CTP Home Page” button to open the Web UI
      • If the browser can’t connect, check CTP is not already running, or try changing the Server port
    10. Login
      • Top RHS banner should show “Welcome admin”
    11. Optional: click “User Manager” to change default usernames/passwords
    12. Optional: click “DICOM Anonymizer” to view/edit anonymiser script
    13. Unzip DCMTK and MrBrain dicom sample
    14. Try sending an dicom to CTP using dcmtk
      cd dcmtk-3.6.5-win64-dynamic/bin
       dcmsend localhost 25055 ../../dicom_viewer_Mrbrain/MRBRAIN.DCM
      -
    15. Login to the XNAT server with an admin account to view Prearchive
      • Use “Upload” → “Go to prearchive”
      • DICOM should appear in “Receiving” status, with project id assigned from step 6
        • Optional: non-admin users need to search by subject/etc
      • Use Refresh to check when “Ready” or it disappears from list (as it has been routed to the project)
      • Debugging: use dcm2xml from DCMTK to check anonymised dicom file under CTP/roots/FileAfterAnonymization25055
    16. Logout and login with the new XNAT user from step 1
    17. Navigate to the project set in step 6
      • You should see the dicom listed as subject “1737775597”
    18. Use subject “1737775597” → “MR Session” → “View Images” to view the uploaded image
    19. Try a dicom send from the scanner using PC address and port 25055 (check windows firewall settings?)
    20. Enable CTP as a Windows Service. Instructions here

    Further information

    If you need a different commit of CTP-installer

    git clone https://github.com/johnperry/CTP
    +
  • Login to the XNAT server with an admin account to view Prearchive
    • Use “Upload” → “Go to prearchive”
    • DICOM should appear in “Receiving” status, with project id assigned from step 6
      • Optional: non-admin users need to search by subject/etc
    • Use Refresh to check when “Ready” or it disappears from list (as it has been routed to the project)
    • Debugging: use dcm2xml from DCMTK to check anonymised dicom file under CTP/roots/FileAfterAnonymization25055
  • Logout and login with the new XNAT user from step 1
  • Navigate to the project set in step 6
    • You should see the dicom listed as subject “1737775597”
  • Use subject “1737775597” → “MR Session” → “View Images” to view the uploaded image
  • Try a dicom send from the scanner using PC address and port 25055 (check windows firewall settings?)
  • Enable CTP as a Windows Service. Instructions here
  • Further information

    If you need a different commit of CTP-installer

    git clone https://github.com/johnperry/CTP
     cd CTP/products
     git checkout <commit> CTP-Installer.jar
     

    If you need other AIS CTP config files

    git clone https://github.com/Australian-Imaging-Service/configuration.git
    @@ -25,9 +26,9 @@
     

    CTP documentation links:

    MIRC CTP Wiki

    CTP DICOM Anonymizer

    1.2 - Proxy Server Settings

    Updating CTP Proxy Server Settings

    If CTP uses a proxy server for internet access, you can update the CTP proxy server settings on Windows as follows

    1. Stop the CTP Windows service

      • If you already have a Services short-cut on the Windows desktop, double-click the short-cut to start Windows Services
      • If not, click the Windows start button, start typing “services” and the Services App icon should appear
        • Click the Services App icon to start Windows Services
      • Locate the CTP service in the list of services, right-click and select Stop from the context menu
    2. Start the CTP Launcher

      • If you already have a CTP Launcher short-cut on the Windows desktop, double-click the short-cut to start the CTP Launcher
      • If not, locate the CTP service in the list of services again, right-click and select Properties from the context menu
        1. Use the Path to executable entry to find the installation folder for CTP. It will be in the form <install folder>\windows\CTP.exe
        2. Open a Windows Command prompt window
          1. Click the Windows Start button, start typing “cmd” and the Command Prompt App icon should appear
          2. Click the Command Prompt App icon to start the Command Prompt
        3. In the Command Prompt window, enter the following commands
        cd <install folder>
         java -jar Launcher.jar
         
    3. Navigate to the CTP Launcher Configuration tab

    4. Use the navigation panel on the left to select Configuration -> Server -> ProxyServer -text

    5. Update the proxy server settings in the right panel as required. You can set an IP address or host name in the proxyIPAddress field

    6. Select File -> Save from the main menu bar to save your changes

    7. Close the CTP Launcher using the Window close button at the top right

    8. Close the Command Prompt window

    9. Re-Start the CTP Windows service using Windows Services

      Locate the CTP service in the list of services, right-click and select Start from the context menu

      text

    Troubleshooting

    • If the CTP Windows service Stop is disabled, try restarting Windows Services as administrator by right-clicking the icon and selecting Run as administrator

    Further information

    1.3 - Windows Service

    Enabling CTP as a Windows Service

    The CTP install.bat script uses Apache procrun. Use the following steps to enable CTP as a Windows service, including an update to use a JRE other than system default (leave out step 2 if using the system default JRE)

    1. Install CTP
      java -jar CTP-installer.jar
      +text

    2. Update the proxy server settings in the right panel as required. You can set an IP address or host name in the proxyIPAddress field

    3. Select File -> Save from the main menu bar to save your changes

    4. Close the CTP Launcher using the Window close button at the top right

    5. Close the Command Prompt window

    6. Re-Start the CTP Windows service using Windows Services

      Locate the CTP service in the list of services, right-click and select Start from the context menu

      text

    Troubleshooting

    • If the CTP Windows service Stop is disabled, try restarting Windows Services as administrator by right-clicking the icon and selecting Run as administrator

    Further information

    1.3 - Windows Service

    Enabling CTP as a Windows Service

    The CTP install.bat script uses Apache procrun. Use the following steps to enable CTP as a Windows service, including an update to use a JRE other than system default (leave out step 2 if using the system default JRE)

    1. Install CTP
      java -jar CTP-installer.jar
       
    2. To use JRE other than system default, edit <ctp-home>/windows/install.bat. Find the –Jvm=auto, add –JavaHome entry and set both as follows
      --JavaHome="<jre home> " ^
       --Jvm="<jre-home>\bin\server\jvm.dll" ^
       
      • ^ is needed to wrap/continue command line in batch file
      • The jvm.dll location under is the same for JRE 1.7 and 1.8 installs. Confirm this is the case for other JREs/JDKs
    3. Run install.bat as Administrator to create the CTP windows service
      cd <ctp-home>/windows
      @@ -41,6 +42,4 @@
       sudo update-rc.d ctpService defaults 98 02
       

      Start and stop CTP using the following commands

      sudo service ctpService start
       sudo service ctpService stop
      -
    - - \ No newline at end of file +
    \ No newline at end of file diff --git a/docs/facility-guides/ctp/_print/index.html b/docs/facility-guides/ctp/_print/index.html index 370bf71..9a97804 100644 --- a/docs/facility-guides/ctp/_print/index.html +++ b/docs/facility-guides/ctp/_print/index.html @@ -1,8 +1,9 @@ -Clinical Trials Processor (CTP) | UQ AIS XNATClinical Trials Processor (CTP) | UQ AIS XNAT +

    This is the multi-page printable view of this section. +">

    This is the multi-page printable view of this section. Click here to print.

    Return to the regular view of this page.

    Clinical Trials Processor (CTP)

    Clinical trials Processor (CTP)

    1 - Installation

    CTP Installation

    Installing CTP on Windows 10

    CTP installation steps

    1. Create a new user for CTP on UQ RCC XNAT (not an AAF/OpenID user) with required project access, without admin access
    2. Download the following files
    3. Install CTP using:
      cd INSTALL_FOLDER (replace with your actual folder)
       java -jar CTP-installer.jar
       
    4. Replace CTP/config.xml with ctp_clinical_site_to_xnat_config.xml
    5. Edit CTP/config.xml
      • Change “xxxx.xxxx” in two “url” tags to “xnat.rcc.uq.edu.au”
      • Change “xxxx” username and password tags to match new user from step 1
      • If CTP internet access is via a proxy server, add the proxy server element to the Server config
        ...
        @@ -17,7 +18,7 @@
         
        Once this element is added proxy server settings can be updated in the CTP Launcher GUI
    6. Add CTP the anonymiser script
      • Copy CTP/scripts/DicomServiceAnonymizer.script to CTP/scripts/dicom-anonymizer-sender.script
      • Add the PROJECTID parameter to the list of parameters at the start of the file
        • <p t="PROJECTID">my xnat project id</p>
      • Change the PatientComments element 0010,4000 to set XNAT project routing info
        • @always()@append(){Project:@param(@PROJECTID) Subject:@contents([0010,0010]) Session:@contents([0008,0050])}
      • Review/set other parameters at the start of the file
        • PROFILENAME, eg. AIS-Clinical-Site-210604
        • DATEINC, eg. 0
        • PROJECTNAME, SITEID, SITENAME, TRIALNAME, TRIALSPONSOR as required
      • Optional: review script to check anonymisation settings are appropriate
    7. Start CTP GUI
      java -jar Launcher.jar
       
    8. Click the CTP “Start” button
    9. Click the “CTP Home Page” button to open the Web UI
      • If the browser can’t connect, check CTP is not already running, or try changing the Server port
    10. Login
      • Top RHS banner should show “Welcome admin”
    11. Optional: click “User Manager” to change default usernames/passwords
    12. Optional: click “DICOM Anonymizer” to view/edit anonymiser script
    13. Unzip DCMTK and MrBrain dicom sample
    14. Try sending an dicom to CTP using dcmtk
      cd dcmtk-3.6.5-win64-dynamic/bin
       dcmsend localhost 25055 ../../dicom_viewer_Mrbrain/MRBRAIN.DCM
      -
    15. Login to the XNAT server with an admin account to view Prearchive
      • Use “Upload” → “Go to prearchive”
      • DICOM should appear in “Receiving” status, with project id assigned from step 6
        • Optional: non-admin users need to search by subject/etc
      • Use Refresh to check when “Ready” or it disappears from list (as it has been routed to the project)
      • Debugging: use dcm2xml from DCMTK to check anonymised dicom file under CTP/roots/FileAfterAnonymization25055
    16. Logout and login with the new XNAT user from step 1
    17. Navigate to the project set in step 6
      • You should see the dicom listed as subject “1737775597”
    18. Use subject “1737775597” → “MR Session” → “View Images” to view the uploaded image
    19. Try a dicom send from the scanner using PC address and port 25055 (check windows firewall settings?)
    20. Enable CTP as a Windows Service. Instructions here

    Further information

    If you need a different commit of CTP-installer

    git clone https://github.com/johnperry/CTP
    +
  • Login to the XNAT server with an admin account to view Prearchive
    • Use “Upload” → “Go to prearchive”
    • DICOM should appear in “Receiving” status, with project id assigned from step 6
      • Optional: non-admin users need to search by subject/etc
    • Use Refresh to check when “Ready” or it disappears from list (as it has been routed to the project)
    • Debugging: use dcm2xml from DCMTK to check anonymised dicom file under CTP/roots/FileAfterAnonymization25055
  • Logout and login with the new XNAT user from step 1
  • Navigate to the project set in step 6
    • You should see the dicom listed as subject “1737775597”
  • Use subject “1737775597” → “MR Session” → “View Images” to view the uploaded image
  • Try a dicom send from the scanner using PC address and port 25055 (check windows firewall settings?)
  • Enable CTP as a Windows Service. Instructions here
  • Further information

    If you need a different commit of CTP-installer

    git clone https://github.com/johnperry/CTP
     cd CTP/products
     git checkout <commit> CTP-Installer.jar
     

    If you need other AIS CTP config files

    git clone https://github.com/Australian-Imaging-Service/configuration.git
    @@ -25,9 +26,9 @@
     

    CTP documentation links:

    MIRC CTP Wiki

    CTP DICOM Anonymizer

    2 - Proxy Server Settings

    Updating CTP Proxy Server Settings

    If CTP uses a proxy server for internet access, you can update the CTP proxy server settings on Windows as follows

    1. Stop the CTP Windows service

      • If you already have a Services short-cut on the Windows desktop, double-click the short-cut to start Windows Services
      • If not, click the Windows start button, start typing “services” and the Services App icon should appear
        • Click the Services App icon to start Windows Services
      • Locate the CTP service in the list of services, right-click and select Stop from the context menu
    2. Start the CTP Launcher

      • If you already have a CTP Launcher short-cut on the Windows desktop, double-click the short-cut to start the CTP Launcher
      • If not, locate the CTP service in the list of services again, right-click and select Properties from the context menu
        1. Use the Path to executable entry to find the installation folder for CTP. It will be in the form <install folder>\windows\CTP.exe
        2. Open a Windows Command prompt window
          1. Click the Windows Start button, start typing “cmd” and the Command Prompt App icon should appear
          2. Click the Command Prompt App icon to start the Command Prompt
        3. In the Command Prompt window, enter the following commands
        cd <install folder>
         java -jar Launcher.jar
         
    3. Navigate to the CTP Launcher Configuration tab

    4. Use the navigation panel on the left to select Configuration -> Server -> ProxyServer -text

    5. Update the proxy server settings in the right panel as required. You can set an IP address or host name in the proxyIPAddress field

    6. Select File -> Save from the main menu bar to save your changes

    7. Close the CTP Launcher using the Window close button at the top right

    8. Close the Command Prompt window

    9. Re-Start the CTP Windows service using Windows Services

      Locate the CTP service in the list of services, right-click and select Start from the context menu

      text

    Troubleshooting

    • If the CTP Windows service Stop is disabled, try restarting Windows Services as administrator by right-clicking the icon and selecting Run as administrator

    Further information

    3 - Windows Service

    Enabling CTP as a Windows Service

    The CTP install.bat script uses Apache procrun. Use the following steps to enable CTP as a Windows service, including an update to use a JRE other than system default (leave out step 2 if using the system default JRE)

    1. Install CTP
      java -jar CTP-installer.jar
      +text

    2. Update the proxy server settings in the right panel as required. You can set an IP address or host name in the proxyIPAddress field

    3. Select File -> Save from the main menu bar to save your changes

    4. Close the CTP Launcher using the Window close button at the top right

    5. Close the Command Prompt window

    6. Re-Start the CTP Windows service using Windows Services

      Locate the CTP service in the list of services, right-click and select Start from the context menu

      text

    Troubleshooting

    • If the CTP Windows service Stop is disabled, try restarting Windows Services as administrator by right-clicking the icon and selecting Run as administrator

    Further information

    3 - Windows Service

    Enabling CTP as a Windows Service

    The CTP install.bat script uses Apache procrun. Use the following steps to enable CTP as a Windows service, including an update to use a JRE other than system default (leave out step 2 if using the system default JRE)

    1. Install CTP
      java -jar CTP-installer.jar
       
    2. To use JRE other than system default, edit <ctp-home>/windows/install.bat. Find the –Jvm=auto, add –JavaHome entry and set both as follows
      --JavaHome="<jre home> " ^
       --Jvm="<jre-home>\bin\server\jvm.dll" ^
       
      • ^ is needed to wrap/continue command line in batch file
      • The jvm.dll location under is the same for JRE 1.7 and 1.8 installs. Confirm this is the case for other JREs/JDKs
    3. Run install.bat as Administrator to create the CTP windows service
      cd <ctp-home>/windows
      @@ -41,6 +42,4 @@
       sudo update-rc.d ctpService defaults 98 02
       

      Start and stop CTP using the following commands

      sudo service ctpService start
       sudo service ctpService stop
      -
    - - \ No newline at end of file +
    \ No newline at end of file diff --git a/docs/facility-guides/ctp/index.html b/docs/facility-guides/ctp/index.html index 3d14ae9..d09d3b9 100644 --- a/docs/facility-guides/ctp/index.html +++ b/docs/facility-guides/ctp/index.html @@ -1,7 +1,6 @@ -Clinical Trials Processor (CTP) | UQ AIS XNATClinical Trials Processor (CTP) | UQ AIS XNAT +
    - - \ No newline at end of file +">
    \ No newline at end of file diff --git a/docs/facility-guides/ctp/index.xml b/docs/facility-guides/ctp/index.xml index be45e61..3c25b68 100644 --- a/docs/facility-guides/ctp/index.xml +++ b/docs/facility-guides/ctp/index.xml @@ -98,7 +98,7 @@ </li> <li>Use subject &ldquo;1737775597&rdquo; → &ldquo;MR Session&rdquo; → &ldquo;View Images&rdquo; to view the uploaded image</li> <li>Try a dicom send from the scanner using PC address and port 25055 (check windows firewall settings?)</li> -<li>Enable CTP as a Windows Service. Instructions <a href="https://docs.xnat.rcc.uq.edu.au/docs/facility-guides/ctp/windows-service">here</a></li> +<li>Enable CTP as a Windows Service. Instructions <a href="https://docs.xnat.rcc.uq.edu.au/docs/facility-guides/ctp/windows-service/">here</a></li> </ol> <h3 id="further-information">Further information</h3> <p>If you need a different commit of CTP-installer</p> @@ -150,7 +150,7 @@ </li> <li> <p>Use the navigation panel on the left to select <strong>Configuration</strong> -&gt; <strong>Server</strong> -&gt; <strong>ProxyServer</strong> -<img src="https://docs.xnat.rcc.uq.edu.au/docs/facility-guides/ctp/proxy-config.png" alt="text"></p> +<img alt="text" src="https://docs.xnat.rcc.uq.edu.au/docs/facility-guides/ctp/proxy-config.png"></p> </li> <li> <p>Update the proxy server settings in the right panel as required. You can set an IP address or host name in the proxyIPAddress field</p> @@ -162,7 +162,7 @@ <p>Close the CTP Launcher using the Window close button at the top right <div class="alert alert-warning" role="alert"> If the following prompt appears, select <strong>No</strong>. -<img src="https://docs.xnat.rcc.uq.edu.au/docs/facility-guides/ctp/close-launcher.png" alt="text"> +<img alt="text" src="https://docs.xnat.rcc.uq.edu.au/docs/facility-guides/ctp/close-launcher.png"> If the CTP is stopped, restart it from the Windows services menu (See below) </div> </p> @@ -173,7 +173,7 @@ If the CTP is stopped, restart it from the Windows services menu (See below) <li> <p>Re-Start the CTP Windows service using Windows Services</p> <p>Locate the CTP service in the list of services, right-click and select <strong>Start</strong> from the context menu</p> -<p><img src="https://docs.xnat.rcc.uq.edu.au/docs/facility-guides/ctp/windows-service.png" alt="text"></p> +<p><img alt="text" src="https://docs.xnat.rcc.uq.edu.au/docs/facility-guides/ctp/windows-service.png"></p> </li> </ol> <h4 id="troubleshooting">Troubleshooting</h4> diff --git a/docs/facility-guides/ctp/installation/index.html b/docs/facility-guides/ctp/installation/index.html index 7cc66cb..ac99c39 100644 --- a/docs/facility-guides/ctp/installation/index.html +++ b/docs/facility-guides/ctp/installation/index.html @@ -1,8 +1,9 @@ -Installation | UQ AIS XNATInstallation | UQ AIS XNAT +

    Installation

    CTP Installation

    Installing CTP on Windows 10

    CTP installation steps

    1. Create a new user for CTP on UQ RCC XNAT (not an AAF/OpenID user) with required project access, without admin access
    2. Download the following files
    3. Install CTP using:
      cd INSTALL_FOLDER (replace with your actual folder)
      +">

      Installation

      CTP Installation

      Installing CTP on Windows 10

      CTP installation steps

      1. Create a new user for CTP on UQ RCC XNAT (not an AAF/OpenID user) with required project access, without admin access
      2. Download the following files
      3. Install CTP using:
        cd INSTALL_FOLDER (replace with your actual folder)
         java -jar CTP-installer.jar
         
      4. Replace CTP/config.xml with ctp_clinical_site_to_xnat_config.xml
      5. Edit CTP/config.xml
        • Change “xxxx.xxxx” in two “url” tags to “xnat.rcc.uq.edu.au”
        • Change “xxxx” username and password tags to match new user from step 1
        • If CTP internet access is via a proxy server, add the proxy server element to the Server config
          ...
           <Server ...>
          @@ -16,11 +17,9 @@
           
          Once this element is added proxy server settings can be updated in the CTP Launcher GUI
      6. Add CTP the anonymiser script
        • Copy CTP/scripts/DicomServiceAnonymizer.script to CTP/scripts/dicom-anonymizer-sender.script
        • Add the PROJECTID parameter to the list of parameters at the start of the file
          • <p t="PROJECTID">my xnat project id</p>
        • Change the PatientComments element 0010,4000 to set XNAT project routing info
          • @always()@append(){Project:@param(@PROJECTID) Subject:@contents([0010,0010]) Session:@contents([0008,0050])}
        • Review/set other parameters at the start of the file
          • PROFILENAME, eg. AIS-Clinical-Site-210604
          • DATEINC, eg. 0
          • PROJECTNAME, SITEID, SITENAME, TRIALNAME, TRIALSPONSOR as required
        • Optional: review script to check anonymisation settings are appropriate
      7. Start CTP GUI
        java -jar Launcher.jar
         
      8. Click the CTP “Start” button
      9. Click the “CTP Home Page” button to open the Web UI
        • If the browser can’t connect, check CTP is not already running, or try changing the Server port
      10. Login
        • Top RHS banner should show “Welcome admin”
      11. Optional: click “User Manager” to change default usernames/passwords
      12. Optional: click “DICOM Anonymizer” to view/edit anonymiser script
      13. Unzip DCMTK and MrBrain dicom sample
      14. Try sending an dicom to CTP using dcmtk
        cd dcmtk-3.6.5-win64-dynamic/bin
         dcmsend localhost 25055 ../../dicom_viewer_Mrbrain/MRBRAIN.DCM
        -
      15. Login to the XNAT server with an admin account to view Prearchive
        • Use “Upload” → “Go to prearchive”
        • DICOM should appear in “Receiving” status, with project id assigned from step 6
          • Optional: non-admin users need to search by subject/etc
        • Use Refresh to check when “Ready” or it disappears from list (as it has been routed to the project)
        • Debugging: use dcm2xml from DCMTK to check anonymised dicom file under CTP/roots/FileAfterAnonymization25055
      16. Logout and login with the new XNAT user from step 1
      17. Navigate to the project set in step 6
        • You should see the dicom listed as subject “1737775597”
      18. Use subject “1737775597” → “MR Session” → “View Images” to view the uploaded image
      19. Try a dicom send from the scanner using PC address and port 25055 (check windows firewall settings?)
      20. Enable CTP as a Windows Service. Instructions here

      Further information

      If you need a different commit of CTP-installer

      git clone https://github.com/johnperry/CTP
      +
    4. Login to the XNAT server with an admin account to view Prearchive
      • Use “Upload” → “Go to prearchive”
      • DICOM should appear in “Receiving” status, with project id assigned from step 6
        • Optional: non-admin users need to search by subject/etc
      • Use Refresh to check when “Ready” or it disappears from list (as it has been routed to the project)
      • Debugging: use dcm2xml from DCMTK to check anonymised dicom file under CTP/roots/FileAfterAnonymization25055
    5. Logout and login with the new XNAT user from step 1
    6. Navigate to the project set in step 6
      • You should see the dicom listed as subject “1737775597”
    7. Use subject “1737775597” → “MR Session” → “View Images” to view the uploaded image
    8. Try a dicom send from the scanner using PC address and port 25055 (check windows firewall settings?)
    9. Enable CTP as a Windows Service. Instructions here

    Further information

    If you need a different commit of CTP-installer

    git clone https://github.com/johnperry/CTP
     cd CTP/products
     git checkout <commit> CTP-Installer.jar
     

    If you need other AIS CTP config files

    git clone https://github.com/Australian-Imaging-Service/configuration.git
     cd configuration/CTP
    -

    CTP documentation links:

    MIRC CTP Wiki

    CTP DICOM Anonymizer

    - - \ No newline at end of file +

    CTP documentation links:

    MIRC CTP Wiki

    CTP DICOM Anonymizer

    \ No newline at end of file diff --git a/docs/facility-guides/ctp/linux-service/index.html b/docs/facility-guides/ctp/linux-service/index.html index f7c60f8..cb48f10 100644 --- a/docs/facility-guides/ctp/linux-service/index.html +++ b/docs/facility-guides/ctp/linux-service/index.html @@ -1,8 +1,9 @@ -Linux Service | UQ AIS XNATLinux Service | UQ AIS XNAT +

    Linux Service

    Enabling CTP as a Linux Service

    Ubuntu

    Open ./linux/ctpService-ubuntu.sh. Update the following parameters:

    USER=ubuntu
    +">
    - - \ No newline at end of file +
    \ No newline at end of file diff --git a/docs/facility-guides/ctp/proxy-server/index.html b/docs/facility-guides/ctp/proxy-server/index.html index 2c2849f..f5f0597 100644 --- a/docs/facility-guides/ctp/proxy-server/index.html +++ b/docs/facility-guides/ctp/proxy-server/index.html @@ -1,12 +1,11 @@ -Proxy Server Settings | UQ AIS XNATProxy Server Settings | UQ AIS XNAT +

    Proxy Server Settings

    Updating CTP Proxy Server Settings

    If CTP uses a proxy server for internet access, you can update the CTP proxy server settings on Windows as follows

    1. Stop the CTP Windows service

      • If you already have a Services short-cut on the Windows desktop, double-click the short-cut to start Windows Services
      • If not, click the Windows start button, start typing “services” and the Services App icon should appear
        • Click the Services App icon to start Windows Services
      • Locate the CTP service in the list of services, right-click and select Stop from the context menu
    2. Start the CTP Launcher

      • If you already have a CTP Launcher short-cut on the Windows desktop, double-click the short-cut to start the CTP Launcher
      • If not, locate the CTP service in the list of services again, right-click and select Properties from the context menu
        1. Use the Path to executable entry to find the installation folder for CTP. It will be in the form <install folder>\windows\CTP.exe
        2. Open a Windows Command prompt window
          1. Click the Windows Start button, start typing “cmd” and the Command Prompt App icon should appear
          2. Click the Command Prompt App icon to start the Command Prompt
        3. In the Command Prompt window, enter the following commands
        cd <install folder>
        +">

        Proxy Server Settings

        Updating CTP Proxy Server Settings

        If CTP uses a proxy server for internet access, you can update the CTP proxy server settings on Windows as follows

        1. Stop the CTP Windows service

          • If you already have a Services short-cut on the Windows desktop, double-click the short-cut to start Windows Services
          • If not, click the Windows start button, start typing “services” and the Services App icon should appear
            • Click the Services App icon to start Windows Services
          • Locate the CTP service in the list of services, right-click and select Stop from the context menu
        2. Start the CTP Launcher

          • If you already have a CTP Launcher short-cut on the Windows desktop, double-click the short-cut to start the CTP Launcher
          • If not, locate the CTP service in the list of services again, right-click and select Properties from the context menu
            1. Use the Path to executable entry to find the installation folder for CTP. It will be in the form <install folder>\windows\CTP.exe
            2. Open a Windows Command prompt window
              1. Click the Windows Start button, start typing “cmd” and the Command Prompt App icon should appear
              2. Click the Command Prompt App icon to start the Command Prompt
            3. In the Command Prompt window, enter the following commands
            cd <install folder>
             java -jar Launcher.jar
             
        3. Navigate to the CTP Launcher Configuration tab

        4. Use the navigation panel on the left to select Configuration -> Server -> ProxyServer -text

        5. Update the proxy server settings in the right panel as required. You can set an IP address or host name in the proxyIPAddress field

        6. Select File -> Save from the main menu bar to save your changes

        7. Close the CTP Launcher using the Window close button at the top right

        8. Close the Command Prompt window

        9. Re-Start the CTP Windows service using Windows Services

          Locate the CTP service in the list of services, right-click and select Start from the context menu

          text

        Troubleshooting

        • If the CTP Windows service Stop is disabled, try restarting Windows Services as administrator by right-clicking the icon and selecting Run as administrator

        Further information

        - - \ No newline at end of file +text

      • Update the proxy server settings in the right panel as required. You can set an IP address or host name in the proxyIPAddress field

      • Select File -> Save from the main menu bar to save your changes

      • Close the CTP Launcher using the Window close button at the top right

      • Close the Command Prompt window

      • Re-Start the CTP Windows service using Windows Services

        Locate the CTP service in the list of services, right-click and select Start from the context menu

        text

    Troubleshooting

    • If the CTP Windows service Stop is disabled, try restarting Windows Services as administrator by right-clicking the icon and selecting Run as administrator

    Further information

    \ No newline at end of file diff --git a/docs/facility-guides/ctp/windows-service/index.html b/docs/facility-guides/ctp/windows-service/index.html index 7cd2c5e..0ba8bc5 100644 --- a/docs/facility-guides/ctp/windows-service/index.html +++ b/docs/facility-guides/ctp/windows-service/index.html @@ -1,12 +1,11 @@ -Windows Service | UQ AIS XNATWindows Service | UQ AIS XNAT +

    Windows Service

    Enabling CTP as a Windows Service

    The CTP install.bat script uses Apache procrun. Use the following steps to enable CTP as a Windows service, including an update to use a JRE other than system default (leave out step 2 if using the system default JRE)

    1. Install CTP
      java -jar CTP-installer.jar
      +">

      Windows Service

      Enabling CTP as a Windows Service

      The CTP install.bat script uses Apache procrun. Use the following steps to enable CTP as a Windows service, including an update to use a JRE other than system default (leave out step 2 if using the system default JRE)

      1. Install CTP
        java -jar CTP-installer.jar
         
      2. To use JRE other than system default, edit <ctp-home>/windows/install.bat. Find the –Jvm=auto, add –JavaHome entry and set both as follows
        --JavaHome="<jre home> " ^
         --Jvm="<jre-home>\bin\server\jvm.dll" ^
         
        • ^ is needed to wrap/continue command line in batch file
        • The jvm.dll location under is the same for JRE 1.7 and 1.8 installs. Confirm this is the case for other JREs/JDKs
      3. Run install.bat as Administrator to create the CTP windows service
        cd <ctp-home>/windows
         install
        -
      4. Open Windows Services as Administrator and start the CTP service
      5. Open CTP administration page in Web browser
      6. Confirm the correct JRE is reported in Admin → System Properties and/or Admin → Log Viewer → ctp.log

      Troubleshooting

      • Installation paths are set in install.bat during CTP install so it won’t work if you move the CTP folder somewhere else after install
      • If removing the service (with uninstall.bat) leaves the service stuck in delete pending state, reboot the system to complete

      Further information

      - - \ No newline at end of file +
    2. Open Windows Services as Administrator and start the CTP service
    3. Open CTP administration page in Web browser
    4. Confirm the correct JRE is reported in Admin → System Properties and/or Admin → Log Viewer → ctp.log

    Troubleshooting

    • Installation paths are set in install.bat during CTP install so it won’t work if you move the CTP folder somewhere else after install
    • If removing the service (with uninstall.bat) leaves the service stuck in delete pending state, reboot the system to complete

    Further information

    \ No newline at end of file diff --git a/docs/facility-guides/index.html b/docs/facility-guides/index.html index 563f575..af7711f 100644 --- a/docs/facility-guides/index.html +++ b/docs/facility-guides/index.html @@ -1,7 +1,6 @@ -Facility Guides | UQ AIS XNATFacility Guides | UQ AIS XNAT +
    - - \ No newline at end of file +">
    \ No newline at end of file diff --git a/docs/index.html b/docs/index.html index 3a59d20..eafbb5d 100644 --- a/docs/index.html +++ b/docs/index.html @@ -1,3 +1,2 @@ -Documentation | UQ AIS XNAT
    - - \ No newline at end of file +Documentation | UQ AIS XNAT +
    \ No newline at end of file diff --git a/docs/index.xml b/docs/index.xml index 33de7b1..1daa5a8 100644 --- a/docs/index.xml +++ b/docs/index.xml @@ -98,7 +98,7 @@ </li> <li>Use subject &ldquo;1737775597&rdquo; → &ldquo;MR Session&rdquo; → &ldquo;View Images&rdquo; to view the uploaded image</li> <li>Try a dicom send from the scanner using PC address and port 25055 (check windows firewall settings?)</li> -<li>Enable CTP as a Windows Service. Instructions <a href="https://docs.xnat.rcc.uq.edu.au/docs/facility-guides/ctp/windows-service">here</a></li> +<li>Enable CTP as a Windows Service. Instructions <a href="https://docs.xnat.rcc.uq.edu.au/docs/facility-guides/ctp/windows-service/">here</a></li> </ol> <h3 id="further-information">Further information</h3> <p>If you need a different commit of CTP-installer</p> @@ -150,7 +150,7 @@ </li> <li> <p>Use the navigation panel on the left to select <strong>Configuration</strong> -&gt; <strong>Server</strong> -&gt; <strong>ProxyServer</strong> -<img src="https://docs.xnat.rcc.uq.edu.au/docs/facility-guides/ctp/proxy-config.png" alt="text"></p> +<img alt="text" src="https://docs.xnat.rcc.uq.edu.au/docs/facility-guides/ctp/proxy-config.png"></p> </li> <li> <p>Update the proxy server settings in the right panel as required. You can set an IP address or host name in the proxyIPAddress field</p> @@ -162,7 +162,7 @@ <p>Close the CTP Launcher using the Window close button at the top right <div class="alert alert-warning" role="alert"> If the following prompt appears, select <strong>No</strong>. -<img src="https://docs.xnat.rcc.uq.edu.au/docs/facility-guides/ctp/close-launcher.png" alt="text"> +<img alt="text" src="https://docs.xnat.rcc.uq.edu.au/docs/facility-guides/ctp/close-launcher.png"> If the CTP is stopped, restart it from the Windows services menu (See below) </div> </p> @@ -173,7 +173,7 @@ If the CTP is stopped, restart it from the Windows services menu (See below) <li> <p>Re-Start the CTP Windows service using Windows Services</p> <p>Locate the CTP service in the list of services, right-click and select <strong>Start</strong> from the context menu</p> -<p><img src="https://docs.xnat.rcc.uq.edu.au/docs/facility-guides/ctp/windows-service.png" alt="text"></p> +<p><img alt="text" src="https://docs.xnat.rcc.uq.edu.au/docs/facility-guides/ctp/windows-service.png"></p> </li> </ol> <h4 id="troubleshooting">Troubleshooting</h4> @@ -377,7 +377,7 @@ Only one member of the project team needs to request for the project <li><strong>Non-HPC collections</strong> end with <strong>-A</strong> (e.g. PROJ001-<strong>A0189</strong>) or <strong>-I</strong> (PROJ001-<strong>I0189</strong>)</li> </ul> <div class="alert alert-warning" role="alert"> -If you have an existing UQ-RDM <strong>HPC collection</strong> (ending with <strong>-Qxxxx</strong>), skip to the <a href="./#step-2-1">next step</a> +If you have an existing UQ-RDM <strong>HPC collection</strong> (ending with <strong>-Qxxxx</strong>), skip to the <a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/#step-2-1">next step</a> </div> <p>To create a new UQ-RDM <strong>HPC Collection</strong>, proceed with the following</p> <p>Open <a href="https://rdm.uq.edu.au/create-record">https://rdm.uq.edu.au/create-record</a> and sign-in</p> @@ -465,7 +465,7 @@ In case of <strong>Background process</strong> errors, expand panel using <li>Collaborating on projects managed on UQ AIS XNAT</li> </ul> <p>Full list of AAF members found <a href="https://aaf.edu.au/subscribers">here</a><br> -For all other organisations, use the <a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/non-aaf-members">Non-AAF members</a> guide</p> +For all other organisations, use the <a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/non-aaf-members/">Non-AAF members</a> guide</p> <h2 id="signing-into-xnat">Signing into XNAT</h2> <hr> <h4 id="step-1">Step 1</h4> @@ -731,7 +731,7 @@ Data Acquisition Site: __________<br> <h4 id="step-2">Step 2</h4> <p>AAF&rsquo;s VHO account will return an email regarding the VHO account registration process</p> <h4 id="step-3">Step 3</h4> -<p><em>After account is provisioned, continue on to the <a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/non-aaf-members#signing-into-xnat">Signing into XNAT guide</a></em></p> +<p><em>After account is provisioned, continue on to the <a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/non-aaf-members/#signing-into-xnat">Signing into XNAT guide</a></em></p> <h2 id="signing-into-xnat">Signing into XNAT</h2> <hr> <h4 id="step-1-1">Step 1</h4> @@ -796,19 +796,19 @@ If you hover over one of them, and click the highlighted view details button. Th <p>Data acquired at HIRF can be sent to the UQ-RCC XNAT repository</p> <p>To get started, refer to the relevant guide below:</p> <ul> -<li><a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/uq-members">UQ members</a> +<li><a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/uq-members/">UQ members</a> <ul> <li>UQ Staff and Students</li> </ul> </li> -<li><a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/other-aaf-members">Other AAF members</a> +<li><a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/other-aaf-members/">Other AAF members</a> <ul> <li>QUT, Griffith, CQU, JCU, USQ, USC, Bond</li> <li>CSIRO, QCIF, Australian Universities</li> <li>Full list of AAF members found <a href="https://aaf.edu.au/subscribers">here</a></li> </ul> </li> -<li><a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/non-aaf-members">Non-AAF members</a> +<li><a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/non-aaf-members/">Non-AAF members</a> <ul> <li>TRI, QIMR</li> <li>QLD Health, QLD Xray, Pacific Radiology</li> @@ -816,9 +816,16 @@ If you hover over one of them, and click the highlighted view details button. Th </li> </ul> <div class="alert alert-warning" role="alert"> -If you have multiple valid affiliations, we&rsquo;d recommend using <a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/uq-members">UQ</a> or <a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/other-aaf-members">AAF</a> affiliation where possible +If you have multiple valid affiliations, we&rsquo;d recommend using <a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/uq-members/">UQ</a> or <a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/other-aaf-members/">AAF</a> affiliation where possible </div> <p>If you have any questions, contact <a href="mailto:rcc-support@uq.edu.au">rcc-support@uq.edu.au</a> or <a href="mailto:HIRFAdministration@health.qld.gov.au">HIRFAdministration@health.qld.gov.au</a></p>Docs:https://docs.xnat.rcc.uq.edu.au/docs/user-guides/faq/Mon, 01 Jan 0001 00:00:00 +0000https://docs.xnat.rcc.uq.edu.au/docs/user-guides/faq/ +<!-- --- +title: "FAQ" +linkTitle: "FAQ" +weight: 1 +description: > +Frequently Asked Questions +--- --> <div> <nav id="TableOfContents"> <ul> diff --git a/docs/user-guides/_print/index.html b/docs/user-guides/_print/index.html index 516ce10..43cc7be 100644 --- a/docs/user-guides/_print/index.html +++ b/docs/user-guides/_print/index.html @@ -1,13 +1,14 @@ -User Guides | UQ AIS XNATUser Guides | UQ AIS XNAT +

    1 - Getting Started

    Signing up and getting started with UQ-RCC XNAT

    1.1 - UQ members

    For UQ Staff and Students

    Signing into XNAT


    Step 1

    Open https://xnat.rcc.uq.edu.au

    Step 2

    Login in with the AAF Single sign-on button (shown below).

    Follow the AAF login process for your organisation

    Step 3

    After the AAF sign-in, you should be redirected back to XNAT (Example below)

    There will be no projects listed when signing in for the first-time, as your user account would have just been created.

    Proceed to to next section for setting up an XNAT project

    Creating XNAT project


    For UQ users, XNAT uses UQ-RDM HPC collections for storage allocation.
    For any general questions about UQ-RDM, please refer to the library guides

    Step 1

    Before creating an XNAT project, you’ll require a UQ-RDM HPC Collection

    • HPC collections ends with -Q and a 4-digit numerical identifier (e.g. PROJ001-Q0189)
    • Non-HPC collections end with -A (e.g. PROJ001-A0189) or -I (PROJ001-I0189)

    To create a new UQ-RDM HPC Collection, proceed with the following

    Open https://rdm.uq.edu.au/create-record and sign-in

    Fill in the record as per your project details

    REQUEST DATA STORAGE when complete

    Move on to the next step after the RDM collection is provisioned
    You should have an RDM collection name ready (e.g. PROJ001-Q0189)

    Step 2

    Open a ticket with RCC support

    Example below (replace __________ with your details)

    Subject: Create XNAT project __________

    Hello RCC support -Can we create an XNAT project for RDM collection __________

    Step 3

    The support ticket will inform you when the project is set up.

    • An XNAT project will be created with the matching name (e.g. PROJ001-Q0189)
    • An xnat directory will be created in the RDM collection for storing the XNAT data files
    • Please do not write or modify anything under the xnat directory

    XNAT Project setup typically takes around ~24 hours from ticket submission
    An automated email from XNAT will be sent through when project is ready, and your user has been added

    1.2 - Other AAF members

    Other AAF members

    This guide is for users from Australian Universities and AAF member organisations, including:

    • QUT, Griffith, CQU, JCU, USQ, USC
    • CSIRO, Australian Universities
    • AAF VHO accounts

    Other AAF members usually require UQ AIS XNAT access for:

    • Management of data acquisition from sites such as CAI, HIRF, TRI
    • Collaborating on projects managed on UQ AIS XNAT

    Full list of AAF members found here
    For all other organisations, use the Non-AAF members guide

    Signing into XNAT


    Step 1

    Open https://xnat.rcc.uq.edu.au

    Step 2

    Login in with the AAF Single sign-on button (See below).

    Follow the AAF login process for your organisation

    Step 3

    After the AAF sign-in, you should be redirected back to XNAT (Example below)

    There will be no projects listed when signing in for the first-time, as your user account would have just been created.

    Accessing XNAT Project


    If you are Acquiring data at HIRF, CAI or TRI

    • The respective facility will organise the project creation.
    • You will receive a follow up email when access has been granted
    • Contact rcc-support@uq.edu.au if you have not received access within 5 working days

    If you are collaborating on an existing XNAT project

    • Contact the project lead to grant you access to the XNAT project

    1.3 - Non-AAF members

    Non-University, non-AAF members and other users

    This is for users from non-AAF member organisations, including:

    • QLD Health, TRI, QIMR, QLD Xray

    Non-AAF members usually require XNAT access for:

    • Management of data acquisition from sites such as CAI, HIRF, TRI
    • Collaborating on projects managed on UQ-RCC XNAT

    XNAT uses AAF for login. QCIF/QRIScloud can provide AAF Virtual Home (VHO) accounts for non-AAF users.

    Creating an AAF VHO account


    Step 1

    Open a ticket with RCC support to request an AAF account

    Example below (replace __________ with your details)

    Subject: XNAT AAF account for project __________

    Hello RCC support -I require an AAF account to access the UQ AIS XNAT service
    My details are below
    Organisation: __________
    Data Acquisition Site: __________

    Step 2

    AAF’s VHO account will return an email regarding the VHO account registration process

    Step 3

    After account is provisioned, continue on to the Signing into XNAT guide

    Signing into XNAT


    Step 1

    Open https://xnat.rcc.uq.edu.au

    Step 2

    Login in with the AAF Single sign-on button (See below).

    Select the AAF Virtual Home option (See below) and login with your AAF VHO credentials.

    +">

    1 - Getting Started

    Signing up and getting started with UQ-RCC XNAT

    1.1 - UQ members

    For UQ Staff and Students

    Signing into XNAT


    Step 1

    Open https://xnat.rcc.uq.edu.au

    Step 2

    Login in with the AAF Single sign-on button (shown below).

    Follow the AAF login process for your organisation

    Step 3

    After the AAF sign-in, you should be redirected back to XNAT (Example below)

    There will be no projects listed when signing in for the first-time, as your user account would have just been created.

    Proceed to to next section for setting up an XNAT project

    Creating XNAT project


    For UQ users, XNAT uses UQ-RDM HPC collections for storage allocation.
    For any general questions about UQ-RDM, please refer to the library guides

    Step 1

    Before creating an XNAT project, you’ll require a UQ-RDM HPC Collection

    • HPC collections ends with -Q and a 4-digit numerical identifier (e.g. PROJ001-Q0189)
    • Non-HPC collections end with -A (e.g. PROJ001-A0189) or -I (PROJ001-I0189)

    To create a new UQ-RDM HPC Collection, proceed with the following

    Open https://rdm.uq.edu.au/create-record and sign-in

    Fill in the record as per your project details

    REQUEST DATA STORAGE when complete

    Move on to the next step after the RDM collection is provisioned
    You should have an RDM collection name ready (e.g. PROJ001-Q0189)

    Step 2

    Open a ticket with RCC support

    Example below (replace __________ with your details)

    Subject: Create XNAT project __________

    Hello RCC support +Can we create an XNAT project for RDM collection __________

    Step 3

    The support ticket will inform you when the project is set up.

    • An XNAT project will be created with the matching name (e.g. PROJ001-Q0189)
    • An xnat directory will be created in the RDM collection for storing the XNAT data files
    • Please do not write or modify anything under the xnat directory

    XNAT Project setup typically takes around ~24 hours from ticket submission
    An automated email from XNAT will be sent through when project is ready, and your user has been added

    1.2 - Other AAF members

    Other AAF members

    This guide is for users from Australian Universities and AAF member organisations, including:

    • QUT, Griffith, CQU, JCU, USQ, USC
    • CSIRO, Australian Universities
    • AAF VHO accounts

    Other AAF members usually require UQ AIS XNAT access for:

    • Management of data acquisition from sites such as CAI, HIRF, TRI
    • Collaborating on projects managed on UQ AIS XNAT

    Full list of AAF members found here
    For all other organisations, use the Non-AAF members guide

    Signing into XNAT


    Step 1

    Open https://xnat.rcc.uq.edu.au

    Step 2

    Login in with the AAF Single sign-on button (See below).

    Follow the AAF login process for your organisation

    Step 3

    After the AAF sign-in, you should be redirected back to XNAT (Example below)

    There will be no projects listed when signing in for the first-time, as your user account would have just been created.

    Accessing XNAT Project


    If you are Acquiring data at HIRF, CAI or TRI

    • The respective facility will organise the project creation.
    • You will receive a follow up email when access has been granted
    • Contact rcc-support@uq.edu.au if you have not received access within 5 working days

    If you are collaborating on an existing XNAT project

    • Contact the project lead to grant you access to the XNAT project

    1.3 - Non-AAF members

    Non-University, non-AAF members and other users

    This is for users from non-AAF member organisations, including:

    • QLD Health, TRI, QIMR, QLD Xray

    Non-AAF members usually require XNAT access for:

    • Management of data acquisition from sites such as CAI, HIRF, TRI
    • Collaborating on projects managed on UQ-RCC XNAT

    XNAT uses AAF for login. QCIF/QRIScloud can provide AAF Virtual Home (VHO) accounts for non-AAF users.

    Creating an AAF VHO account


    Step 1

    Open a ticket with RCC support to request an AAF account

    Example below (replace __________ with your details)

    Subject: XNAT AAF account for project __________

    Hello RCC support +I require an AAF account to access the UQ AIS XNAT service
    My details are below
    Organisation: __________
    Data Acquisition Site: __________

    Step 2

    AAF’s VHO account will return an email regarding the VHO account registration process

    Step 3

    After account is provisioned, continue on to the Signing into XNAT guide

    Signing into XNAT


    Step 1

    Open https://xnat.rcc.uq.edu.au

    Step 2

    Login in with the AAF Single sign-on button (See below).

    Select the AAF Virtual Home option (See below) and login with your AAF VHO credentials.

    -

    Step 3

    After the AAF sign-in, you should be redirected back to XNAT (Example below)

    There will be no projects listed when signing in for the first-time, as your user account would have just been created.

    Accessing XNAT Project


    If you are Acquiring data at HIRF, CAI or TRI

    • The respective facility will organise the project creation.
    • You will receive a follow up email when access has been granted
    • Contact rcc-support@uq.edu.au if you have not received access within 5 working days

    If you are collaborating on an existing XNAT project

    • Contact the project lead to grant you access to the XNAT project

    1.4 - HIRF users

    For users acquiring data at HIRF

    Data acquired at HIRF can be sent to the UQ-RCC XNAT repository

    To get started, refer to the relevant guide below:

    If you have any questions, contact rcc-support@uq.edu.au or HIRFAdministration@health.qld.gov.au

    2 - Logging into XNAT

    Logging into XNAT

    AAF

    If your organisation is part of the Australian Access Federation (AAF), you can use your AAF credentials to sign up. See here

    For more details on the Australian Access Federation, see https://aaf.edu.au

    RCC Authenticate

    To use this login, you would have received an email from a UQ XNAT administrator with the login information.

    2.1 - AAF login

    Login using Australian Access Federation (AAF)

    If your organisation is part of the Australian Access Federation (AAF), you can use your AAF credentials to sign up. Follow the steps below to sign-up/login using AAF.

    1. Open https://xnat.rcc.uq.edu.au
    2. Login in with the AAF Single sign-on button (shown below)

    This will take you to your XNAT home page.

    2.2 - RCC Authenticate

    Login using RCC Authenticate

    To use this login, you would have received an email from a UQ XNAT administrator with the login information.

    1. Login in with the RCC Authenticate button (shown below)

    1. You’ll be taken to a UQ RCC SERVICES (shown below)

    1. Enter your user name and password to sign in. +

      Step 3

      After the AAF sign-in, you should be redirected back to XNAT (Example below)

      There will be no projects listed when signing in for the first-time, as your user account would have just been created.

      Accessing XNAT Project


      If you are Acquiring data at HIRF, CAI or TRI

      • The respective facility will organise the project creation.
      • You will receive a follow up email when access has been granted
      • Contact rcc-support@uq.edu.au if you have not received access within 5 working days

      If you are collaborating on an existing XNAT project

      • Contact the project lead to grant you access to the XNAT project

    1.4 - HIRF users

    For users acquiring data at HIRF

    Data acquired at HIRF can be sent to the UQ-RCC XNAT repository

    To get started, refer to the relevant guide below:

    If you have any questions, contact rcc-support@uq.edu.au or HIRFAdministration@health.qld.gov.au

    2 - Logging into XNAT

    Logging into XNAT

    AAF

    If your organisation is part of the Australian Access Federation (AAF), you can use your AAF credentials to sign up. See here

    For more details on the Australian Access Federation, see https://aaf.edu.au

    RCC Authenticate

    To use this login, you would have received an email from a UQ XNAT administrator with the login information.

    2.1 - AAF login

    Login using Australian Access Federation (AAF)

    If your organisation is part of the Australian Access Federation (AAF), you can use your AAF credentials to sign up. Follow the steps below to sign-up/login using AAF.

    1. Open https://xnat.rcc.uq.edu.au
    2. Login in with the AAF Single sign-on button (shown below)

    This will take you to your XNAT home page.

    2.2 - RCC Authenticate

    Login using RCC Authenticate

    To use this login, you would have received an email from a UQ XNAT administrator with the login information.

    1. Login in with the RCC Authenticate button (shown below)

    1. You’ll be taken to a UQ RCC SERVICES (shown below)

    1. Enter your user name and password to sign in. This will take you to your XNAT home page.

    2.3 - Alias tokens

    Alias tokens

    AAF is used for logging into the XNAT website itself.

    But there are a lot of tools and services that will require a connect to the XNAT server externally

    These could include

    • Windows or Mac desktop clients, like XNAT Desktop
    • Command line tools such as xnatpy, pyxnat, xnatutils etc
    • XSYNC

    All of these tools and services need a way to authenticating to your XNAT account without AAF.

    An alias token is a time-limited, long, randomised username and password used for authenticating from external services, without compromising your AAF account or credentials. They can be generated and revoked easily

    We’ll look at how to generate them next

    Generating Alias tokens

    To access the alias token Click your name on the top right of the website. This will take you to your user profile management page

    Then click the “Manage Alias Tokens” option

    There, you’ll find the option to “Create an Alias Token”

    When you create the alias token, it will appear as a new entry

    Alias tokens expire 60 days after creation @@ -22,7 +23,7 @@ Click modify, and then submit for the changes to take effect.

    Just note, subject renaming can take a few minutes to take effect

    3.3 - Sessions

    Managing Scan Sessions

    Sessions are divided into three types, based on modality information extracted from the DICOM metadata

    • MR
    • CT
    • PET

    The following is an example MR session

    Editing Sessions

    We can edit session details and metadata from the actions panel on the right

    Here we can change some of the key properties of the sessions, such as

    • Change session name
    • Move sessions to other projects
    • Move sessions to other subjects
    • Create a new subject, and move session to that subject
    • Fix invalid or blank session names

    3.3.1 - Scans

    Accessing individual Scans

    The Scans themselves are listed at the bottom with the relevant series descriptions and other information If you hover over one of them, and click the highlighted view details button. This will open up a more details and an image preview window

    Here we can also view View DICOM headers

    And see the DICOM headers as shown on the right

    3.4 - Search

    Search across Projects, Subjects and Sessions

    You can search across Projects, Subjects or Sessions And Sessions are broken up into MR, PET and CT

    For instance, we can fill a couple of fields on the MR Sessions search -You don’t have to specify all the fields

    And XNAT will provide a list of results.

    4 - Managing Data

    Managing Data

    4.1 - Downloading Data

    Downloading data from XNAT Projects
    1. Navigate to Scan or Session (See guide on browsing data)
    2. Select Download from controls on top right.
    3. Use the following settings for downloading dataset as zip text

    For further information refer to the XNAT official guide on downloading data

    4.1.1 - Zip Download

    Downloading data as Zip using the XNAT UI

    The Project, Subject and Sessions page has the option to Download Images from the right hand side menu

    +You don’t have to specify all the fields

    And XNAT will provide a list of results.

    4 - Managing Data

    Managing Data

    4.1 - Downloading Data

    Downloading data from XNAT Projects
    1. Navigate to Scan or Session (See guide on browsing data)
    2. Select Download from controls on top right.
    3. Use the following settings for downloading dataset as zip text

    For further information refer to the XNAT official guide on downloading data

    4.1.1 - Zip Download

    Downloading data as Zip using the XNAT UI

    The Project, Subject and Sessions page has the option to Download Images from the right hand side menu

    Select Option 2: ZIP download

    Filter out the Session and scans from the first two columns and select Submit

    4.1.2 - Desktop client

    Downloading data using the XNAT Desktop client

    The XNAT Desktop client is maintained by the XNAT development team. For information see the link below.

    XNAT Desktop client
    https://www.xnat.org/download/desktop-client/

    Install client

    Download and install the client for you operating system

    Download images

    The Project, Subject and Sessions page has the option to Download Images from the right hand side menu

    Select Option 1: Download via Desktop Client

    Click Download Via App

    Select a local destination folder

    Download should start, and progress can be monitored

    4.1.3 - Download Scan

    Downloading induvidual Scans using the XNAT UI

    Induvidual scans can be downloaded from the Sessions page

    Multiple scans can be selected and downloaded using Bulk Actions

    4.2 - Viewing Images

    Viewing Images in the XNAT OHIF Viewer

    XNAT OHIF Viewer

    AIS XNAT instances come with the XNAT OHIF Image viewer Which is a plugin developed by the Institute for Cancer Research in London

    Just note, if your publication uses the OHIF viewer, they have an article for citation. @@ -39,6 +40,4 @@

    Authenticating using .netrc

    1. Create an alias token. Or use an existing alias token
    2. Create a .netrc file in your home directory with the following details
    machine https://xnat.rcc.uq.edu.au
     user <your-alias-token>
     password <your-alias-secret>
    -

    xnatpy

    https://xnat.readthedocs.io/en/latest/

    Pyxnat

    https://pyxnat.github.io/pyxnat

    6 -

    Example

    Example

    - - \ No newline at end of file +

    xnatpy

    https://xnat.readthedocs.io/en/latest/

    Pyxnat

    https://pyxnat.github.io/pyxnat

    6 -

    Example

    Example

    \ No newline at end of file diff --git a/docs/user-guides/browsing-xnat/_print/index.html b/docs/user-guides/browsing-xnat/_print/index.html index 3a79837..3714acf 100644 --- a/docs/user-guides/browsing-xnat/_print/index.html +++ b/docs/user-guides/browsing-xnat/_print/index.html @@ -1,14 +1,13 @@ -Browsing XNAT | UQ AIS XNATBrowsing XNAT | UQ AIS XNAT +

    This is the multi-page printable view of this section. +">

    This is the multi-page printable view of this section. Click here to print.

    Return to the regular view of this page.

    Browsing XNAT

    Browsing XNAT

    For further information refer to the XNAT official guides on browsing data

    1 - Projects

    Managing Projects

    When you login into the home page, the list of projects that you have access to will be on the left

    • All datasets have to go into Projects
    • User access is controlled at the project level

    1.1 - Granting Access

    Granting project access to other users

    Switch to the Access tab. Use Add User or Add Users from List to select the user to add

    Select role from

    1. Owners
    2. Members
    3. Collaborators

    User roles

    The following table outlines the permissions given to each role.

    PermissionOwnersMembersCollaborators
    Data - Create
    Data - Read/Download
    Data - Update
    Data - Delete
    User - Add/Remove
    User - Change role

    2 - Subjects

    Managing Subjects

    The Project page will have a list of Subjects If we click one of the subjects… it will take us to the subject page

    The Subject will have some associated metadata and name extracted from the DICOM headers of the datasets

    Editing Subjects

    We can edit subject details and metadata from the actions panel on the right

    For instance, if you want to rename the subject You click the button next to the Subject ID

    This will pop-up the following dialog box for you enter the new subject. Click modify, and then submit for the changes to take effect.

    Just note, subject renaming can take a few minutes to take effect

    3 - Sessions

    Managing Scan Sessions

    Sessions are divided into three types, based on modality information extracted from the DICOM metadata

    • MR
    • CT
    • PET

    The following is an example MR session

    Editing Sessions

    We can edit session details and metadata from the actions panel on the right

    Here we can change some of the key properties of the sessions, such as

    • Change session name
    • Move sessions to other projects
    • Move sessions to other subjects
    • Create a new subject, and move session to that subject
    • Fix invalid or blank session names

    3.1 - Scans

    Accessing individual Scans

    The Scans themselves are listed at the bottom with the relevant series descriptions and other information If you hover over one of them, and click the highlighted view details button. This will open up a more details and an image preview window

    Here we can also view View DICOM headers

    And see the DICOM headers as shown on the right

    4 - Search

    Search across Projects, Subjects and Sessions

    You can search across Projects, Subjects or Sessions And Sessions are broken up into MR, PET and CT

    For instance, we can fill a couple of fields on the MR Sessions search -You don’t have to specify all the fields

    And XNAT will provide a list of results.

    - - \ No newline at end of file +You don’t have to specify all the fields

    And XNAT will provide a list of results.

    \ No newline at end of file diff --git a/docs/user-guides/browsing-xnat/index.html b/docs/user-guides/browsing-xnat/index.html index 74a25bc..43d3ce9 100644 --- a/docs/user-guides/browsing-xnat/index.html +++ b/docs/user-guides/browsing-xnat/index.html @@ -1,7 +1,6 @@ -Browsing XNAT | UQ AIS XNATBrowsing XNAT | UQ AIS XNAT +
    - - \ No newline at end of file +">
    \ No newline at end of file diff --git a/docs/user-guides/browsing-xnat/projects/_print/index.html b/docs/user-guides/browsing-xnat/projects/_print/index.html index 1698452..1a248e1 100644 --- a/docs/user-guides/browsing-xnat/projects/_print/index.html +++ b/docs/user-guides/browsing-xnat/projects/_print/index.html @@ -1,8 +1,7 @@ -Projects | UQ AIS XNATProjects | UQ AIS XNAT +

    This is the multi-page printable view of this section. -Click here to print.

    Return to the regular view of this page.

    Projects

    Managing Projects

    When you login into the home page, the list of projects that you have access to will be on the left

    • All datasets have to go into Projects
    • User access is controlled at the project level

    1 - Granting Access

    Granting project access to other users

    Switch to the Access tab. Use Add User or Add Users from List to select the user to add

    Select role from

    1. Owners
    2. Members
    3. Collaborators

    User roles

    The following table outlines the permissions given to each role.

    PermissionOwnersMembersCollaborators
    Data - Create
    Data - Read/Download
    Data - Update
    Data - Delete
    User - Add/Remove
    User - Change role
    - - \ No newline at end of file +">

    This is the multi-page printable view of this section. +Click here to print.

    Return to the regular view of this page.

    Projects

    Managing Projects

    When you login into the home page, the list of projects that you have access to will be on the left

    • All datasets have to go into Projects
    • User access is controlled at the project level

    1 - Granting Access

    Granting project access to other users

    Switch to the Access tab. Use Add User or Add Users from List to select the user to add

    Select role from

    1. Owners
    2. Members
    3. Collaborators

    User roles

    The following table outlines the permissions given to each role.

    PermissionOwnersMembersCollaborators
    Data - Create
    Data - Read/Download
    Data - Update
    Data - Delete
    User - Add/Remove
    User - Change role
    \ No newline at end of file diff --git a/docs/user-guides/browsing-xnat/projects/granting-access/index.html b/docs/user-guides/browsing-xnat/projects/granting-access/index.html index 03732ad..0c51ef8 100644 --- a/docs/user-guides/browsing-xnat/projects/granting-access/index.html +++ b/docs/user-guides/browsing-xnat/projects/granting-access/index.html @@ -1,7 +1,6 @@ -Granting Access | UQ AIS XNATGranting Access | UQ AIS XNAT +

    Granting Access

    Granting project access to other users

    Switch to the Access tab. Use Add User or Add Users from List to select the user to add

    Select role from

    1. Owners
    2. Members
    3. Collaborators

    User roles

    The following table outlines the permissions given to each role.

    PermissionOwnersMembersCollaborators
    Data - Create
    Data - Read/Download
    Data - Update
    Data - Delete
    User - Add/Remove
    User - Change role
    - - \ No newline at end of file +">

    Granting Access

    Granting project access to other users

    Switch to the Access tab. Use Add User or Add Users from List to select the user to add

    Select role from

    1. Owners
    2. Members
    3. Collaborators

    User roles

    The following table outlines the permissions given to each role.

    PermissionOwnersMembersCollaborators
    Data - Create
    Data - Read/Download
    Data - Update
    Data - Delete
    User - Add/Remove
    User - Change role
    \ No newline at end of file diff --git a/docs/user-guides/browsing-xnat/projects/index.html b/docs/user-guides/browsing-xnat/projects/index.html index 0358260..f4bdbd8 100644 --- a/docs/user-guides/browsing-xnat/projects/index.html +++ b/docs/user-guides/browsing-xnat/projects/index.html @@ -1,7 +1,6 @@ -Projects | UQ AIS XNATProjects | UQ AIS XNAT +
    - - \ No newline at end of file +">
    \ No newline at end of file diff --git a/docs/user-guides/browsing-xnat/search/_print/index.html b/docs/user-guides/browsing-xnat/search/_print/index.html index 6a22a7d..dc174d1 100644 --- a/docs/user-guides/browsing-xnat/search/_print/index.html +++ b/docs/user-guides/browsing-xnat/search/_print/index.html @@ -1,10 +1,9 @@ -Search | UQ AIS XNATSearch | UQ AIS XNAT +

    This is the multi-page printable view of this section. +">

    This is the multi-page printable view of this section. Click here to print.

    Return to the regular view of this page.

    Search

    Search across Projects, Subjects and Sessions

      You can search across Projects, Subjects or Sessions And Sessions are broken up into MR, PET and CT

      For instance, we can fill a couple of fields on the MR Sessions search -You don’t have to specify all the fields

      And XNAT will provide a list of results.

      - - \ No newline at end of file +You don’t have to specify all the fields

      And XNAT will provide a list of results.

      \ No newline at end of file diff --git a/docs/user-guides/browsing-xnat/search/index.html b/docs/user-guides/browsing-xnat/search/index.html index 3b1f2e1..3adcadf 100644 --- a/docs/user-guides/browsing-xnat/search/index.html +++ b/docs/user-guides/browsing-xnat/search/index.html @@ -1,9 +1,8 @@ -Search | UQ AIS XNATSearch | UQ AIS XNAT +

      Search

      Search across Projects, Subjects and Sessions

      You can search across Projects, Subjects or Sessions +">

      - - \ No newline at end of file +You don’t have to specify all the fields

      And XNAT will provide a list of results.

      \ No newline at end of file diff --git a/docs/user-guides/browsing-xnat/sessions/_print/index.html b/docs/user-guides/browsing-xnat/sessions/_print/index.html index 1a75493..69d899f 100644 --- a/docs/user-guides/browsing-xnat/sessions/_print/index.html +++ b/docs/user-guides/browsing-xnat/sessions/_print/index.html @@ -1,9 +1,8 @@ -Sessions | UQ AIS XNATSessions | UQ AIS XNAT +

      This is the multi-page printable view of this section. +">

      This is the multi-page printable view of this section. Click here to print.

      Return to the regular view of this page.

      Sessions

      Managing Scan Sessions

      Sessions are divided into three types, based on modality information extracted from the DICOM metadata

      • MR
      • CT
      • PET

      The following is an example MR session

      Editing Sessions

      We can edit session details and metadata from the actions panel on the right

      Here we can change some of the key properties of the sessions, such as

      • Change session name
      • Move sessions to other projects
      • Move sessions to other subjects
      • Create a new subject, and move session to that subject
      • Fix invalid or blank session names

      1 - Scans

      Accessing individual Scans

      The Scans themselves are listed at the bottom with the relevant series descriptions and other information -If you hover over one of them, and click the highlighted view details button. This will open up a more details and an image preview window

      Here we can also view View DICOM headers

      And see the DICOM headers as shown on the right

      - - \ No newline at end of file +If you hover over one of them, and click the highlighted view details button. This will open up a more details and an image preview window

      Here we can also view View DICOM headers

      And see the DICOM headers as shown on the right

      \ No newline at end of file diff --git a/docs/user-guides/browsing-xnat/sessions/index.html b/docs/user-guides/browsing-xnat/sessions/index.html index 268065a..08a2f78 100644 --- a/docs/user-guides/browsing-xnat/sessions/index.html +++ b/docs/user-guides/browsing-xnat/sessions/index.html @@ -1,7 +1,6 @@ -Sessions | UQ AIS XNATSessions | UQ AIS XNAT +

      Sessions

      Managing Scan Sessions

      Sessions are divided into three types, based on modality information extracted from the DICOM metadata

      • MR
      • CT
      • PET

      The following is an example MR session

      Editing Sessions

      We can edit session details and metadata from the actions panel on the right

      Here we can change some of the key properties of the sessions, such as

      • Change session name
      • Move sessions to other projects
      • Move sessions to other subjects
      • Create a new subject, and move session to that subject
      • Fix invalid or blank session names


      Scans

      Accessing individual Scans

      - - \ No newline at end of file +">

      Sessions

      Managing Scan Sessions

      Sessions are divided into three types, based on modality information extracted from the DICOM metadata

      • MR
      • CT
      • PET

      The following is an example MR session

      Editing Sessions

      We can edit session details and metadata from the actions panel on the right

      Here we can change some of the key properties of the sessions, such as

      • Change session name
      • Move sessions to other projects
      • Move sessions to other subjects
      • Create a new subject, and move session to that subject
      • Fix invalid or blank session names


      Scans

      Accessing individual Scans

      \ No newline at end of file diff --git a/docs/user-guides/browsing-xnat/sessions/scans/index.html b/docs/user-guides/browsing-xnat/sessions/scans/index.html index c9cad38..76e33dd 100644 --- a/docs/user-guides/browsing-xnat/sessions/scans/index.html +++ b/docs/user-guides/browsing-xnat/sessions/scans/index.html @@ -1,8 +1,7 @@ -Scans | UQ AIS XNATScans | UQ AIS XNAT +
      - - \ No newline at end of file +">
      \ No newline at end of file diff --git a/docs/user-guides/browsing-xnat/subjects/_print/index.html b/docs/user-guides/browsing-xnat/subjects/_print/index.html index e0965af..ab60ca9 100644 --- a/docs/user-guides/browsing-xnat/subjects/_print/index.html +++ b/docs/user-guides/browsing-xnat/subjects/_print/index.html @@ -1,11 +1,10 @@ -Subjects | UQ AIS XNATSubjects | UQ AIS XNAT +

      This is the multi-page printable view of this section. +">

      This is the multi-page printable view of this section. Click here to print.

      Return to the regular view of this page.

      Subjects

      Managing Subjects

        The Project page will have a list of Subjects If we click one of the subjects… it will take us to the subject page

        The Subject will have some associated metadata and name extracted from the DICOM headers of the datasets

        Editing Subjects

        We can edit subject details and metadata from the actions panel on the right

        For instance, if you want to rename the subject You click the button next to the Subject ID

        This will pop-up the following dialog box for you enter the new subject. - Click modify, and then submit for the changes to take effect.

        Just note, subject renaming can take a few minutes to take effect

        - - \ No newline at end of file + Click modify, and then submit for the changes to take effect.

        Just note, subject renaming can take a few minutes to take effect

        \ No newline at end of file diff --git a/docs/user-guides/browsing-xnat/subjects/index.html b/docs/user-guides/browsing-xnat/subjects/index.html index c05c53d..13e63ec 100644 --- a/docs/user-guides/browsing-xnat/subjects/index.html +++ b/docs/user-guides/browsing-xnat/subjects/index.html @@ -1,10 +1,9 @@ -Subjects | UQ AIS XNATSubjects | UQ AIS XNAT +

        Subjects

        Managing Subjects

        The Project page will have a list of Subjects +">

        Subjects

        Managing Subjects

        The Project page will have a list of Subjects If we click one of the subjects… it will take us to the subject page

        The Subject will have some associated metadata and name extracted from the DICOM headers of the datasets

        Editing Subjects

        We can edit subject details and metadata from the actions panel on the right

        For instance, if you want to rename the subject You click the button next to the Subject ID

        This will pop-up the following dialog box for you enter the new subject. - Click modify, and then submit for the changes to take effect.

        Just note, subject renaming can take a few minutes to take effect

        - - \ No newline at end of file + Click modify, and then submit for the changes to take effect.

        Just note, subject renaming can take a few minutes to take effect

        \ No newline at end of file diff --git a/docs/user-guides/create-xnat-project/create-q-collection-non-uq-users/index.html b/docs/user-guides/create-xnat-project/create-q-collection-non-uq-users/index.html index 21739d1..bbcba45 100644 --- a/docs/user-guides/create-xnat-project/create-q-collection-non-uq-users/index.html +++ b/docs/user-guides/create-xnat-project/create-q-collection-non-uq-users/index.html @@ -1 +1,2 @@ -https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/other-aaf-members/ \ No newline at end of file +https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/other-aaf-members/ + \ No newline at end of file diff --git a/docs/user-guides/create-xnat-project/create-q-collection-uq-users/index.html b/docs/user-guides/create-xnat-project/create-q-collection-uq-users/index.html index c32831c..a92dae8 100644 --- a/docs/user-guides/create-xnat-project/create-q-collection-uq-users/index.html +++ b/docs/user-guides/create-xnat-project/create-q-collection-uq-users/index.html @@ -1 +1,2 @@ -https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/uq-members/ \ No newline at end of file +https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/uq-members/ + \ No newline at end of file diff --git a/docs/user-guides/create-xnat-project/index.html b/docs/user-guides/create-xnat-project/index.html index 5e3ea88..64fe480 100644 --- a/docs/user-guides/create-xnat-project/index.html +++ b/docs/user-guides/create-xnat-project/index.html @@ -1 +1,2 @@ -https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/ \ No newline at end of file +https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/ + \ No newline at end of file diff --git a/docs/user-guides/faq/index.html b/docs/user-guides/faq/index.html index 91c5f3e..c2d2f4d 100644 --- a/docs/user-guides/faq/index.html +++ b/docs/user-guides/faq/index.html @@ -1,3 +1,2 @@ -UQ AIS XNAT
        - - \ No newline at end of file +UQ AIS XNAT +
        \ No newline at end of file diff --git a/docs/user-guides/getting-started/_print/index.html b/docs/user-guides/getting-started/_print/index.html index 363948d..5bb91e5 100644 --- a/docs/user-guides/getting-started/_print/index.html +++ b/docs/user-guides/getting-started/_print/index.html @@ -1,12 +1,11 @@ -Getting Started | UQ AIS XNATGetting Started | UQ AIS XNAT +

        This is the multi-page printable view of this section. -Click here to print.

        Return to the regular view of this page.

        Getting Started

        Signing up and getting started with UQ-RCC XNAT

        1 - UQ members

        For UQ Staff and Students

        Signing into XNAT


        Step 1

        Open https://xnat.rcc.uq.edu.au

        Step 2

        Login in with the AAF Single sign-on button (shown below).

        Follow the AAF login process for your organisation

        Step 3

        After the AAF sign-in, you should be redirected back to XNAT (Example below)

        There will be no projects listed when signing in for the first-time, as your user account would have just been created.

        Proceed to to next section for setting up an XNAT project

        Creating XNAT project


        For UQ users, XNAT uses UQ-RDM HPC collections for storage allocation.
        For any general questions about UQ-RDM, please refer to the library guides

        Step 1

        Before creating an XNAT project, you’ll require a UQ-RDM HPC Collection

        • HPC collections ends with -Q and a 4-digit numerical identifier (e.g. PROJ001-Q0189)
        • Non-HPC collections end with -A (e.g. PROJ001-A0189) or -I (PROJ001-I0189)

        To create a new UQ-RDM HPC Collection, proceed with the following

        Open https://rdm.uq.edu.au/create-record and sign-in

        Fill in the record as per your project details

        REQUEST DATA STORAGE when complete

        Move on to the next step after the RDM collection is provisioned
        You should have an RDM collection name ready (e.g. PROJ001-Q0189)

        Step 2

        Open a ticket with RCC support

        Example below (replace __________ with your details)

        Subject: Create XNAT project __________

        Hello RCC support -Can we create an XNAT project for RDM collection __________

        Step 3

        The support ticket will inform you when the project is set up.

        • An XNAT project will be created with the matching name (e.g. PROJ001-Q0189)
        • An xnat directory will be created in the RDM collection for storing the XNAT data files
        • Please do not write or modify anything under the xnat directory

        XNAT Project setup typically takes around ~24 hours from ticket submission
        An automated email from XNAT will be sent through when project is ready, and your user has been added

        2 - Other AAF members

        Other AAF members

        This guide is for users from Australian Universities and AAF member organisations, including:

        • QUT, Griffith, CQU, JCU, USQ, USC
        • CSIRO, Australian Universities
        • AAF VHO accounts

        Other AAF members usually require UQ AIS XNAT access for:

        • Management of data acquisition from sites such as CAI, HIRF, TRI
        • Collaborating on projects managed on UQ AIS XNAT

        Full list of AAF members found here
        For all other organisations, use the Non-AAF members guide

        Signing into XNAT


        Step 1

        Open https://xnat.rcc.uq.edu.au

        Step 2

        Login in with the AAF Single sign-on button (See below).

        Follow the AAF login process for your organisation

        Step 3

        After the AAF sign-in, you should be redirected back to XNAT (Example below)

        There will be no projects listed when signing in for the first-time, as your user account would have just been created.

        Accessing XNAT Project


        If you are Acquiring data at HIRF, CAI or TRI

        • The respective facility will organise the project creation.
        • You will receive a follow up email when access has been granted
        • Contact rcc-support@uq.edu.au if you have not received access within 5 working days

        If you are collaborating on an existing XNAT project

        • Contact the project lead to grant you access to the XNAT project

        3 - Non-AAF members

        Non-University, non-AAF members and other users

        This is for users from non-AAF member organisations, including:

        • QLD Health, TRI, QIMR, QLD Xray

        Non-AAF members usually require XNAT access for:

        • Management of data acquisition from sites such as CAI, HIRF, TRI
        • Collaborating on projects managed on UQ-RCC XNAT

        XNAT uses AAF for login. QCIF/QRIScloud can provide AAF Virtual Home (VHO) accounts for non-AAF users.

        Creating an AAF VHO account


        Step 1

        Open a ticket with RCC support to request an AAF account

        Example below (replace __________ with your details)

        Subject: XNAT AAF account for project __________

        Hello RCC support -I require an AAF account to access the UQ AIS XNAT service
        My details are below
        Organisation: __________
        Data Acquisition Site: __________

        Step 2

        AAF’s VHO account will return an email regarding the VHO account registration process

        Step 3

        After account is provisioned, continue on to the Signing into XNAT guide

        Signing into XNAT


        Step 1

        Open https://xnat.rcc.uq.edu.au

        Step 2

        Login in with the AAF Single sign-on button (See below).

        Select the AAF Virtual Home option (See below) and login with your AAF VHO credentials.

        +">

        This is the multi-page printable view of this section. +Click here to print.

        Return to the regular view of this page.

        Getting Started

        Signing up and getting started with UQ-RCC XNAT

        1 - UQ members

        For UQ Staff and Students

        Signing into XNAT


        Step 1

        Open https://xnat.rcc.uq.edu.au

        Step 2

        Login in with the AAF Single sign-on button (shown below).

        Follow the AAF login process for your organisation

        Step 3

        After the AAF sign-in, you should be redirected back to XNAT (Example below)

        There will be no projects listed when signing in for the first-time, as your user account would have just been created.

        Proceed to to next section for setting up an XNAT project

        Creating XNAT project


        For UQ users, XNAT uses UQ-RDM HPC collections for storage allocation.
        For any general questions about UQ-RDM, please refer to the library guides

        Step 1

        Before creating an XNAT project, you’ll require a UQ-RDM HPC Collection

        • HPC collections ends with -Q and a 4-digit numerical identifier (e.g. PROJ001-Q0189)
        • Non-HPC collections end with -A (e.g. PROJ001-A0189) or -I (PROJ001-I0189)

        To create a new UQ-RDM HPC Collection, proceed with the following

        Open https://rdm.uq.edu.au/create-record and sign-in

        Fill in the record as per your project details

        REQUEST DATA STORAGE when complete

        Move on to the next step after the RDM collection is provisioned
        You should have an RDM collection name ready (e.g. PROJ001-Q0189)

        Step 2

        Open a ticket with RCC support

        Example below (replace __________ with your details)

        Subject: Create XNAT project __________

        Hello RCC support +Can we create an XNAT project for RDM collection __________

        Step 3

        The support ticket will inform you when the project is set up.

        • An XNAT project will be created with the matching name (e.g. PROJ001-Q0189)
        • An xnat directory will be created in the RDM collection for storing the XNAT data files
        • Please do not write or modify anything under the xnat directory

        XNAT Project setup typically takes around ~24 hours from ticket submission
        An automated email from XNAT will be sent through when project is ready, and your user has been added

        2 - Other AAF members

        Other AAF members

        This guide is for users from Australian Universities and AAF member organisations, including:

        • QUT, Griffith, CQU, JCU, USQ, USC
        • CSIRO, Australian Universities
        • AAF VHO accounts

        Other AAF members usually require UQ AIS XNAT access for:

        • Management of data acquisition from sites such as CAI, HIRF, TRI
        • Collaborating on projects managed on UQ AIS XNAT

        Full list of AAF members found here
        For all other organisations, use the Non-AAF members guide

        Signing into XNAT


        Step 1

        Open https://xnat.rcc.uq.edu.au

        Step 2

        Login in with the AAF Single sign-on button (See below).

        Follow the AAF login process for your organisation

        Step 3

        After the AAF sign-in, you should be redirected back to XNAT (Example below)

        There will be no projects listed when signing in for the first-time, as your user account would have just been created.

        Accessing XNAT Project


        If you are Acquiring data at HIRF, CAI or TRI

        • The respective facility will organise the project creation.
        • You will receive a follow up email when access has been granted
        • Contact rcc-support@uq.edu.au if you have not received access within 5 working days

        If you are collaborating on an existing XNAT project

        • Contact the project lead to grant you access to the XNAT project

        3 - Non-AAF members

        Non-University, non-AAF members and other users

        This is for users from non-AAF member organisations, including:

        • QLD Health, TRI, QIMR, QLD Xray

        Non-AAF members usually require XNAT access for:

        • Management of data acquisition from sites such as CAI, HIRF, TRI
        • Collaborating on projects managed on UQ-RCC XNAT

        XNAT uses AAF for login. QCIF/QRIScloud can provide AAF Virtual Home (VHO) accounts for non-AAF users.

        Creating an AAF VHO account


        Step 1

        Open a ticket with RCC support to request an AAF account

        Example below (replace __________ with your details)

        Subject: XNAT AAF account for project __________

        Hello RCC support +I require an AAF account to access the UQ AIS XNAT service
        My details are below
        Organisation: __________
        Data Acquisition Site: __________

        Step 2

        AAF’s VHO account will return an email regarding the VHO account registration process

        Step 3

        After account is provisioned, continue on to the Signing into XNAT guide

        Signing into XNAT


        Step 1

        Open https://xnat.rcc.uq.edu.au

        Step 2

        Login in with the AAF Single sign-on button (See below).

        Select the AAF Virtual Home option (See below) and login with your AAF VHO credentials.

        -

        Step 3

        After the AAF sign-in, you should be redirected back to XNAT (Example below)

        There will be no projects listed when signing in for the first-time, as your user account would have just been created.

        Accessing XNAT Project


        If you are Acquiring data at HIRF, CAI or TRI

        • The respective facility will organise the project creation.
        • You will receive a follow up email when access has been granted
        • Contact rcc-support@uq.edu.au if you have not received access within 5 working days

        If you are collaborating on an existing XNAT project

        • Contact the project lead to grant you access to the XNAT project

        4 - HIRF users

        For users acquiring data at HIRF

        Data acquired at HIRF can be sent to the UQ-RCC XNAT repository

        To get started, refer to the relevant guide below:

        If you have any questions, contact rcc-support@uq.edu.au or HIRFAdministration@health.qld.gov.au

        - - \ No newline at end of file +

        Step 3

        After the AAF sign-in, you should be redirected back to XNAT (Example below)

        There will be no projects listed when signing in for the first-time, as your user account would have just been created.

        Accessing XNAT Project


        If you are Acquiring data at HIRF, CAI or TRI

        • The respective facility will organise the project creation.
        • You will receive a follow up email when access has been granted
        • Contact rcc-support@uq.edu.au if you have not received access within 5 working days

        If you are collaborating on an existing XNAT project

        • Contact the project lead to grant you access to the XNAT project

        4 - HIRF users

        For users acquiring data at HIRF

        Data acquired at HIRF can be sent to the UQ-RCC XNAT repository

        To get started, refer to the relevant guide below:

        If you have any questions, contact rcc-support@uq.edu.au or HIRFAdministration@health.qld.gov.au

        \ No newline at end of file diff --git a/docs/user-guides/getting-started/hirf-users/index.html b/docs/user-guides/getting-started/hirf-users/index.html index 58ef0c2..261a2b8 100644 --- a/docs/user-guides/getting-started/hirf-users/index.html +++ b/docs/user-guides/getting-started/hirf-users/index.html @@ -1,7 +1,6 @@ -HIRF users | UQ AIS XNATHIRF users | UQ AIS XNAT +

        HIRF users

        For users acquiring data at HIRF

        Data acquired at HIRF can be sent to the UQ-RCC XNAT repository

        To get started, refer to the relevant guide below:

        If you have any questions, contact rcc-support@uq.edu.au or HIRFAdministration@health.qld.gov.au

        - - \ No newline at end of file +">

        HIRF users

        For users acquiring data at HIRF

        Data acquired at HIRF can be sent to the UQ-RCC XNAT repository

        To get started, refer to the relevant guide below:

        If you have any questions, contact rcc-support@uq.edu.au or HIRFAdministration@health.qld.gov.au

        \ No newline at end of file diff --git a/docs/user-guides/getting-started/index.html b/docs/user-guides/getting-started/index.html index 51eaf69..bf13d4f 100644 --- a/docs/user-guides/getting-started/index.html +++ b/docs/user-guides/getting-started/index.html @@ -1,7 +1,6 @@ -Getting Started | UQ AIS XNATGetting Started | UQ AIS XNAT +
        - - \ No newline at end of file +">
        \ No newline at end of file diff --git a/docs/user-guides/getting-started/index.xml b/docs/user-guides/getting-started/index.xml index 32da9c0..48d6e56 100644 --- a/docs/user-guides/getting-started/index.xml +++ b/docs/user-guides/getting-started/index.xml @@ -38,7 +38,7 @@ Only one member of the project team needs to request for the project <li><strong>Non-HPC collections</strong> end with <strong>-A</strong> (e.g. PROJ001-<strong>A0189</strong>) or <strong>-I</strong> (PROJ001-<strong>I0189</strong>)</li> </ul> <div class="alert alert-warning" role="alert"> -If you have an existing UQ-RDM <strong>HPC collection</strong> (ending with <strong>-Qxxxx</strong>), skip to the <a href="./#step-2-1">next step</a> +If you have an existing UQ-RDM <strong>HPC collection</strong> (ending with <strong>-Qxxxx</strong>), skip to the <a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/#step-2-1">next step</a> </div> <p>To create a new UQ-RDM <strong>HPC Collection</strong>, proceed with the following</p> <p>Open <a href="https://rdm.uq.edu.au/create-record">https://rdm.uq.edu.au/create-record</a> and sign-in</p> @@ -89,7 +89,7 @@ An automated email from XNAT will be sent through when project is ready, and you <li>Collaborating on projects managed on UQ AIS XNAT</li> </ul> <p>Full list of AAF members found <a href="https://aaf.edu.au/subscribers">here</a><br> -For all other organisations, use the <a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/non-aaf-members">Non-AAF members</a> guide</p> +For all other organisations, use the <a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/non-aaf-members/">Non-AAF members</a> guide</p> <h2 id="signing-into-xnat">Signing into XNAT</h2> <hr> <h4 id="step-1">Step 1</h4> @@ -159,7 +159,7 @@ Data Acquisition Site: __________<br> <h4 id="step-2">Step 2</h4> <p>AAF&rsquo;s VHO account will return an email regarding the VHO account registration process</p> <h4 id="step-3">Step 3</h4> -<p><em>After account is provisioned, continue on to the <a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/non-aaf-members#signing-into-xnat">Signing into XNAT guide</a></em></p> +<p><em>After account is provisioned, continue on to the <a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/non-aaf-members/#signing-into-xnat">Signing into XNAT guide</a></em></p> <h2 id="signing-into-xnat">Signing into XNAT</h2> <hr> <h4 id="step-1-1">Step 1</h4> @@ -194,19 +194,19 @@ This is the link to the UQ AIS XNAT. If you have been provided with a project sp <p>Data acquired at HIRF can be sent to the UQ-RCC XNAT repository</p> <p>To get started, refer to the relevant guide below:</p> <ul> -<li><a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/uq-members">UQ members</a> +<li><a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/uq-members/">UQ members</a> <ul> <li>UQ Staff and Students</li> </ul> </li> -<li><a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/other-aaf-members">Other AAF members</a> +<li><a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/other-aaf-members/">Other AAF members</a> <ul> <li>QUT, Griffith, CQU, JCU, USQ, USC, Bond</li> <li>CSIRO, QCIF, Australian Universities</li> <li>Full list of AAF members found <a href="https://aaf.edu.au/subscribers">here</a></li> </ul> </li> -<li><a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/non-aaf-members">Non-AAF members</a> +<li><a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/non-aaf-members/">Non-AAF members</a> <ul> <li>TRI, QIMR</li> <li>QLD Health, QLD Xray, Pacific Radiology</li> @@ -214,6 +214,6 @@ This is the link to the UQ AIS XNAT. If you have been provided with a project sp </li> </ul> <div class="alert alert-warning" role="alert"> -If you have multiple valid affiliations, we&rsquo;d recommend using <a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/uq-members">UQ</a> or <a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/other-aaf-members">AAF</a> affiliation where possible +If you have multiple valid affiliations, we&rsquo;d recommend using <a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/uq-members/">UQ</a> or <a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/other-aaf-members/">AAF</a> affiliation where possible </div> <p>If you have any questions, contact <a href="mailto:rcc-support@uq.edu.au">rcc-support@uq.edu.au</a> or <a href="mailto:HIRFAdministration@health.qld.gov.au">HIRFAdministration@health.qld.gov.au</a></p> \ No newline at end of file diff --git a/docs/user-guides/getting-started/non-aaf-members/index.html b/docs/user-guides/getting-started/non-aaf-members/index.html index 0e31b21..f728a45 100644 --- a/docs/user-guides/getting-started/non-aaf-members/index.html +++ b/docs/user-guides/getting-started/non-aaf-members/index.html @@ -1,10 +1,9 @@ -Non-AAF members | UQ AIS XNATNon-AAF members | UQ AIS XNAT +

        Non-AAF members

        Non-University, non-AAF members and other users

        This is for users from non-AAF member organisations, including:

        • QLD Health, TRI, QIMR, QLD Xray

        Non-AAF members usually require XNAT access for:

        • Management of data acquisition from sites such as CAI, HIRF, TRI
        • Collaborating on projects managed on UQ-RCC XNAT

        XNAT uses AAF for login. QCIF/QRIScloud can provide AAF Virtual Home (VHO) accounts for non-AAF users.

        Creating an AAF VHO account


        Step 1

        Open a ticket with RCC support to request an AAF account

        Example below (replace __________ with your details)

        Subject: XNAT AAF account for project __________

        Hello RCC support -I require an AAF account to access the UQ AIS XNAT service
        My details are below
        Organisation: __________
        Data Acquisition Site: __________

        Step 2

        AAF’s VHO account will return an email regarding the VHO account registration process

        Step 3

        After account is provisioned, continue on to the Signing into XNAT guide

        Signing into XNAT


        Step 1

        Open https://xnat.rcc.uq.edu.au

        Step 2

        Login in with the AAF Single sign-on button (See below).

        Select the AAF Virtual Home option (See below) and login with your AAF VHO credentials.

        +">

        Non-AAF members

        Non-University, non-AAF members and other users

        This is for users from non-AAF member organisations, including:

        • QLD Health, TRI, QIMR, QLD Xray

        Non-AAF members usually require XNAT access for:

        • Management of data acquisition from sites such as CAI, HIRF, TRI
        • Collaborating on projects managed on UQ-RCC XNAT

        XNAT uses AAF for login. QCIF/QRIScloud can provide AAF Virtual Home (VHO) accounts for non-AAF users.

        Creating an AAF VHO account


        Step 1

        Open a ticket with RCC support to request an AAF account

        Example below (replace __________ with your details)

        Subject: XNAT AAF account for project __________

        Hello RCC support +I require an AAF account to access the UQ AIS XNAT service
        My details are below
        Organisation: __________
        Data Acquisition Site: __________

        Step 2

        AAF’s VHO account will return an email regarding the VHO account registration process

        Step 3

        After account is provisioned, continue on to the Signing into XNAT guide

        Signing into XNAT


        Step 1

        Open https://xnat.rcc.uq.edu.au

        Step 2

        Login in with the AAF Single sign-on button (See below).

        Select the AAF Virtual Home option (See below) and login with your AAF VHO credentials.

        -

        Step 3

        After the AAF sign-in, you should be redirected back to XNAT (Example below)

        There will be no projects listed when signing in for the first-time, as your user account would have just been created.

        Accessing XNAT Project


        If you are Acquiring data at HIRF, CAI or TRI

        • The respective facility will organise the project creation.
        • You will receive a follow up email when access has been granted
        • Contact rcc-support@uq.edu.au if you have not received access within 5 working days

        If you are collaborating on an existing XNAT project

        • Contact the project lead to grant you access to the XNAT project
        - - \ No newline at end of file +

        Step 3

        After the AAF sign-in, you should be redirected back to XNAT (Example below)

        There will be no projects listed when signing in for the first-time, as your user account would have just been created.

        Accessing XNAT Project


        If you are Acquiring data at HIRF, CAI or TRI

        • The respective facility will organise the project creation.
        • You will receive a follow up email when access has been granted
        • Contact rcc-support@uq.edu.au if you have not received access within 5 working days

        If you are collaborating on an existing XNAT project

        • Contact the project lead to grant you access to the XNAT project
        \ No newline at end of file diff --git a/docs/user-guides/getting-started/other-aaf-members/index.html b/docs/user-guides/getting-started/other-aaf-members/index.html index ccdd1c3..31c0a05 100644 --- a/docs/user-guides/getting-started/other-aaf-members/index.html +++ b/docs/user-guides/getting-started/other-aaf-members/index.html @@ -1,7 +1,6 @@ -Other AAF members | UQ AIS XNATOther AAF members | UQ AIS XNAT +

        Other AAF members

        Other AAF members

        This guide is for users from Australian Universities and AAF member organisations, including:

        • QUT, Griffith, CQU, JCU, USQ, USC
        • CSIRO, Australian Universities
        • AAF VHO accounts

        Other AAF members usually require UQ AIS XNAT access for:

        • Management of data acquisition from sites such as CAI, HIRF, TRI
        • Collaborating on projects managed on UQ AIS XNAT

        Full list of AAF members found here
        For all other organisations, use the Non-AAF members guide

        Signing into XNAT


        Step 1

        Open https://xnat.rcc.uq.edu.au

        Step 2

        Login in with the AAF Single sign-on button (See below).

        Follow the AAF login process for your organisation

        Step 3

        After the AAF sign-in, you should be redirected back to XNAT (Example below)

        There will be no projects listed when signing in for the first-time, as your user account would have just been created.

        Accessing XNAT Project


        If you are Acquiring data at HIRF, CAI or TRI

        • The respective facility will organise the project creation.
        • You will receive a follow up email when access has been granted
        • Contact rcc-support@uq.edu.au if you have not received access within 5 working days

        If you are collaborating on an existing XNAT project

        • Contact the project lead to grant you access to the XNAT project
        - - \ No newline at end of file +">

        Other AAF members

        Other AAF members

        This guide is for users from Australian Universities and AAF member organisations, including:

        • QUT, Griffith, CQU, JCU, USQ, USC
        • CSIRO, Australian Universities
        • AAF VHO accounts

        Other AAF members usually require UQ AIS XNAT access for:

        • Management of data acquisition from sites such as CAI, HIRF, TRI
        • Collaborating on projects managed on UQ AIS XNAT

        Full list of AAF members found here
        For all other organisations, use the Non-AAF members guide

        Signing into XNAT


        Step 1

        Open https://xnat.rcc.uq.edu.au

        Step 2

        Login in with the AAF Single sign-on button (See below).

        Follow the AAF login process for your organisation

        Step 3

        After the AAF sign-in, you should be redirected back to XNAT (Example below)

        There will be no projects listed when signing in for the first-time, as your user account would have just been created.

        Accessing XNAT Project


        If you are Acquiring data at HIRF, CAI or TRI

        • The respective facility will organise the project creation.
        • You will receive a follow up email when access has been granted
        • Contact rcc-support@uq.edu.au if you have not received access within 5 working days

        If you are collaborating on an existing XNAT project

        • Contact the project lead to grant you access to the XNAT project
        \ No newline at end of file diff --git a/docs/user-guides/getting-started/uq-members/index.html b/docs/user-guides/getting-started/uq-members/index.html index f8436fc..d63af8d 100644 --- a/docs/user-guides/getting-started/uq-members/index.html +++ b/docs/user-guides/getting-started/uq-members/index.html @@ -1,8 +1,7 @@ -UQ members | UQ AIS XNATUQ members | UQ AIS XNAT +

        UQ members

        For UQ Staff and Students

        Signing into XNAT


        Step 1

        Open https://xnat.rcc.uq.edu.au

        Step 2

        Login in with the AAF Single sign-on button (shown below).

        Follow the AAF login process for your organisation

        Step 3

        After the AAF sign-in, you should be redirected back to XNAT (Example below)

        There will be no projects listed when signing in for the first-time, as your user account would have just been created.

        Proceed to to next section for setting up an XNAT project

        Creating XNAT project


        For UQ users, XNAT uses UQ-RDM HPC collections for storage allocation.
        For any general questions about UQ-RDM, please refer to the library guides

        Step 1

        Before creating an XNAT project, you’ll require a UQ-RDM HPC Collection

        • HPC collections ends with -Q and a 4-digit numerical identifier (e.g. PROJ001-Q0189)
        • Non-HPC collections end with -A (e.g. PROJ001-A0189) or -I (PROJ001-I0189)

        To create a new UQ-RDM HPC Collection, proceed with the following

        Open https://rdm.uq.edu.au/create-record and sign-in

        Fill in the record as per your project details

        REQUEST DATA STORAGE when complete

        Move on to the next step after the RDM collection is provisioned
        You should have an RDM collection name ready (e.g. PROJ001-Q0189)

        Step 2

        Open a ticket with RCC support

        Example below (replace __________ with your details)

        Subject: Create XNAT project __________

        Hello RCC support -Can we create an XNAT project for RDM collection __________

        Step 3

        The support ticket will inform you when the project is set up.

        • An XNAT project will be created with the matching name (e.g. PROJ001-Q0189)
        • An xnat directory will be created in the RDM collection for storing the XNAT data files
        • Please do not write or modify anything under the xnat directory

        XNAT Project setup typically takes around ~24 hours from ticket submission
        An automated email from XNAT will be sent through when project is ready, and your user has been added

        - - \ No newline at end of file +">

        UQ members

        For UQ Staff and Students

        Signing into XNAT


        Step 1

        Open https://xnat.rcc.uq.edu.au

        Step 2

        Login in with the AAF Single sign-on button (shown below).

        Follow the AAF login process for your organisation

        Step 3

        After the AAF sign-in, you should be redirected back to XNAT (Example below)

        There will be no projects listed when signing in for the first-time, as your user account would have just been created.

        Proceed to to next section for setting up an XNAT project

        Creating XNAT project


        For UQ users, XNAT uses UQ-RDM HPC collections for storage allocation.
        For any general questions about UQ-RDM, please refer to the library guides

        Step 1

        Before creating an XNAT project, you’ll require a UQ-RDM HPC Collection

        • HPC collections ends with -Q and a 4-digit numerical identifier (e.g. PROJ001-Q0189)
        • Non-HPC collections end with -A (e.g. PROJ001-A0189) or -I (PROJ001-I0189)

        To create a new UQ-RDM HPC Collection, proceed with the following

        Open https://rdm.uq.edu.au/create-record and sign-in

        Fill in the record as per your project details

        REQUEST DATA STORAGE when complete

        Move on to the next step after the RDM collection is provisioned
        You should have an RDM collection name ready (e.g. PROJ001-Q0189)

        Step 2

        Open a ticket with RCC support

        Example below (replace __________ with your details)

        Subject: Create XNAT project __________

        Hello RCC support +Can we create an XNAT project for RDM collection __________

        Step 3

        The support ticket will inform you when the project is set up.

        • An XNAT project will be created with the matching name (e.g. PROJ001-Q0189)
        • An xnat directory will be created in the RDM collection for storing the XNAT data files
        • Please do not write or modify anything under the xnat directory

        XNAT Project setup typically takes around ~24 hours from ticket submission
        An automated email from XNAT will be sent through when project is ready, and your user has been added

        \ No newline at end of file diff --git a/docs/user-guides/index.html b/docs/user-guides/index.html index 21c83cf..e7c546e 100644 --- a/docs/user-guides/index.html +++ b/docs/user-guides/index.html @@ -1,7 +1,6 @@ -User Guides | UQ AIS XNATUser Guides | UQ AIS XNAT +
        - - \ No newline at end of file +">
        \ No newline at end of file diff --git a/docs/user-guides/index.xml b/docs/user-guides/index.xml index a753bca..781b5a3 100644 --- a/docs/user-guides/index.xml +++ b/docs/user-guides/index.xml @@ -1,12 +1,12 @@ UQ AIS XNAT – User Guideshttps://docs.xnat.rcc.uq.edu.au/docs/user-guides/Recent content in User Guides on UQ AIS XNATHugo -- gohugo.ioenDocs: Getting Startedhttps://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/Mon, 01 Jan 0001 00:00:00 +0000https://docs.xnat.rcc.uq.edu.au/docs/user-guides/getting-started/Docs: Logging into XNAThttps://docs.xnat.rcc.uq.edu.au/docs/user-guides/logging-into-xnat/Mon, 01 Jan 0001 00:00:00 +0000https://docs.xnat.rcc.uq.edu.au/docs/user-guides/logging-into-xnat/ -<h2 id="aafaaf-login"><a href="aaf-login">AAF</a></h2> +<h2 id="aafaaf-login"><a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/logging-into-xnat/aaf-login/">AAF</a></h2> <div class="alert alert-primary" role="alert"> <p>AAF is the recommended way to sign up and login to XNAT.</p> <p>If your organisation is not in the AAF list during the sign-up process, please contact the respective XNAT support for further options</p> </div> -<p>If your organisation is part of the Australian Access Federation (AAF), you can use your AAF credentials to sign up. See <a href="aaf-login">here</a></p> +<p>If your organisation is part of the Australian Access Federation (AAF), you can use your AAF credentials to sign up. See <a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/logging-into-xnat/aaf-login/">here</a></p> <p>For more details on the Australian Access Federation, see <a href="https://aaf.edu.au">https://aaf.edu.au</a></p> -<h2 id="rcc-authenticatercc-login"><a href="rcc-login">RCC Authenticate</a></h2> +<h2 id="rcc-authenticatercc-login"><a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/logging-into-xnat/rcc-login/">RCC Authenticate</a></h2> <p>To use this login, you would have received an email from a UQ XNAT administrator with the login information.</p> <div class="alert alert-warning" role="alert"> <h4 class="alert-heading">Note</h4> @@ -14,6 +14,13 @@ <p>RCC Authenticate credentials are <strong>NOT</strong> your UQ or institutional username and password</p> </div>Docs: Browsing XNAThttps://docs.xnat.rcc.uq.edu.au/docs/user-guides/browsing-xnat/Mon, 01 Jan 0001 00:00:00 +0000https://docs.xnat.rcc.uq.edu.au/docs/user-guides/browsing-xnat/ <p>For further information refer to the <a href="https://wiki.xnat.org/documentation/how-to-use-xnat/using-the-standard-search/browsing-data-types">XNAT official guides on browsing data</a></p>Docs: Managing Datahttps://docs.xnat.rcc.uq.edu.au/docs/user-guides/managing-data/Mon, 01 Jan 0001 00:00:00 +0000https://docs.xnat.rcc.uq.edu.au/docs/user-guides/managing-data/Docs: Processing Datahttps://docs.xnat.rcc.uq.edu.au/docs/user-guides/processing-data/Mon, 01 Jan 0001 00:00:00 +0000https://docs.xnat.rcc.uq.edu.au/docs/user-guides/processing-data/Docs:https://docs.xnat.rcc.uq.edu.au/docs/user-guides/faq/Mon, 01 Jan 0001 00:00:00 +0000https://docs.xnat.rcc.uq.edu.au/docs/user-guides/faq/ +<!-- --- +title: "FAQ" +linkTitle: "FAQ" +weight: 1 +description: > +Frequently Asked Questions +--- --> <div> <nav id="TableOfContents"> <ul> diff --git a/docs/user-guides/logging-into-xnat/_print/index.html b/docs/user-guides/logging-into-xnat/_print/index.html index d58fde2..34a5f44 100644 --- a/docs/user-guides/logging-into-xnat/_print/index.html +++ b/docs/user-guides/logging-into-xnat/_print/index.html @@ -1,9 +1,10 @@ -Logging into XNAT | UQ AIS XNATLogging into XNAT | UQ AIS XNAT +

        This is the multi-page printable view of this section. -Click here to print.

        Return to the regular view of this page.

        Logging into XNAT

        Logging into XNAT

        AAF

        If your organisation is part of the Australian Access Federation (AAF), you can use your AAF credentials to sign up. See here

        For more details on the Australian Access Federation, see https://aaf.edu.au

        RCC Authenticate

        To use this login, you would have received an email from a UQ XNAT administrator with the login information.

        1 - AAF login

        Login using Australian Access Federation (AAF)

        If your organisation is part of the Australian Access Federation (AAF), you can use your AAF credentials to sign up. Follow the steps below to sign-up/login using AAF.

        1. Open https://xnat.rcc.uq.edu.au
        2. Login in with the AAF Single sign-on button (shown below)

        This will take you to your XNAT home page.

        2 - RCC Authenticate

        Login using RCC Authenticate

        To use this login, you would have received an email from a UQ XNAT administrator with the login information.

        1. Login in with the RCC Authenticate button (shown below)

        1. You’ll be taken to a UQ RCC SERVICES (shown below)

        1. Enter your user name and password to sign in. +">

          This is the multi-page printable view of this section. +Click here to print.

          Return to the regular view of this page.

          Logging into XNAT

          Logging into XNAT

          AAF

          If your organisation is part of the Australian Access Federation (AAF), you can use your AAF credentials to sign up. See here

          For more details on the Australian Access Federation, see https://aaf.edu.au

          RCC Authenticate

          To use this login, you would have received an email from a UQ XNAT administrator with the login information.

          1 - AAF login

          Login using Australian Access Federation (AAF)

          If your organisation is part of the Australian Access Federation (AAF), you can use your AAF credentials to sign up. Follow the steps below to sign-up/login using AAF.

          1. Open https://xnat.rcc.uq.edu.au
          2. Login in with the AAF Single sign-on button (shown below)

          This will take you to your XNAT home page.

          2 - RCC Authenticate

          Login using RCC Authenticate

          To use this login, you would have received an email from a UQ XNAT administrator with the login information.

          1. Login in with the RCC Authenticate button (shown below)

          1. You’ll be taken to a UQ RCC SERVICES (shown below)

          1. Enter your user name and password to sign in. This will take you to your XNAT home page.

          3 - Alias tokens

          Alias tokens

          AAF is used for logging into the XNAT website itself.

          But there are a lot of tools and services that will require a connect to the XNAT server externally

          These could include

          • Windows or Mac desktop clients, like XNAT Desktop
          • Command line tools such as xnatpy, pyxnat, xnatutils etc
          • XSYNC

          All of these tools and services need a way to authenticating to your XNAT account without AAF.

          An alias token is a time-limited, long, randomised username and password used for authenticating from external services, without compromising your AAF account or credentials. They can be generated and revoked easily

          We’ll look at how to generate them next

          Generating Alias tokens

          To access the alias token Click your name on the top right of the website. This will take you to your user profile management page

          Then click the “Manage Alias Tokens” option

          There, you’ll find the option to “Create an Alias Token”

          When you create the alias token, it will appear as a new entry

          Alias tokens expire 60 days after creation @@ -12,6 +13,4 @@ The alias is your username And secret is your password

          So you can use the alias and secret for any external clients requesting a username and password.

          Just note, the alias and secret are effectively a temporary set of login credentials. Do not reveal the secret. It is effectively your temporary password. -If you no longer require the alias token, or suspect a secret has been compromised, just delete the alias token.

          - - \ No newline at end of file +If you no longer require the alias token, or suspect a secret has been compromised, just delete the alias token.

        \ No newline at end of file diff --git a/docs/user-guides/logging-into-xnat/aaf-login/index.html b/docs/user-guides/logging-into-xnat/aaf-login/index.html index 7d0dc83..8e635af 100644 --- a/docs/user-guides/logging-into-xnat/aaf-login/index.html +++ b/docs/user-guides/logging-into-xnat/aaf-login/index.html @@ -1,7 +1,6 @@ -AAF login | UQ AIS XNATAAF login | UQ AIS XNAT +

        AAF login

        Login using Australian Access Federation (AAF)

        If your organisation is part of the Australian Access Federation (AAF), you can use your AAF credentials to sign up. Follow the steps below to sign-up/login using AAF.

        1. Open https://xnat.rcc.uq.edu.au
        2. Login in with the AAF Single sign-on button (shown below)

        This will take you to your XNAT home page.

        - - \ No newline at end of file +">

        AAF login

        Login using Australian Access Federation (AAF)

        If your organisation is part of the Australian Access Federation (AAF), you can use your AAF credentials to sign up. Follow the steps below to sign-up/login using AAF.

        1. Open https://xnat.rcc.uq.edu.au
        2. Login in with the AAF Single sign-on button (shown below)

        This will take you to your XNAT home page.

        \ No newline at end of file diff --git a/docs/user-guides/logging-into-xnat/alias-tokens/index.html b/docs/user-guides/logging-into-xnat/alias-tokens/index.html index 89a4efc..19a001b 100644 --- a/docs/user-guides/logging-into-xnat/alias-tokens/index.html +++ b/docs/user-guides/logging-into-xnat/alias-tokens/index.html @@ -1,8 +1,9 @@ -Alias tokens | UQ AIS XNATAlias tokens | UQ AIS XNAT +

        Alias tokens

        Alias tokens

        AAF is used for logging into the XNAT website itself.

        But there are a lot of tools and services that will require a connect to the XNAT server externally

        These could include

        • Windows or Mac desktop clients, like XNAT Desktop
        • Command line tools such as xnatpy, pyxnat, xnatutils etc
        • XSYNC

        All of these tools and services need a way to authenticating to your XNAT account without AAF.

        An alias token is a time-limited, long, randomised username and password used for authenticating from external services, without compromising your AAF account or credentials. They can be generated and revoked easily

        We’ll look at how to generate them next

        Generating Alias tokens

        To access the alias token +">

        Alias tokens

        Alias tokens

        AAF is used for logging into the XNAT website itself.

        But there are a lot of tools and services that will require a connect to the XNAT server externally

        These could include

        • Windows or Mac desktop clients, like XNAT Desktop
        • Command line tools such as xnatpy, pyxnat, xnatutils etc
        • XSYNC

        All of these tools and services need a way to authenticating to your XNAT account without AAF.

        An alias token is a time-limited, long, randomised username and password used for authenticating from external services, without compromising your AAF account or credentials. They can be generated and revoked easily

        We’ll look at how to generate them next

        Generating Alias tokens

        To access the alias token Click your name on the top right of the website. This will take you to your user profile management page

        Then click the “Manage Alias Tokens” option

        There, you’ll find the option to “Create an Alias Token”

        When you create the alias token, it will appear as a new entry

        Alias tokens expire 60 days after creation There will be an expiration date column.

        You can have multiple alias tokens. And they can be deleted and created as needed to revoke permissions. @@ -10,6 +11,4 @@ The alias is your username And secret is your password

        So you can use the alias and secret for any external clients requesting a username and password.

        Just note, the alias and secret are effectively a temporary set of login credentials. Do not reveal the secret. It is effectively your temporary password. -If you no longer require the alias token, or suspect a secret has been compromised, just delete the alias token.

        - - \ No newline at end of file +If you no longer require the alias token, or suspect a secret has been compromised, just delete the alias token.

        \ No newline at end of file diff --git a/docs/user-guides/logging-into-xnat/index.html b/docs/user-guides/logging-into-xnat/index.html index 26d9c90..81f2f70 100644 --- a/docs/user-guides/logging-into-xnat/index.html +++ b/docs/user-guides/logging-into-xnat/index.html @@ -1,7 +1,6 @@ -Logging into XNAT | UQ AIS XNATLogging into XNAT | UQ AIS XNAT +

        Logging into XNAT

        Logging into XNAT

        AAF

        If your organisation is part of the Australian Access Federation (AAF), you can use your AAF credentials to sign up. See here

        For more details on the Australian Access Federation, see https://aaf.edu.au

        RCC Authenticate

        To use this login, you would have received an email from a UQ XNAT administrator with the login information.


        AAF login

        Login using Australian Access Federation (AAF)

        RCC Authenticate

        Login using RCC Authenticate

        Alias tokens

        Alias tokens

        - - \ No newline at end of file +">

        Logging into XNAT

        Logging into XNAT

        AAF

        If your organisation is part of the Australian Access Federation (AAF), you can use your AAF credentials to sign up. See here

        For more details on the Australian Access Federation, see https://aaf.edu.au

        RCC Authenticate

        To use this login, you would have received an email from a UQ XNAT administrator with the login information.


        AAF login

        Login using Australian Access Federation (AAF)

        RCC Authenticate

        Login using RCC Authenticate

        Alias tokens

        Alias tokens

        \ No newline at end of file diff --git a/docs/user-guides/logging-into-xnat/rcc-login/index.html b/docs/user-guides/logging-into-xnat/rcc-login/index.html index 13a4183..168119f 100644 --- a/docs/user-guides/logging-into-xnat/rcc-login/index.html +++ b/docs/user-guides/logging-into-xnat/rcc-login/index.html @@ -1,8 +1,7 @@ -RCC Authenticate | UQ AIS XNATRCC Authenticate | UQ AIS XNAT +

        RCC Authenticate

        Login using RCC Authenticate

        To use this login, you would have received an email from a UQ XNAT administrator with the login information.

        1. Login in with the RCC Authenticate button (shown below)

        1. You’ll be taken to a UQ RCC SERVICES (shown below)

        1. Enter your user name and password to sign in. -This will take you to your XNAT home page.
        - - \ No newline at end of file +">

        RCC Authenticate

        Login using RCC Authenticate

        To use this login, you would have received an email from a UQ XNAT administrator with the login information.

        1. Login in with the RCC Authenticate button (shown below)

        1. You’ll be taken to a UQ RCC SERVICES (shown below)

        1. Enter your user name and password to sign in. +This will take you to your XNAT home page.
        \ No newline at end of file diff --git a/docs/user-guides/login-to-xnat/aaf-login/index.html b/docs/user-guides/login-to-xnat/aaf-login/index.html index 6c5c05a..1781c8a 100644 --- a/docs/user-guides/login-to-xnat/aaf-login/index.html +++ b/docs/user-guides/login-to-xnat/aaf-login/index.html @@ -1 +1,2 @@ -https://docs.xnat.rcc.uq.edu.au/docs/user-guides/logging-into-xnat/aaf-login/ \ No newline at end of file +https://docs.xnat.rcc.uq.edu.au/docs/user-guides/logging-into-xnat/aaf-login/ + \ No newline at end of file diff --git a/docs/user-guides/login-to-xnat/index.html b/docs/user-guides/login-to-xnat/index.html index 6583cdd..66a0608 100644 --- a/docs/user-guides/login-to-xnat/index.html +++ b/docs/user-guides/login-to-xnat/index.html @@ -1 +1,2 @@ -https://docs.xnat.rcc.uq.edu.au/docs/user-guides/logging-into-xnat/ \ No newline at end of file +https://docs.xnat.rcc.uq.edu.au/docs/user-guides/logging-into-xnat/ + \ No newline at end of file diff --git a/docs/user-guides/login-to-xnat/rcc-login/index.html b/docs/user-guides/login-to-xnat/rcc-login/index.html index f388ec8..0ea96ff 100644 --- a/docs/user-guides/login-to-xnat/rcc-login/index.html +++ b/docs/user-guides/login-to-xnat/rcc-login/index.html @@ -1 +1,2 @@ -https://docs.xnat.rcc.uq.edu.au/docs/user-guides/logging-into-xnat/rcc-login/ \ No newline at end of file +https://docs.xnat.rcc.uq.edu.au/docs/user-guides/logging-into-xnat/rcc-login/ + \ No newline at end of file diff --git a/docs/user-guides/managing-data/_print/index.html b/docs/user-guides/managing-data/_print/index.html index b28ddc5..62b61b0 100644 --- a/docs/user-guides/managing-data/_print/index.html +++ b/docs/user-guides/managing-data/_print/index.html @@ -1,9 +1,10 @@ -Managing Data | UQ AIS XNATManaging Data | UQ AIS XNAT +

        1 - Downloading Data

        Downloading data from XNAT Projects
        1. Navigate to Scan or Session (See guide on browsing data)
        2. Select Download from controls on top right.
        3. Use the following settings for downloading dataset as zip text

        For further information refer to the XNAT official guide on downloading data

        1.1 - Zip Download

        Downloading data as Zip using the XNAT UI

        The Project, Subject and Sessions page has the option to Download Images from the right hand side menu

        +">

        1 - Downloading Data

        Downloading data from XNAT Projects
        1. Navigate to Scan or Session (See guide on browsing data)
        2. Select Download from controls on top right.
        3. Use the following settings for downloading dataset as zip text

        For further information refer to the XNAT official guide on downloading data

        1.1 - Zip Download

        Downloading data as Zip using the XNAT UI

        The Project, Subject and Sessions page has the option to Download Images from the right hand side menu

        Select Option 2: ZIP download

        Filter out the Session and scans from the first two columns and select Submit

        1.2 - Desktop client

        Downloading data using the XNAT Desktop client

        The XNAT Desktop client is maintained by the XNAT development team. For information see the link below.

        XNAT Desktop client
        https://www.xnat.org/download/desktop-client/

        Install client

        Download and install the client for you operating system

        Download images

        The Project, Subject and Sessions page has the option to Download Images from the right hand side menu

        Select Option 1: Download via Desktop Client

        Click Download Via App

        Select a local destination folder

        Download should start, and progress can be monitored

        1.3 - Download Scan

        Downloading induvidual Scans using the XNAT UI

        Induvidual scans can be downloaded from the Sessions page

        Multiple scans can be selected and downloaded using Bulk Actions

        2 - Viewing Images

        Viewing Images in the XNAT OHIF Viewer

        XNAT OHIF Viewer

        AIS XNAT instances come with the XNAT OHIF Image viewer Which is a plugin developed by the Institute for Cancer Research in London

        Just note, if your publication uses the OHIF viewer, they have an article for citation. @@ -16,6 +17,4 @@ project != "Unassigned" ? (0008,1030) := project (0010,0010) := subject (0010,0020) := session -

        The example in this screenshot basically replicates the behaviour in the HIRF onsite anonymiser for remapping the ReferringPhysicianName, PatientName and PatientID

        You can use DICOMedit to enforce a particular naming and tagging scheme across your entire project this way.

        Anonymising existing sesssions

        The Project level anonymiser works best for new sessions, as it runs when the dataset is being ingested into the XNAT archive, or when sessions are renamed. By default, it does not anonymise sessions that are sitting in the archive already.

        If you need to trigger your anonymisation on an existing session

        • Edit a session name. Modify
        • Then edit it back to its original name

        This will trigger the anonymisation script.

        5.2 - Site anonymiser

        Site anonymiser

        HIRF and CAI data are anonymised on-site by default with the following protocols

        Modified Tags

        DICOM TagOriginal valueNew value
        PatientBirthDate10/12/20001/1/2000
        PatientCommentsXXXXXXXXProject:Proj001 Subject:TEST_MR Session:TEST_MR-20210405T1220
        ReferringPhysicianNameProj001Proj001
        PatientNameXXXXXXXXTEST_MR
        PatientIDTEST_MRTEST_MR-20210405T1220

        Blanked Tags

        DICOM Tag
        AccessionNumber
        ImageComments
        OperatorName
        OtherPatientIDs
        AdditionalPatientHistory
        AdmittingDiagnosisDescription
        MedicalRecordLocator
        NameOfPhysicianReadingStudy
        Occupation
        OtherPatientNames
        PatientBirthTime
        PerformingPhysicianName
        PhysicianOfRecord
        ReferringPhysicianAddress
        ReferringPhysicianPhoneNumbers
        - - \ No newline at end of file +

        The example in this screenshot basically replicates the behaviour in the HIRF onsite anonymiser for remapping the ReferringPhysicianName, PatientName and PatientID

        You can use DICOMedit to enforce a particular naming and tagging scheme across your entire project this way.

        Anonymising existing sesssions

        The Project level anonymiser works best for new sessions, as it runs when the dataset is being ingested into the XNAT archive, or when sessions are renamed. By default, it does not anonymise sessions that are sitting in the archive already.

        If you need to trigger your anonymisation on an existing session

        • Edit a session name. Modify
        • Then edit it back to its original name

        This will trigger the anonymisation script.

        5.2 - Site anonymiser

        Site anonymiser

        HIRF and CAI data are anonymised on-site by default with the following protocols

        Modified Tags

        DICOM TagOriginal valueNew value
        PatientBirthDate10/12/20001/1/2000
        PatientCommentsXXXXXXXXProject:Proj001 Subject:TEST_MR Session:TEST_MR-20210405T1220
        ReferringPhysicianNameProj001Proj001
        PatientNameXXXXXXXXTEST_MR
        PatientIDTEST_MRTEST_MR-20210405T1220

        Blanked Tags

        DICOM Tag
        AccessionNumber
        ImageComments
        OperatorName
        OtherPatientIDs
        AdditionalPatientHistory
        AdmittingDiagnosisDescription
        MedicalRecordLocator
        NameOfPhysicianReadingStudy
        Occupation
        OtherPatientNames
        PatientBirthTime
        PerformingPhysicianName
        PhysicianOfRecord
        ReferringPhysicianAddress
        ReferringPhysicianPhoneNumbers
        \ No newline at end of file diff --git a/docs/user-guides/managing-data/anonymising-data/_print/index.html b/docs/user-guides/managing-data/anonymising-data/_print/index.html index 62a0f4d..8a533d0 100644 --- a/docs/user-guides/managing-data/anonymising-data/_print/index.html +++ b/docs/user-guides/managing-data/anonymising-data/_print/index.html @@ -1,13 +1,12 @@ -Anonymising Data | UQ AIS XNATAnonymising Data | UQ AIS XNAT +

        This is the multi-page printable view of this section. +">

        This is the multi-page printable view of this section. Click here to print.

        Return to the regular view of this page.

        Anonymising Data

        Anonymising Data

        1 - Project anonymiser

        Project anonymiser

        The Project level anonymiser uses a scripting syntax called DicomEdit to modify, reassign or blank DICOM tags. You can actually use this to create automated workflow for renaming DICOM metadata on datasets

        Dicomedit
        https://wiki.xnat.org/xnat-tools/dicomedit/dicomedit-6-3-language-reference
        version "6.1"
         project != "Unassigned" ? (0008,1030) := project
         (0010,0010) := subject
         (0010,0020) := session
        -

        The example in this screenshot basically replicates the behaviour in the HIRF onsite anonymiser for remapping the ReferringPhysicianName, PatientName and PatientID

        You can use DICOMedit to enforce a particular naming and tagging scheme across your entire project this way.

        Anonymising existing sesssions

        The Project level anonymiser works best for new sessions, as it runs when the dataset is being ingested into the XNAT archive, or when sessions are renamed. By default, it does not anonymise sessions that are sitting in the archive already.

        If you need to trigger your anonymisation on an existing session

        • Edit a session name. Modify
        • Then edit it back to its original name

        This will trigger the anonymisation script.

        2 - Site anonymiser

        Site anonymiser

        HIRF and CAI data are anonymised on-site by default with the following protocols

        Modified Tags

        DICOM TagOriginal valueNew value
        PatientBirthDate10/12/20001/1/2000
        PatientCommentsXXXXXXXXProject:Proj001 Subject:TEST_MR Session:TEST_MR-20210405T1220
        ReferringPhysicianNameProj001Proj001
        PatientNameXXXXXXXXTEST_MR
        PatientIDTEST_MRTEST_MR-20210405T1220

        Blanked Tags

        DICOM Tag
        AccessionNumber
        ImageComments
        OperatorName
        OtherPatientIDs
        AdditionalPatientHistory
        AdmittingDiagnosisDescription
        MedicalRecordLocator
        NameOfPhysicianReadingStudy
        Occupation
        OtherPatientNames
        PatientBirthTime
        PerformingPhysicianName
        PhysicianOfRecord
        ReferringPhysicianAddress
        ReferringPhysicianPhoneNumbers
        - - \ No newline at end of file +

        The example in this screenshot basically replicates the behaviour in the HIRF onsite anonymiser for remapping the ReferringPhysicianName, PatientName and PatientID

        You can use DICOMedit to enforce a particular naming and tagging scheme across your entire project this way.

        Anonymising existing sesssions

        The Project level anonymiser works best for new sessions, as it runs when the dataset is being ingested into the XNAT archive, or when sessions are renamed. By default, it does not anonymise sessions that are sitting in the archive already.

        If you need to trigger your anonymisation on an existing session

        • Edit a session name. Modify
        • Then edit it back to its original name

        This will trigger the anonymisation script.

        2 - Site anonymiser

        Site anonymiser

        HIRF and CAI data are anonymised on-site by default with the following protocols

        Modified Tags

        DICOM TagOriginal valueNew value
        PatientBirthDate10/12/20001/1/2000
        PatientCommentsXXXXXXXXProject:Proj001 Subject:TEST_MR Session:TEST_MR-20210405T1220
        ReferringPhysicianNameProj001Proj001
        PatientNameXXXXXXXXTEST_MR
        PatientIDTEST_MRTEST_MR-20210405T1220

        Blanked Tags

        DICOM Tag
        AccessionNumber
        ImageComments
        OperatorName
        OtherPatientIDs
        AdditionalPatientHistory
        AdmittingDiagnosisDescription
        MedicalRecordLocator
        NameOfPhysicianReadingStudy
        Occupation
        OtherPatientNames
        PatientBirthTime
        PerformingPhysicianName
        PhysicianOfRecord
        ReferringPhysicianAddress
        ReferringPhysicianPhoneNumbers
        \ No newline at end of file diff --git a/docs/user-guides/managing-data/anonymising-data/index.html b/docs/user-guides/managing-data/anonymising-data/index.html index 8ede07b..3ccf18a 100644 --- a/docs/user-guides/managing-data/anonymising-data/index.html +++ b/docs/user-guides/managing-data/anonymising-data/index.html @@ -1,7 +1,6 @@ -Anonymising Data | UQ AIS XNATAnonymising Data | UQ AIS XNAT +
        - - \ No newline at end of file +">
        \ No newline at end of file diff --git a/docs/user-guides/managing-data/anonymising-data/project-anonymiser/index.html b/docs/user-guides/managing-data/anonymising-data/project-anonymiser/index.html index 88d0dee..eb1229c 100644 --- a/docs/user-guides/managing-data/anonymising-data/project-anonymiser/index.html +++ b/docs/user-guides/managing-data/anonymising-data/project-anonymiser/index.html @@ -1,12 +1,11 @@ -Project anonymiser | UQ AIS XNATProject anonymiser | UQ AIS XNAT +

        Project anonymiser

        Project anonymiser

        The Project level anonymiser uses a scripting syntax called DicomEdit to modify, reassign or blank DICOM tags. +">

        Project anonymiser

        Project anonymiser

        The Project level anonymiser uses a scripting syntax called DicomEdit to modify, reassign or blank DICOM tags. You can actually use this to create automated workflow for renaming DICOM metadata on datasets

        Dicomedit
        https://wiki.xnat.org/xnat-tools/dicomedit/dicomedit-6-3-language-reference
        version "6.1"
         project != "Unassigned" ? (0008,1030) := project
         (0010,0010) := subject
         (0010,0020) := session
        -

        The example in this screenshot basically replicates the behaviour in the HIRF onsite anonymiser for remapping the ReferringPhysicianName, PatientName and PatientID

        You can use DICOMedit to enforce a particular naming and tagging scheme across your entire project this way.

        Anonymising existing sesssions

        The Project level anonymiser works best for new sessions, as it runs when the dataset is being ingested into the XNAT archive, or when sessions are renamed. By default, it does not anonymise sessions that are sitting in the archive already.

        If you need to trigger your anonymisation on an existing session

        • Edit a session name. Modify
        • Then edit it back to its original name

        This will trigger the anonymisation script.

        - - \ No newline at end of file +

        The example in this screenshot basically replicates the behaviour in the HIRF onsite anonymiser for remapping the ReferringPhysicianName, PatientName and PatientID

        You can use DICOMedit to enforce a particular naming and tagging scheme across your entire project this way.

        Anonymising existing sesssions

        The Project level anonymiser works best for new sessions, as it runs when the dataset is being ingested into the XNAT archive, or when sessions are renamed. By default, it does not anonymise sessions that are sitting in the archive already.

        If you need to trigger your anonymisation on an existing session

        • Edit a session name. Modify
        • Then edit it back to its original name

        This will trigger the anonymisation script.

        \ No newline at end of file diff --git a/docs/user-guides/managing-data/anonymising-data/site-anonymiser/index.html b/docs/user-guides/managing-data/anonymising-data/site-anonymiser/index.html index 8a9c171..9eef150 100644 --- a/docs/user-guides/managing-data/anonymising-data/site-anonymiser/index.html +++ b/docs/user-guides/managing-data/anonymising-data/site-anonymiser/index.html @@ -1,7 +1,6 @@ -Site anonymiser | UQ AIS XNATSite anonymiser | UQ AIS XNAT +

        Site anonymiser

        Site anonymiser

        HIRF and CAI data are anonymised on-site by default with the following protocols

        Modified Tags

        DICOM TagOriginal valueNew value
        PatientBirthDate10/12/20001/1/2000
        PatientCommentsXXXXXXXXProject:Proj001 Subject:TEST_MR Session:TEST_MR-20210405T1220
        ReferringPhysicianNameProj001Proj001
        PatientNameXXXXXXXXTEST_MR
        PatientIDTEST_MRTEST_MR-20210405T1220

        Blanked Tags

        DICOM Tag
        AccessionNumber
        ImageComments
        OperatorName
        OtherPatientIDs
        AdditionalPatientHistory
        AdmittingDiagnosisDescription
        MedicalRecordLocator
        NameOfPhysicianReadingStudy
        Occupation
        OtherPatientNames
        PatientBirthTime
        PerformingPhysicianName
        PhysicianOfRecord
        ReferringPhysicianAddress
        ReferringPhysicianPhoneNumbers
        - - \ No newline at end of file +">

        Site anonymiser

        Site anonymiser

        HIRF and CAI data are anonymised on-site by default with the following protocols

        Modified Tags

        DICOM TagOriginal valueNew value
        PatientBirthDate10/12/20001/1/2000
        PatientCommentsXXXXXXXXProject:Proj001 Subject:TEST_MR Session:TEST_MR-20210405T1220
        ReferringPhysicianNameProj001Proj001
        PatientNameXXXXXXXXTEST_MR
        PatientIDTEST_MRTEST_MR-20210405T1220

        Blanked Tags

        DICOM Tag
        AccessionNumber
        ImageComments
        OperatorName
        OtherPatientIDs
        AdditionalPatientHistory
        AdmittingDiagnosisDescription
        MedicalRecordLocator
        NameOfPhysicianReadingStudy
        Occupation
        OtherPatientNames
        PatientBirthTime
        PerformingPhysicianName
        PhysicianOfRecord
        ReferringPhysicianAddress
        ReferringPhysicianPhoneNumbers
        \ No newline at end of file diff --git a/docs/user-guides/managing-data/downloading-data/_print/index.html b/docs/user-guides/managing-data/downloading-data/_print/index.html index bd02936..c21113f 100644 --- a/docs/user-guides/managing-data/downloading-data/_print/index.html +++ b/docs/user-guides/managing-data/downloading-data/_print/index.html @@ -1,10 +1,9 @@ -Downloading Data | UQ AIS XNATDownloading Data | UQ AIS XNAT +

        This is the multi-page printable view of this section. -Click here to print.

        Return to the regular view of this page.

        Downloading Data

        Downloading data from XNAT Projects
        1. Navigate to Scan or Session (See guide on browsing data)
        2. Select Download from controls on top right.
        3. Use the following settings for downloading dataset as zip text

        For further information refer to the XNAT official guide on downloading data

        1 - Zip Download

        Downloading data as Zip using the XNAT UI

        The Project, Subject and Sessions page has the option to Download Images from the right hand side menu

        +">

        This is the multi-page printable view of this section. +Click here to print.

        Return to the regular view of this page.

        Downloading Data

        Downloading data from XNAT Projects
        1. Navigate to Scan or Session (See guide on browsing data)
        2. Select Download from controls on top right.
        3. Use the following settings for downloading dataset as zip text

        For further information refer to the XNAT official guide on downloading data

        1 - Zip Download

        Downloading data as Zip using the XNAT UI

        The Project, Subject and Sessions page has the option to Download Images from the right hand side menu

        -

        Select Option 2: ZIP download

        Filter out the Session and scans from the first two columns and select Submit

        2 - Desktop client

        Downloading data using the XNAT Desktop client

        The XNAT Desktop client is maintained by the XNAT development team. For information see the link below.

        XNAT Desktop client
        https://www.xnat.org/download/desktop-client/

        Install client

        Download and install the client for you operating system

        Download images

        The Project, Subject and Sessions page has the option to Download Images from the right hand side menu

        Select Option 1: Download via Desktop Client

        Click Download Via App

        Select a local destination folder

        Download should start, and progress can be monitored

        3 - Download Scan

        Downloading induvidual Scans using the XNAT UI

        Induvidual scans can be downloaded from the Sessions page

        Multiple scans can be selected and downloaded using Bulk Actions

        - - \ No newline at end of file +

        Select Option 2: ZIP download

        Filter out the Session and scans from the first two columns and select Submit

        2 - Desktop client

        Downloading data using the XNAT Desktop client

        The XNAT Desktop client is maintained by the XNAT development team. For information see the link below.

        XNAT Desktop client
        https://www.xnat.org/download/desktop-client/

        Install client

        Download and install the client for you operating system

        Download images

        The Project, Subject and Sessions page has the option to Download Images from the right hand side menu

        Select Option 1: Download via Desktop Client

        Click Download Via App

        Select a local destination folder

        Download should start, and progress can be monitored

        3 - Download Scan

        Downloading induvidual Scans using the XNAT UI

        Induvidual scans can be downloaded from the Sessions page

        Multiple scans can be selected and downloaded using Bulk Actions

        \ No newline at end of file diff --git a/docs/user-guides/managing-data/downloading-data/desktop-client/index.html b/docs/user-guides/managing-data/downloading-data/desktop-client/index.html index 2514a21..fe7b88e 100644 --- a/docs/user-guides/managing-data/downloading-data/desktop-client/index.html +++ b/docs/user-guides/managing-data/downloading-data/desktop-client/index.html @@ -1,7 +1,6 @@ -Desktop client | UQ AIS XNATDesktop client | UQ AIS XNAT +

        Desktop client

        Downloading data using the XNAT Desktop client

        The XNAT Desktop client is maintained by the XNAT development team. For information see the link below.

        XNAT Desktop client
        https://www.xnat.org/download/desktop-client/

        Install client

        Download and install the client for you operating system

        Download images

        The Project, Subject and Sessions page has the option to Download Images from the right hand side menu

        Select Option 1: Download via Desktop Client

        Click Download Via App

        Select a local destination folder

        Download should start, and progress can be monitored

        - - \ No newline at end of file +">

        Desktop client

        Downloading data using the XNAT Desktop client

        The XNAT Desktop client is maintained by the XNAT development team. For information see the link below.

        XNAT Desktop client
        https://www.xnat.org/download/desktop-client/

        Install client

        Download and install the client for you operating system

        Download images

        The Project, Subject and Sessions page has the option to Download Images from the right hand side menu

        Select Option 1: Download via Desktop Client

        Click Download Via App

        Select a local destination folder

        Download should start, and progress can be monitored

        \ No newline at end of file diff --git a/docs/user-guides/managing-data/downloading-data/download-scan/index.html b/docs/user-guides/managing-data/downloading-data/download-scan/index.html index 6ba04ab..a545643 100644 --- a/docs/user-guides/managing-data/downloading-data/download-scan/index.html +++ b/docs/user-guides/managing-data/downloading-data/download-scan/index.html @@ -1,7 +1,6 @@ -Download Scan | UQ AIS XNATDownload Scan | UQ AIS XNAT +
        - - \ No newline at end of file +">
        \ No newline at end of file diff --git a/docs/user-guides/managing-data/downloading-data/index.html b/docs/user-guides/managing-data/downloading-data/index.html index 32b88fd..2ff5224 100644 --- a/docs/user-guides/managing-data/downloading-data/index.html +++ b/docs/user-guides/managing-data/downloading-data/index.html @@ -1,7 +1,6 @@ -Downloading Data | UQ AIS XNATDownloading Data | UQ AIS XNAT +
        - - \ No newline at end of file +">
        \ No newline at end of file diff --git a/docs/user-guides/managing-data/downloading-data/zip-download/index.html b/docs/user-guides/managing-data/downloading-data/zip-download/index.html index 55785ed..df7e7b5 100644 --- a/docs/user-guides/managing-data/downloading-data/zip-download/index.html +++ b/docs/user-guides/managing-data/downloading-data/zip-download/index.html @@ -1,9 +1,8 @@ -Zip Download | UQ AIS XNATZip Download | UQ AIS XNAT +

        Zip Download

        Downloading data as Zip using the XNAT UI

        The Project, Subject and Sessions page has the option to Download Images from the right hand side menu

        +">

        - - \ No newline at end of file +

        Select Option 2: ZIP download

        Filter out the Session and scans from the first two columns and select Submit

        \ No newline at end of file diff --git a/docs/user-guides/managing-data/index.html b/docs/user-guides/managing-data/index.html index 7c1f455..3a1e882 100644 --- a/docs/user-guides/managing-data/index.html +++ b/docs/user-guides/managing-data/index.html @@ -1,7 +1,6 @@ -Managing Data | UQ AIS XNATManaging Data | UQ AIS XNAT +
        - - \ No newline at end of file +">
        \ No newline at end of file diff --git a/docs/user-guides/managing-data/index.xml b/docs/user-guides/managing-data/index.xml index 176dd52..5a09dc6 100644 --- a/docs/user-guides/managing-data/index.xml +++ b/docs/user-guides/managing-data/index.xml @@ -2,7 +2,7 @@ <ol> <li>Navigate to Scan or Session (See guide on <a href="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/browsing-data">browsing data</a>)</li> <li>Select <code>Download</code> from controls on top right.</li> -<li>Use the following settings for downloading dataset as zip <img src="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/xnat-data-download-options.png" alt="text"></li> +<li>Use the following settings for downloading dataset as zip <img alt="text" src="https://docs.xnat.rcc.uq.edu.au/docs/user-guides/xnat-data-download-options.png"></li> </ol> <p>For further information refer to the <a href="https://wiki.xnat.org/documentation/how-to-use-xnat/how-to-download-image-data-from-xnat-projects">XNAT official guide on downloading data</a></p>
        Docs: Viewing Imageshttps://docs.xnat.rcc.uq.edu.au/docs/user-guides/managing-data/viewing-images/Mon, 01 Jan 0001 00:00:00 +0000https://docs.xnat.rcc.uq.edu.au/docs/user-guides/managing-data/viewing-images/ <h2 id="xnat-ohif-viewer">XNAT OHIF Viewer</h2> diff --git a/docs/user-guides/managing-data/syncing-data/_print/index.html b/docs/user-guides/managing-data/syncing-data/_print/index.html index bab11a4..87c294d 100644 --- a/docs/user-guides/managing-data/syncing-data/_print/index.html +++ b/docs/user-guides/managing-data/syncing-data/_print/index.html @@ -1,8 +1,7 @@ -Syncing Data | UQ AIS XNATSyncing Data | UQ AIS XNAT +

        This is the multi-page printable view of this section. -Click here to print.

        Return to the regular view of this page.

        Syncing Data

        Syncing data to other XNAT Projects

          The UQ-RCC XNAT may be able to sync datasets to other XNATs in Australia.

          To see if your project is able to be synced, send a ticket to RCC support (rcc-support@uq.edu.au)

          They will need the details of the XNAT that you wish to share data with.

          - - \ No newline at end of file +">

          This is the multi-page printable view of this section. +Click here to print.

          Return to the regular view of this page.

          Syncing Data

          Syncing data to other XNAT Projects

            The UQ-RCC XNAT may be able to sync datasets to other XNATs in Australia.

            To see if your project is able to be synced, send a ticket to RCC support (rcc-support@uq.edu.au)

            They will need the details of the XNAT that you wish to share data with.

            \ No newline at end of file diff --git a/docs/user-guides/managing-data/syncing-data/index.html b/docs/user-guides/managing-data/syncing-data/index.html index 3a0d3ce..cfdc685 100644 --- a/docs/user-guides/managing-data/syncing-data/index.html +++ b/docs/user-guides/managing-data/syncing-data/index.html @@ -1,7 +1,6 @@ -Syncing Data | UQ AIS XNATSyncing Data | UQ AIS XNAT +
            - - \ No newline at end of file +">
            \ No newline at end of file diff --git a/docs/user-guides/managing-data/uploading-data/_print/index.html b/docs/user-guides/managing-data/uploading-data/_print/index.html index 9e1018f..4206922 100644 --- a/docs/user-guides/managing-data/uploading-data/_print/index.html +++ b/docs/user-guides/managing-data/uploading-data/_print/index.html @@ -1,12 +1,11 @@ -Uploading Data | UQ AIS XNATUploading Data | UQ AIS XNAT +

            This is the multi-page printable view of this section. +">

            This is the multi-page printable view of this section. Click here to print.

            Return to the regular view of this page.

            Uploading Data

            Upload data to XNAT Projects
            1. Web Upload (Compressed image uploader)
            2. XNAT data client
            3. CTP

            For further information refer to the image session upload methods in XNAT

            1 - Web Upload

            Upload using XNAT compressed uploader

            Uploading DICOM datasets

            This is for uploading de-identified DICOM files using the uploader directly from the XNAT website

            1. De-identify DICOM on scanner or upload pc
            2. Zip DICOM files into a zip file
            3. Login to XNAT (see Login to XNAT)
            4. From the top panel, select Upload → Images → Compressed Uploader

            1. Specify the following options:
              • Project
              • Destination: Select Prearchive
              • Choose file to select zipped file with DICOMs

            1. Click Begin Upload Wait for:
              • Upload percent bar to finish (**percent bar may not appear for small datasets)
              • Background processes panel to appear on bottom right
              • Green tick on under Upload extraction/review for archival

            For further information refer to the XNAT official guide on using the compressed image uploader

            2 - Resource uploader

            Resource uploader

            This is to create a web upload form for repeated uploads of any data type.

            Navigate to Project → Manage → Project Resource Settings → Start

            Select Image Sessions. Enter the following required fields

            • Title: e.g. Rawdata
            • Resource Folder: e.g. RAW
            • Extract compressed files by default

            Select Add when complete

            To upload file(s) using the resource uploader, Upload Additional Files from the Sessions page

            3 - Prearchive

            XNAT Prearchive

            If a dataset has not arrived into your XNAT project, the prearchive would be the place to check

            This usually happens when:

            • a DICOM dataset matching an existing session gets resent
            • a part of a session gets uploaded separately

            Accessing the prearchive

            Go to Upload on the top menu, and Go to prearchive

            The following is an example of a session that is in conflict. We can select the session and choose Details.

            Here we can download the session, or individual scans. -And review the datasets

            • Choose Archive if you want the dataset merged into the existing one on the archive,
            • choose Modify and Archive if any details need to be changed before archiving, or if you don’t want this dataset to merge with the existing one

            - - \ No newline at end of file +And review the datasets

            • Choose Archive if you want the dataset merged into the existing one on the archive,
            • choose Modify and Archive if any details need to be changed before archiving, or if you don’t want this dataset to merge with the existing one

            \ No newline at end of file diff --git a/docs/user-guides/managing-data/uploading-data/index.html b/docs/user-guides/managing-data/uploading-data/index.html index 0395b39..4aca3be 100644 --- a/docs/user-guides/managing-data/uploading-data/index.html +++ b/docs/user-guides/managing-data/uploading-data/index.html @@ -1,7 +1,6 @@ -Uploading Data | UQ AIS XNATUploading Data | UQ AIS XNAT +
            - - \ No newline at end of file +">
            \ No newline at end of file diff --git a/docs/user-guides/managing-data/uploading-data/prearchive/index.html b/docs/user-guides/managing-data/uploading-data/prearchive/index.html index a9ade58..cfb2cb5 100644 --- a/docs/user-guides/managing-data/uploading-data/prearchive/index.html +++ b/docs/user-guides/managing-data/uploading-data/prearchive/index.html @@ -1,9 +1,8 @@ -Prearchive | UQ AIS XNATPrearchive | UQ AIS XNAT +

            Prearchive

            XNAT Prearchive

            If a dataset has not arrived into your XNAT project, the prearchive would be the place to check

            This usually happens when:

            • a DICOM dataset matching an existing session gets resent
            • a part of a session gets uploaded separately

            Accessing the prearchive

            Go to Upload on the top menu, and Go to prearchive

            The following is an example of a session that is in conflict. +">

            Prearchive

            XNAT Prearchive

            If a dataset has not arrived into your XNAT project, the prearchive would be the place to check

            This usually happens when:

            • a DICOM dataset matching an existing session gets resent
            • a part of a session gets uploaded separately

            Accessing the prearchive

            Go to Upload on the top menu, and Go to prearchive

            The following is an example of a session that is in conflict. We can select the session and choose Details.

            Here we can download the session, or individual scans. -And review the datasets

            • Choose Archive if you want the dataset merged into the existing one on the archive,
            • choose Modify and Archive if any details need to be changed before archiving, or if you don’t want this dataset to merge with the existing one

            - - \ No newline at end of file +And review the datasets

            • Choose Archive if you want the dataset merged into the existing one on the archive,
            • choose Modify and Archive if any details need to be changed before archiving, or if you don’t want this dataset to merge with the existing one

            \ No newline at end of file diff --git a/docs/user-guides/managing-data/uploading-data/resource-uploader/index.html b/docs/user-guides/managing-data/uploading-data/resource-uploader/index.html index edffe4c..0bfeb41 100644 --- a/docs/user-guides/managing-data/uploading-data/resource-uploader/index.html +++ b/docs/user-guides/managing-data/uploading-data/resource-uploader/index.html @@ -1,7 +1,6 @@ -Resource uploader | UQ AIS XNATResource uploader | UQ AIS XNAT +

            Resource uploader

            Resource uploader

            This is to create a web upload form for repeated uploads of any data type.

            Navigate to Project → Manage → Project Resource Settings → Start

            Select Image Sessions. Enter the following required fields

            • Title: e.g. Rawdata
            • Resource Folder: e.g. RAW
            • Extract compressed files by default

            Select Add when complete

            To upload file(s) using the resource uploader, Upload Additional Files from the Sessions page

            - - \ No newline at end of file +">

            Resource uploader

            Resource uploader

            This is to create a web upload form for repeated uploads of any data type.

            Navigate to Project → Manage → Project Resource Settings → Start

            Select Image Sessions. Enter the following required fields

            • Title: e.g. Rawdata
            • Resource Folder: e.g. RAW
            • Extract compressed files by default

            Select Add when complete

            To upload file(s) using the resource uploader, Upload Additional Files from the Sessions page

            \ No newline at end of file diff --git a/docs/user-guides/managing-data/uploading-data/web-upload/index.html b/docs/user-guides/managing-data/uploading-data/web-upload/index.html index a68c14d..3e7853c 100644 --- a/docs/user-guides/managing-data/uploading-data/web-upload/index.html +++ b/docs/user-guides/managing-data/uploading-data/web-upload/index.html @@ -1,9 +1,8 @@ -Web Upload | UQ AIS XNATWeb Upload | UQ AIS XNAT +

            Web Upload

            Upload using XNAT compressed uploader

            Uploading DICOM datasets

            This is for uploading de-identified DICOM files using the uploader directly from the XNAT website

            1. De-identify DICOM on scanner or upload pc
            2. Zip DICOM files into a zip file
            3. Login to XNAT (see Login to XNAT)
            4. From the top panel, select Upload → Images → Compressed Uploader

            1. Specify the following options:
              • Project
              • Destination: Select Prearchive
              • Choose file to select zipped file with DICOMs

            1. Click Begin Upload +">

              Web Upload

              Upload using XNAT compressed uploader

              Uploading DICOM datasets

              This is for uploading de-identified DICOM files using the uploader directly from the XNAT website

              1. De-identify DICOM on scanner or upload pc
              2. Zip DICOM files into a zip file
              3. Login to XNAT (see Login to XNAT)
              4. From the top panel, select Upload → Images → Compressed Uploader

              1. Specify the following options:
                • Project
                • Destination: Select Prearchive
                • Choose file to select zipped file with DICOMs

              1. Click Begin Upload Wait for:
                • Upload percent bar to finish (**percent bar may not appear for small datasets)
                • Background processes panel to appear on bottom right
                • Green tick on under Upload extraction/review for archival

              For further information refer to the XNAT official guide on using the compressed image uploader

              - - \ No newline at end of file +

            For further information refer to the XNAT official guide on using the compressed image uploader

            \ No newline at end of file diff --git a/docs/user-guides/managing-data/viewing-images/_print/index.html b/docs/user-guides/managing-data/viewing-images/_print/index.html index e06e56e..33cbd08 100644 --- a/docs/user-guides/managing-data/viewing-images/_print/index.html +++ b/docs/user-guides/managing-data/viewing-images/_print/index.html @@ -1,10 +1,9 @@ -Viewing Images | UQ AIS XNATViewing Images | UQ AIS XNAT +

            This is the multi-page printable view of this section. +">

            This is the multi-page printable view of this section. Click here to print.

            Return to the regular view of this page.

            Viewing Images

            Viewing Images in the XNAT OHIF Viewer

              XNAT OHIF Viewer

              AIS XNAT instances come with the XNAT OHIF Image viewer Which is a plugin developed by the Institute for Cancer Research in London

              Just note, if your publication uses the OHIF viewer, they have an article for citation. -This information is all available at the link below

              Documentation
              https://wiki.xnat.org/documentation/xnat-ohif-viewer
              Using the XNAT OHIF Viewer
              https://wiki.xnat.org/documentation/xnat-ohif-viewer/using-the-xnat-ohif-viewer-122978515.html

              Opening images in OHIF viewer

              You can access the viewer from Session page

              Just click View Image on the actions panel

              This will take you to the OHIF Viewer

              - - \ No newline at end of file +This information is all available at the link below

              Documentation
              https://wiki.xnat.org/documentation/xnat-ohif-viewer
              Using the XNAT OHIF Viewer
              https://wiki.xnat.org/documentation/xnat-ohif-viewer/using-the-xnat-ohif-viewer-122978515.html

              Opening images in OHIF viewer

              You can access the viewer from Session page

              Just click View Image on the actions panel

              This will take you to the OHIF Viewer

              \ No newline at end of file diff --git a/docs/user-guides/managing-data/viewing-images/index.html b/docs/user-guides/managing-data/viewing-images/index.html index 166539d..50209b0 100644 --- a/docs/user-guides/managing-data/viewing-images/index.html +++ b/docs/user-guides/managing-data/viewing-images/index.html @@ -1,9 +1,8 @@ -Viewing Images | UQ AIS XNATViewing Images | UQ AIS XNAT +

              Viewing Images

              Viewing Images in the XNAT OHIF Viewer

              XNAT OHIF Viewer

              AIS XNAT instances come with the XNAT OHIF Image viewer +">

              Viewing Images

              Viewing Images in the XNAT OHIF Viewer

              XNAT OHIF Viewer

              AIS XNAT instances come with the XNAT OHIF Image viewer Which is a plugin developed by the Institute for Cancer Research in London

              Just note, if your publication uses the OHIF viewer, they have an article for citation. -This information is all available at the link below

              Documentation
              https://wiki.xnat.org/documentation/xnat-ohif-viewer
              Using the XNAT OHIF Viewer
              https://wiki.xnat.org/documentation/xnat-ohif-viewer/using-the-xnat-ohif-viewer-122978515.html

              Opening images in OHIF viewer

              You can access the viewer from Session page

              Just click View Image on the actions panel

              This will take you to the OHIF Viewer

              - - \ No newline at end of file +This information is all available at the link below

              Documentation
              https://wiki.xnat.org/documentation/xnat-ohif-viewer
              Using the XNAT OHIF Viewer
              https://wiki.xnat.org/documentation/xnat-ohif-viewer/using-the-xnat-ohif-viewer-122978515.html

              Opening images in OHIF viewer

              You can access the viewer from Session page

              Just click View Image on the actions panel

              This will take you to the OHIF Viewer

              \ No newline at end of file diff --git a/docs/user-guides/processing-data/_print/index.html b/docs/user-guides/processing-data/_print/index.html index b2ecb60..e963898 100644 --- a/docs/user-guides/processing-data/_print/index.html +++ b/docs/user-guides/processing-data/_print/index.html @@ -1,12 +1,11 @@ -Processing Data | UQ AIS XNATProcessing Data | UQ AIS XNAT +

              This is the multi-page printable view of this section. +">

              This is the multi-page printable view of this section. Click here to print.

              Return to the regular view of this page.

              Processing Data

              Processing Data

              1 - Command line tools

              Command line tools

              XnatUtils

              https://github.com/Australian-Imaging-Service/xnatutils

              Install xnatutils using

              pip3 install xnatutils
               

              Authenticating using .netrc

              1. Create an alias token. Or use an existing alias token
              2. Create a .netrc file in your home directory with the following details
              machine https://xnat.rcc.uq.edu.au
               user <your-alias-token>
               password <your-alias-secret>
              -

              xnatpy

              https://xnat.readthedocs.io/en/latest/

              Pyxnat

              https://pyxnat.github.io/pyxnat

              - - \ No newline at end of file +

              xnatpy

              https://xnat.readthedocs.io/en/latest/

              Pyxnat

              https://pyxnat.github.io/pyxnat

              \ No newline at end of file diff --git a/docs/user-guides/processing-data/command-line-tools/_print/index.html b/docs/user-guides/processing-data/command-line-tools/_print/index.html index a955b77..790d725 100644 --- a/docs/user-guides/processing-data/command-line-tools/_print/index.html +++ b/docs/user-guides/processing-data/command-line-tools/_print/index.html @@ -1,12 +1,11 @@ -Command line tools | UQ AIS XNATCommand line tools | UQ AIS XNAT +

              This is the multi-page printable view of this section. +">

              This is the multi-page printable view of this section. Click here to print.

              Return to the regular view of this page.

              Command line tools

              Command line tools

                XnatUtils

                https://github.com/Australian-Imaging-Service/xnatutils

                Install xnatutils using

                pip3 install xnatutils
                 

                Authenticating using .netrc

                1. Create an alias token. Or use an existing alias token
                2. Create a .netrc file in your home directory with the following details
                machine https://xnat.rcc.uq.edu.au
                 user <your-alias-token>
                 password <your-alias-secret>
                -

                xnatpy

                https://xnat.readthedocs.io/en/latest/

                Pyxnat

                https://pyxnat.github.io/pyxnat

                - - \ No newline at end of file +

                xnatpy

                https://xnat.readthedocs.io/en/latest/

                Pyxnat

                https://pyxnat.github.io/pyxnat

                \ No newline at end of file diff --git a/docs/user-guides/processing-data/command-line-tools/index.html b/docs/user-guides/processing-data/command-line-tools/index.html index e58fb9a..1f20ae2 100644 --- a/docs/user-guides/processing-data/command-line-tools/index.html +++ b/docs/user-guides/processing-data/command-line-tools/index.html @@ -1,11 +1,10 @@ -Command line tools | UQ AIS XNATCommand line tools | UQ AIS XNAT +
                \ No newline at end of file diff --git a/docs/user-guides/processing-data/index.html b/docs/user-guides/processing-data/index.html index 0827c4b..21d3f9e 100644 --- a/docs/user-guides/processing-data/index.html +++ b/docs/user-guides/processing-data/index.html @@ -1,7 +1,6 @@ -Processing Data | UQ AIS XNATProcessing Data | UQ AIS XNAT +
                - - \ No newline at end of file +">
                \ No newline at end of file diff --git a/index.html b/index.html index 623b901..e66a5f1 100644 --- a/index.html +++ b/index.html @@ -1,10 +1,8 @@ -UQ AIS XNAT

                UQ AIS XNAT

                Storing, managing and analysing de-identified imaging data for UQ projects and collaborators

                Learn more about AIS   -Documentation   -Go to UQ AIS XNAT  

                Project specific UQ XNAT repositories (may require UQ Network or VPN)

                opex.qbi.uq.edu.au -irc5.qbi.uq.edu.au -braininjury.qbi.uq.edu.au
                +UQ AIS XNAT +

                UQ AIS XNAT

                Storing, managing and analysing de-identified imaging data for UQ projects and collaborators

                Learn more about AIS   +Documentation   +Go to UQ AIS XNAT  

                Project specific UQ XNAT repositories (may require UQ Network or VPN)

                opex.qbi.uq.edu.au +irc5.qbi.uq.edu.au
                Multi-center Studies
                Imaging and Clinical Data
                -Data sharing
                Provided by
                UQ Research Computing Centre (RCC) and Australian National Imaging Facility (ANIF)
                - - \ No newline at end of file +Data sharing
                Provided by
                UQ Research Computing Centre (RCC) and Australian National Imaging Facility (ANIF)
                \ No newline at end of file diff --git a/js/main.min.b24653df39aba6780742323257d59bc1d785ebeeca70a6d45af47b9784701cee.js b/js/main.min.b24653df39aba6780742323257d59bc1d785ebeeca70a6d45af47b9784701cee.js deleted file mode 100644 index ce9b29c..0000000 --- a/js/main.min.b24653df39aba6780742323257d59bc1d785ebeeca70a6d45af47b9784701cee.js +++ /dev/null @@ -1,5 +0,0 @@ -/*! - * Bootstrap v5.2.3 (https://getbootstrap.com/) - * Copyright 2011-2022 The Bootstrap Authors (https://github.com/twbs/bootstrap/graphs/contributors) - * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE) - */(function(e,t){typeof exports=="object"&&typeof module!="undefined"?module.exports=t():typeof define=="function"&&define.amd?define(t):(e=typeof globalThis!="undefined"?globalThis:e||self,e.bootstrap=t())})(this,function(){"use strict";const ro=1e6,Jr=1e3,ut="transitionend",Xr=e=>e==null?`${e}`:Object.prototype.toString.call(e).match(/\s([a-z]+)/i)[1].toLowerCase(),Gr=e=>{do 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e=this.getWidth();this._disableOverFlow(),this._setElementAttributes(this._element,me,t=>t+e),this._setElementAttributes(wt,me,t=>t+e),this._setElementAttributes(Ot,xt,t=>t-e)}reset(){this._resetElementAttributes(this._element,"overflow"),this._resetElementAttributes(this._element,me),this._resetElementAttributes(wt,me),this._resetElementAttributes(Ot,xt)}isOverflowing(){return this.getWidth()>0}_disableOverFlow(){this._saveInitialAttribute(this._element,"overflow"),this._element.style.overflow="hidden"}_setElementAttributes(e,t,n){const s=this.getWidth(),o=e=>{if(e!==this._element&&window.innerWidth>e.clientWidth+s)return;this._saveInitialAttribute(e,t);const o=window.getComputedStyle(e).getPropertyValue(t);e.style.setProperty(t,`${n(Number.parseFloat(o))}px`)};this._applyManipulationCallback(e,o)}_saveInitialAttribute(e,t){const n=e.style.getPropertyValue(t);n&&b.setDataAttribute(e,t,n)}_resetElementAttributes(e,t){const n=e=>{const n=b.getDataAttribute(e,t);if(n===null){e.style.removeProperty(t);return}b.removeDataAttribute(e,t),e.style.setProperty(t,n)};this._applyManipulationCallback(e,n)}_applyManipulationCallback(e,n){if(g(e)){n(e);return}for(const s of t.find(e,this._element))n(s)}}const Ft="backdrop",Ho="fade",pt="show",Dt=`mousedown.bs.${Ft}`,Vo={className:"modal-backdrop",clickCallback:null,isAnimated:!1,isVisible:!0,rootElement:"body"},$o={className:"string",clickCallback:"(function|null)",isAnimated:"boolean",isVisible:"boolean",rootElement:"(element|string)"};class Nt extends te{constructor(e){super(),this._config=this._getConfig(e),this._isAppended=!1,this._element=null}static get Default(){return Vo}static get DefaultType(){return $o}static get NAME(){return Ft}show(e){if(!this._config.isVisible){y(e);return}this._append();const t=this._getElement();this._config.isAnimated&&ne(t),t.classList.add(pt),this._emulateAnimation(()=>{y(e)})}hide(e){if(!this._config.isVisible){y(e);return}this._getElement().classList.remove(pt),this._emulateAnimation(()=>{this.dispose(),y(e)})}dispose(){if(!this._isAppended)return;e.off(this._element,Dt),this._element.remove(),this._isAppended=!1}_getElement(){if(!this._element){const e=document.createElement("div");e.className=this._config.className,this._config.isAnimated&&e.classList.add(Ho),this._element=e}return this._element}_configAfterMerge(e){return e.rootElement=E(e.rootElement),e}_append(){if(this._isAppended)return;const t=this._getElement();this._config.rootElement.append(t),e.on(t,Dt,()=>{y(this._config.clickCallback)}),this._isAppended=!0}_emulateAnimation(e){Yn(e,this._getElement(),this._config.isAnimated)}}const Uo="focustrap",Ko="bs.focustrap",_e=`.${Ko}`,Yo=`focusin${_e}`,Go=`keydown.tab${_e}`,Xo="Tab",Qo="forward",Rt="backward",Jo={autofocus:!0,trapElement:null},ei={autofocus:"boolean",trapElement:"element"};class Pt extends te{constructor(e){super(),this._config=this._getConfig(e),this._isActive=!1,this._lastTabNavDirection=null}static get Default(){return Jo}static get DefaultType(){return ei}static get NAME(){return Uo}activate(){if(this._isActive)return;this._config.autofocus&&this._config.trapElement.focus(),e.off(document,_e),e.on(document,Yo,e=>this._handleFocusin(e)),e.on(document,Go,e=>this._handleKeydown(e)),this._isActive=!0}deactivate(){if(!this._isActive)return;this._isActive=!1,e.off(document,_e)}_handleFocusin(e){const{trapElement:n}=this._config;if(e.target===document||e.target===n||n.contains(e.target))return;const s=t.focusableChildren(n);s.length===0?n.focus():this._lastTabNavDirection===Rt?s[s.length-1].focus():s[0].focus()}_handleKeydown(e){if(e.key!==Xo)return;this._lastTabNavDirection=e.shiftKey?Rt:Qo}}const ni="modal",si="bs.modal",d=`.${si}`,ii=".data-api",ai="Escape",ri=`hide${d}`,ci=`hidePrevented${d}`,Ht=`hidden${d}`,It=`show${d}`,ui=`shown${d}`,hi=`resize${d}`,mi=`click.dismiss${d}`,fi=`mousedown.dismiss${d}`,pi=`keydown.dismiss${d}`,gi=`click${d}${ii}`,Bt="modal-open",bi="fade",Vt="show",Ne="modal-static",_i=".modal.show",wi=".modal-dialog",Oi=".modal-body",xi='[data-bs-toggle="modal"]',Ci={backdrop:!0,focus:!0,keyboard:!0},Ei={backdrop:"(boolean|string)",focus:"boolean",keyboard:"boolean"};class B extends u{constructor(e,n){super(e,n),this._dialog=t.findOne(wi,this._element),this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._isShown=!1,this._isTransitioning=!1,this._scrollBar=new tt,this._addEventListeners()}static get Default(){return Ci}static get DefaultType(){return Ei}static get NAME(){return ni}toggle(e){return this._isShown?this.hide():this.show(e)}show(t){if(this._isShown||this._isTransitioning)return;const n=e.trigger(this._element,It,{relatedTarget:t});if(n.defaultPrevented)return;this._isShown=!0,this._isTransitioning=!0,this._scrollBar.hide(),document.body.classList.add(Bt),this._adjustDialog(),this._backdrop.show(()=>this._showElement(t))}hide(){if(!this._isShown||this._isTransitioning)return;const t=e.trigger(this._element,ri);if(t.defaultPrevented)return;this._isShown=!1,this._isTransitioning=!0,this._focustrap.deactivate(),this._element.classList.remove(Vt),this._queueCallback(()=>this._hideModal(),this._element,this._isAnimated())}dispose(){for(const t of[window,this._dialog])e.off(t,d);this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}handleUpdate(){this._adjustDialog()}_initializeBackDrop(){return new Nt({isVisible:Boolean(this._config.backdrop),isAnimated:this._isAnimated()})}_initializeFocusTrap(){return new Pt({trapElement:this._element})}_showElement(n){document.body.contains(this._element)||document.body.append(this._element),this._element.style.display="block",this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.scrollTop=0;const s=t.findOne(Oi,this._dialog);s&&(s.scrollTop=0),ne(this._element),this._element.classList.add(Vt);const o=()=>{this._config.focus&&this._focustrap.activate(),this._isTransitioning=!1,e.trigger(this._element,ui,{relatedTarget:n})};this._queueCallback(o,this._dialog,this._isAnimated())}_addEventListeners(){e.on(this._element,pi,e=>{if(e.key!==ai)return;if(this._config.keyboard){e.preventDefault(),this.hide();return}this._triggerBackdropTransition()}),e.on(window,hi,()=>{this._isShown&&!this._isTransitioning&&this._adjustDialog()}),e.on(this._element,fi,t=>{e.one(this._element,mi,e=>{if(this._element!==t.target||this._element!==e.target)return;if(this._config.backdrop==="static"){this._triggerBackdropTransition();return}this._config.backdrop&&this.hide()})})}_hideModal(){this._element.style.display="none",this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._isTransitioning=!1,this._backdrop.hide(()=>{document.body.classList.remove(Bt),this._resetAdjustments(),this._scrollBar.reset(),e.trigger(this._element,Ht)})}_isAnimated(){return this._element.classList.contains(bi)}_triggerBackdropTransition(){const n=e.trigger(this._element,ci);if(n.defaultPrevented)return;const s=this._element.scrollHeight>document.documentElement.clientHeight,t=this._element.style.overflowY;if(t==="hidden"||this._element.classList.contains(Ne))return;s||(this._element.style.overflowY="hidden"),this._element.classList.add(Ne),this._queueCallback(()=>{this._element.classList.remove(Ne),this._queueCallback(()=>{this._element.style.overflowY=t},this._dialog)},this._dialog),this._element.focus()}_adjustDialog(){const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._scrollBar.getWidth(),n=e>0;if(n&&!t){const t=a()?"paddingLeft":"paddingRight";this._element.style[t]=`${e}px`}if(!n&&t){const t=a()?"paddingRight":"paddingLeft";this._element.style[t]=`${e}px`}}_resetAdjustments(){this._element.style.paddingLeft="",this._element.style.paddingRight=""}static jQueryInterface(e,t){return this.each(function(){const n=B.getOrCreateInstance(this,e);if(typeof e!="string")return;if(typeof n[e]=="undefined")throw new TypeError(`No method named "${e}"`);n[e](t)})}}e.on(document,gi,xi,function(n){const s=v(this);["A","AREA"].includes(this.tagName)&&n.preventDefault(),e.one(s,It,t=>{if(t.defaultPrevented)return;e.one(s,Ht,()=>{H(this)&&this.focus()})});const o=t.findOne(_i);o&&B.getInstance(o).hide();const i=B.getOrCreateInstance(s);i.toggle(this)}),Se(B),c(B);const Ai="offcanvas",Si="bs.offcanvas",j=`.${Si}`,Ut=".data-api",Ti=`load${j}${Ut}`,zi="Escape",qt="show",Yt="showing",an="hiding",Ri="offcanvas-backdrop",rn=".offcanvas.show",Hi=`show${j}`,Ii=`shown${j}`,Bi=`hide${j}`,cn=`hidePrevented${j}`,ln=`hidden${j}`,Wi=`resize${j}`,Ui=`click${j}${Ut}`,Ki=`keydown.dismiss${j}`,qi='[data-bs-toggle="offcanvas"]',Yi={backdrop:!0,keyboard:!0,scroll:!1},Gi={backdrop:"(boolean|string)",keyboard:"boolean",scroll:"boolean"};class A extends u{constructor(e,t){super(e,t),this._isShown=!1,this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._addEventListeners()}static get Default(){return Yi}static get DefaultType(){return Gi}static get NAME(){return Ai}toggle(e){return this._isShown?this.hide():this.show(e)}show(t){if(this._isShown)return;const n=e.trigger(this._element,Hi,{relatedTarget:t});if(n.defaultPrevented)return;this._isShown=!0,this._backdrop.show(),this._config.scroll||(new tt).hide(),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.classList.add(Yt);const s=()=>{(!this._config.scroll||this._config.backdrop)&&this._focustrap.activate(),this._element.classList.add(qt),this._element.classList.remove(Yt),e.trigger(this._element,Ii,{relatedTarget:t})};this._queueCallback(s,this._element,!0)}hide(){if(!this._isShown)return;const t=e.trigger(this._element,Bi);if(t.defaultPrevented)return;this._focustrap.deactivate(),this._element.blur(),this._isShown=!1,this._element.classList.add(an),this._backdrop.hide();const n=()=>{this._element.classList.remove(qt,an),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._config.scroll||(new tt).reset(),e.trigger(this._element,ln)};this._queueCallback(n,this._element,!0)}dispose(){this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}_initializeBackDrop(){const n=()=>{if(this._config.backdrop==="static"){e.trigger(this._element,cn);return}this.hide()},t=Boolean(this._config.backdrop);return new Nt({className:Ri,isVisible:t,isAnimated:!0,rootElement:this._element.parentNode,clickCallback:t?n:null})}_initializeFocusTrap(){return new Pt({trapElement:this._element})}_addEventListeners(){e.on(this._element,Ki,t=>{if(t.key!==zi)return;if(!this._config.keyboard){e.trigger(this._element,cn);return}this.hide()})}static jQueryInterface(e){return this.each(function(){const t=A.getOrCreateInstance(this,e);if(typeof e!="string")return;if(t[e]===void 0||e.startsWith("_")||e==="constructor")throw new TypeError(`No method named "${e}"`);t[e](this)})}}e.on(document,Ui,qi,function(n){const s=v(this);if(["A","AREA"].includes(this.tagName)&&n.preventDefault(),w(this))return;e.one(s,ln,()=>{H(this)&&this.focus()});const o=t.findOne(rn);o&&o!==s&&A.getInstance(o).hide();const i=A.getOrCreateInstance(s);i.toggle(this)}),e.on(window,Ti,()=>{for(const e of t.find(rn))A.getOrCreateInstance(e).show()}),e.on(window,Wi,()=>{for(const e of t.find("[aria-modal][class*=show][class*=offcanvas-]"))getComputedStyle(e).position!=="fixed"&&A.getOrCreateInstance(e).hide()}),Se(A),c(A);const Qi=new Set(["background","cite","href","itemtype","longdesc","poster","src","xlink:href"]),Zi=/^aria-[\w-]*$/i,Ji=/^(?:(?:https?|mailto|ftp|tel|file|sms):|[^#&/:?]*(?:[#/?]|$))/i,ea=/^data:(?:image\/(?:bmp|gif|jpeg|jpg|png|tiff|webp)|video\/(?:mpeg|mp4|ogg|webm)|audio\/(?:mp3|oga|ogg|opus));base64,[\d+/a-z]+=*$/i,ta=(e,t)=>{const n=e.nodeName.toLowerCase();return t.includes(n)?!Qi.has(n)||Boolean(Ji.test(e.nodeValue)||ea.test(e.nodeValue)):t.filter(e=>e instanceof RegExp).some(e=>e.test(n))},dn={"*":["class","dir","id","lang","role",Zi],a:["target","href","title","rel"],area:[],b:[],br:[],col:[],code:[],div:[],em:[],hr:[],h1:[],h2:[],h3:[],h4:[],h5:[],h6:[],i:[],img:["src","srcset","alt","title","width","height"],li:[],ol:[],p:[],pre:[],s:[],small:[],span:[],sub:[],sup:[],strong:[],u:[],ul:[]};function sa(e,t,n){if(!e.length)return e;if(n&&typeof n=="function")return n(e);const o=new window.DOMParser,s=o.parseFromString(e,"text/html"),i=[].concat(...s.body.querySelectorAll("*"));for(const e of i){const n=e.nodeName.toLowerCase();if(!Object.keys(t).includes(n)){e.remove();continue}const s=[].concat(...e.attributes),o=[].concat(t["*"]||[],t[n]||[]);for(const t of s)ta(t,o)||e.removeAttribute(t.nodeName)}return s.body.innerHTML}const oa="TemplateFactory",ia={allowList:dn,content:{},extraClass:"",html:!1,sanitize:!0,sanitizeFn:null,template:"
                "},aa={allowList:"object",content:"object",extraClass:"(string|function)",html:"boolean",sanitize:"boolean",sanitizeFn:"(null|function)",template:"string"},ra={entry:"(string|element|function|null)",selector:"(string|element)"};class ca extends te{constructor(e){super(),this._config=this._getConfig(e)}static get Default(){return ia}static get DefaultType(){return aa}static get NAME(){return oa}getContent(){return Object.values(this._config.content).map(e=>this._resolvePossibleFunction(e)).filter(Boolean)}hasContent(){return this.getContent().length>0}changeContent(e){return this._checkContent(e),this._config.content={...this._config.content,...e},this}toHtml(){const e=document.createElement("div");e.innerHTML=this._maybeSanitize(this._config.template);for(const[t,n]of Object.entries(this._config.content))this._setContent(e,n,t);const t=e.children[0],n=this._resolvePossibleFunction(this._config.extraClass);return n&&t.classList.add(...n.split(" ")),t}_typeCheckConfig(e){super._typeCheckConfig(e),this._checkContent(e.content)}_checkContent(e){for(const[t,n]of Object.entries(e))super._typeCheckConfig({selector:t,entry:n},ra)}_setContent(e,n,s){const o=t.findOne(s,e);if(!o)return;if(n=this._resolvePossibleFunction(n),!n){o.remove();return}if(g(n)){this._putElementInTemplate(E(n),o);return}if(this._config.html){o.innerHTML=this._maybeSanitize(n);return}o.textContent=n}_maybeSanitize(e){return this._config.sanitize?sa(e,this._config.allowList,this._config.sanitizeFn):e}_resolvePossibleFunction(e){return typeof e=="function"?e(this):e}_putElementInTemplate(e,t){if(this._config.html){t.innerHTML="",t.append(e);return}t.textContent=e.textContent}}const la="tooltip",da=new Set(["sanitize","allowList","sanitizeFn"]),Xe="fade",ha="modal",ue="show",fa=".tooltip-inner",hn=`.${ha}`,mn="hide.bs.modal",J="hover",ot="focus",ja="click",ya="manual",_a="hide",wa="hidden",Oa="show",xa="shown",Ca="inserted",Ea="click",ka="focusin",Aa="focusout",Sa="mouseenter",Ma="mouseleave",Fa={AUTO:"auto",TOP:"top",RIGHT:a()?"left":"right",BOTTOM:"bottom",LEFT:a()?"right":"left"},Ta={allowList:dn,animation:!0,boundary:"clippingParents",container:!1,customClass:"",delay:0,fallbackPlacements:["top","right","bottom","left"],html:!1,offset:[0,0],placement:"top",popperConfig:null,sanitize:!0,sanitizeFn:null,selector:!1,template:'',title:"",trigger:"hover focus"},za={allowList:"object",animation:"boolean",boundary:"(string|element)",container:"(string|element|boolean)",customClass:"(string|function)",delay:"(number|object)",fallbackPlacements:"array",html:"boolean",offset:"(array|string|function)",placement:"(string|function)",popperConfig:"(null|object|function)",sanitize:"boolean",sanitizeFn:"(null|function)",selector:"(string|boolean)",template:"string",title:"(string|element|function)",trigger:"string"};class U extends u{constructor(e,t){if(typeof _t=="undefined")throw new TypeError("Bootstrap's tooltips require Popper (https://popper.js.org)");super(e,t),this._isEnabled=!0,this._timeout=0,this._isHovered=null,this._activeTrigger={},this._popper=null,this._templateFactory=null,this._newContent=null,this.tip=null,this._setListeners(),this._config.selector||this._fixTitle()}static get Default(){return Ta}static get DefaultType(){return za}static get NAME(){return la}enable(){this._isEnabled=!0}disable(){this._isEnabled=!1}toggleEnabled(){this._isEnabled=!this._isEnabled}toggle(){if(!this._isEnabled)return;if(this._activeTrigger.click=!this._activeTrigger.click,this._isShown()){this._leave();return}this._enter()}dispose(){clearTimeout(this._timeout),e.off(this._element.closest(hn),mn,this._hideModalHandler),this._element.getAttribute("data-bs-original-title")&&this._element.setAttribute("title",this._element.getAttribute("data-bs-original-title")),this._disposePopper(),super.dispose()}show(){if(this._element.style.display==="none")throw new Error("Please use show on visible elements");if(!this._isWithContent()||!this._isEnabled)return;const n=e.trigger(this._element,this.constructor.eventName(Oa)),s=Jn(this._element),o=(s||this._element.ownerDocument.documentElement).contains(this._element);if(n.defaultPrevented||!o)return;this._disposePopper();const t=this._getTipElement();this._element.setAttribute("aria-describedby",t.getAttribute("id"));const{container:i}=this._config;if(this._element.ownerDocument.documentElement.contains(this.tip)||(i.append(t),e.trigger(this._element,this.constructor.eventName(Ca))),this._popper=this._createPopper(t),t.classList.add(ue),"ontouchstart"in document.documentElement)for(const t of[].concat(...document.body.children))e.on(t,"mouseover",Oe);const a=()=>{e.trigger(this._element,this.constructor.eventName(xa)),this._isHovered===!1&&this._leave(),this._isHovered=!1};this._queueCallback(a,this.tip,this._isAnimated())}hide(){if(!this._isShown())return;const t=e.trigger(this._element,this.constructor.eventName(_a));if(t.defaultPrevented)return;const n=this._getTipElement();if(n.classList.remove(ue),"ontouchstart"in document.documentElement)for(const t of[].concat(...document.body.children))e.off(t,"mouseover",Oe);this._activeTrigger[ja]=!1,this._activeTrigger[ot]=!1,this._activeTrigger[J]=!1,this._isHovered=null;const s=()=>{if(this._isWithActiveTrigger())return;this._isHovered||this._disposePopper(),this._element.removeAttribute("aria-describedby"),e.trigger(this._element,this.constructor.eventName(wa))};this._queueCallback(s,this.tip,this._isAnimated())}update(){this._popper&&this._popper.update()}_isWithContent(){return Boolean(this._getTitle())}_getTipElement(){return this.tip||(this.tip=this._createTipElement(this._newContent||this._getContentForTemplate())),this.tip}_createTipElement(e){const t=this._getTemplateFactory(e).toHtml();if(!t)return null;t.classList.remove(Xe,ue),t.classList.add(`bs-${this.constructor.NAME}-auto`);const n=Gr(this.constructor.NAME).toString();return t.setAttribute("id",n),this._isAnimated()&&t.classList.add(Xe),t}setContent(e){this._newContent=e,this._isShown()&&(this._disposePopper(),this.show())}_getTemplateFactory(e){return this._templateFactory?this._templateFactory.changeContent(e):this._templateFactory=new ca({...this._config,content:e,extraClass:this._resolvePossibleFunction(this._config.customClass)}),this._templateFactory}_getContentForTemplate(){return{[fa]:this._getTitle()}}_getTitle(){return this._resolvePossibleFunction(this._config.title)||this._element.getAttribute("data-bs-original-title")}_initializeOnDelegatedTarget(e){return this.constructor.getOrCreateInstance(e.delegateTarget,this._getDelegateConfig())}_isAnimated(){return this._config.animation||this.tip&&this.tip.classList.contains(Xe)}_isShown(){return this.tip&&this.tip.classList.contains(ue)}_createPopper(e){const t=typeof 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t=e.trigger(this._element,Bi);if(t.defaultPrevented)return;this._focustrap.deactivate(),this._element.blur(),this._isShown=!1,this._element.classList.add(an),this._backdrop.hide();const n=()=>{this._element.classList.remove(qt,an),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._config.scroll||(new tt).reset(),e.trigger(this._element,ln)};this._queueCallback(n,this._element,!0)}dispose(){this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}_initializeBackDrop(){const n=()=>{if(this._config.backdrop==="static"){e.trigger(this._element,cn);return}this.hide()},t=Boolean(this._config.backdrop);return new Nt({className:Ri,isVisible:t,isAnimated:!0,rootElement:this._element.parentNode,clickCallback:t?n:null})}_initializeFocusTrap(){return new Pt({trapElement:this._element})}_addEventListeners(){e.on(this._element,Ki,t=>{if(t.key!==zi)return;if(!this._config.keyboard){e.trigger(this._element,cn);return}this.hide()})}static 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of i){const n=e.nodeName.toLowerCase();if(!Object.keys(t).includes(n)){e.remove();continue}const s=[].concat(...e.attributes),o=[].concat(t["*"]||[],t[n]||[]);for(const t of s)ta(t,o)||e.removeAttribute(t.nodeName)}return s.body.innerHTML}const oa="TemplateFactory",ia={allowList:dn,content:{},extraClass:"",html:!1,sanitize:!0,sanitizeFn:null,template:"
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e.container=e.container===!1?document.body:E(e.container),typeof e.delay=="number"&&(e.delay={show:e.delay,hide:e.delay}),typeof e.title=="number"&&(e.title=e.title.toString()),typeof e.content=="number"&&(e.content=e.content.toString()),e}_getDelegateConfig(){const e={};for(const t in this._config)this.constructor.Default[t]!==this._config[t]&&(e[t]=this._config[t]);return e.selector=!1,e.trigger="manual",e}_disposePopper(){this._popper&&(this._popper.destroy(),this._popper=null),this.tip&&(this.tip.remove(),this.tip=null)}static jQueryInterface(e){return this.each(function(){const t=U.getOrCreateInstance(this,e);if(typeof e!="string")return;if(typeof t[e]=="undefined")throw new TypeError(`No method named "${e}"`);t[e]()})}}c(U);const Na="popover",La=".popover-header",Ra=".popover-body",Pa={...U.Default,content:"",offset:[0,8],placement:"right",template:'',trigger:"click"},Ha={...U.DefaultType,content:"(null|string|element|function)"};class ct extends U{static get Default(){return 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