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Merge pull request #215 from kaitj/feat/getting-started-page
Add getting started page
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,203 @@ | ||
| <!-- Home page --> | ||
| {% extends "base.html" %} | ||
| {% block title %} | ||
| Home | ||
| {% endblock title %} | ||
| {% block | ||
| app_content %} | ||
| <div class="container"> | ||
| <!-- Getting started --> | ||
| <div class="row"> | ||
| <div class="col"> | ||
| <div class="card my-3"> | ||
| <div class="card-body"> | ||
| <h1 class="card-title">Getting started!</h1> | ||
| <p class="card-text"> | ||
| This page provides some information to help you get started with autobids, | ||
| detailing the steps taken to convert data acquired from a CFMM scanner to | ||
| a <a href="https://bids.neuroimaging.io/" target="_blank" rel="noopener">BIDS</a> | ||
| dataset. | ||
| </p> | ||
| <p class="card-text"> | ||
| If you haven't already, please | ||
| <a href="{{ url_for("portal_blueprint.register") }}" | ||
| target="_blank" | ||
| rel="noopener">create an account</a> in order to interact with and | ||
| manage your study. | ||
| </p> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| <!-- New study --> | ||
| <div class="row"> | ||
| <div class="col"> | ||
| <div class="card my-3"> | ||
| <div class="card-body"> | ||
| <h2 class="card-title">New study</h2> | ||
| <p class="card-text"> | ||
| After you have acquired some data from a CFMM scanner, a request can be | ||
| made for autobids conversion: | ||
| <ol type="1"> | ||
| <li> | ||
| Request a new study from the | ||
| <a href="{{ url_for("portal_blueprint.new_study") }}">"New Study"</a> | ||
| tab. | ||
| </li> | ||
| <li> | ||
| Have the PI (or study manager) add "bidsdump" as an authorized user | ||
| for the study on the CFMM DICOM server. A step-by-step guide can be found | ||
| <a href="https://github.com/khanlab/autobids/wiki/Granting-access-to-bidsdump" | ||
| target="_blank" | ||
| rel="noopener">here</a>. | ||
| </li> | ||
| <li> | ||
| Sign up for a <a href="https://app.globus.org/" target="_blank" rel="noopener">Globus</a> | ||
| in order to download the converted data. | ||
| </li> | ||
| </ol> | ||
| An admin will review the new study, enable it, and grant you access if | ||
| there are no issues. Additional users can be granted access to the study. | ||
| For autobids to work on the study, the "Active" option needs to be checked | ||
| in the study config. | ||
| </p> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| <!-- Cfmm2tar --> | ||
| <div class="row"> | ||
| <div class="col"> | ||
| <div class="card my-3"> | ||
| <div class="card-body"> | ||
| <h2 class="card-title">DICOM retrieval</h2> | ||
| <p class="card-text"> | ||
| <em> | ||
| (This step makes use of | ||
| <a href="https://github.com/khanlab/cfmm2tar" | ||
| target="_blank" | ||
| rel="noopener">cfmm2tar</a>) | ||
| </em> | ||
| </p> | ||
| <p class="card-text"> | ||
| The first step of autobids queries the CFMM DICOM server for study data | ||
| based on information that was provided when creating a new study. | ||
| For each newly acquired scan that is found, a tarball file will be | ||
| created containing all of the associated DICOMS for a given participant. | ||
| This tarball file will be named based on a combination of values pulled | ||
| from the DICOM server and autobids database (which will be created if it | ||
| can't be found): | ||
| <br> | ||
| <br> | ||
| <code>PI_ProjectDescription_ScanDate_PatientName_StudyID.Hash.tar</code> | ||
| </p> | ||
| <p class="card-text"> | ||
| All created tarballs can be found under the "Tar Files" table within a given | ||
| study. It is important that these tarballs are named consistently as | ||
| these names are used to organize the data in the next step. The easiest | ||
| way to ensure this is to have a consistent patient naming patterns when | ||
| acquiring the data. If renaming is necessary, it can be done by clicking | ||
| the "Rename" button for each tarball. | ||
| </p> | ||
| <p class="card-text"> | ||
| <!-- Individual subjects --> | ||
| If you wish to manage individual participants (e.g. exclude from | ||
| conversion), you can do so by querying the DICOM server via autobids by | ||
| clicking "All matching scans" on the study page. | ||
| </p> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| <!-- Tar2bids --> | ||
| <div class="row"> | ||
| <div class="col"> | ||
| <div class="card my-3"> | ||
| <div class="card-body"> | ||
| <h2 class="card-title">BIDS-ify data</h2> | ||
| <p class="card-text"> | ||
| <em> | ||
| (This step makes use of | ||
| <a href="https://github.com/khanlab/tar2bids" | ||
| target="_blank" | ||
| rel="noopener">tar2bids</a>) | ||
| </em> | ||
| </p> | ||
| <p class="card-text"> | ||
| The next step of autobids uses the previously created tarballs and custom | ||
| heuristics to map the DICOMS to NifTIs organized according to BIDS. There | ||
| are two important settings under the study's config page: | ||
| <ol> | ||
| <li> | ||
| Heuristic - study specific mapping of DICOM values (to add or update | ||
| an existing heuristic, create a pull request to the | ||
| <a href="https://github.com/khanlab/tar2bids-heuristics" | ||
| target="_blank" | ||
| rel="noopener">heuristics repository</a>) | ||
| </li> | ||
| <li> | ||
| Tar2bids Patient Name Search String - extraction of patient names | ||
| and session labels (if necessary) | ||
| </li> | ||
| </ol> | ||
| After the data has been converted, it will be validated according to the | ||
| BIDS specification. Any errors or warnings will appear here! If the files | ||
| you converted are not part of the specification, you can add the pattern | ||
| to the .bidsignore content under the study configuration to exclude them | ||
| from validation. | ||
| </p> | ||
| <p class="card-text"> | ||
| If the study was acquired on the 7T scanner, distortion correction is | ||
| automatically performed on the converted data after validation. | ||
| Additionally, optional defacing can be performed by checking | ||
| the option under the study config. | ||
| </p> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| <!-- Archiving --> | ||
| <div class="row"> | ||
| <div class="col"> | ||
| <div class="card my-3"> | ||
| <div class="card-body"> | ||
| <h2 class="card-title">Accessing the data</h2> | ||
| <p class="card-text"> | ||
| Ensure a globus identity has been granted access to the study under the | ||
| study config, as converted data is archived and shared via globus. Note | ||
| the study id, which will be in the name of the shared globus collection. | ||
| In each collection, one zip archive will be created containing the | ||
| converted data since the last time tar2bids has been run. | ||
| </p> | ||
| <p class="card-text"> | ||
| Instructions for accessing the converted data can be found in the study | ||
| page. | ||
| </p> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| <!-- Notes --> | ||
| <div class="row"> | ||
| <div class="col"> | ||
| <div class="card my-3"> | ||
| <div class="card-body"> | ||
| <h2 class="card-title">Notes</h2> | ||
| <p class="card-text"> | ||
| <li> | ||
| For any questions concerning autobids, please post them on the | ||
| <a href="https://cbs-discourse.uwo.ca" target="_blank" rel="noopener"> | ||
| CBS Discourse | ||
| </a>. | ||
| </li> | ||
| <li> | ||
| Each step noted is automatically run throughout the day, | ||
| but can also be triggered manually | ||
| </li> | ||
| </p> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| {% endblock app_content %} |
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