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Only measurement definitions with the Session model as their content type should be included.

Following TheLabbingProject/django_analyses#58, integrate the QuerySetRunner class to simplify the existing CAT12 segmentation and ReconAll execution modules.

Describe the solution you'd like
Create an interface for fMRIprep via signularity/docker containers.

Including -1 in the sequence type filter input should return scans with an undefined sequence type.

A SequenceType instance can currently be associated with only one scanning_sequence and sequence_variant combination. However, some sequences may have a couple of different combinations.
I think we should either split SequenceType into two models, one to save the title and description and one to specify scanning_sequence and sequence_variant and associate with an instance of the former, or convert these two fields under SequenceType to be ArrayFields or simply a single JSONField, so that it can hold multiple specifications.

Show runs the scan was an input for in the Scan model's admin.

We need to create a Session model that will group scans that were acquired together.

• The Subject association should probably be moved to that Session model.
• I'm not yet entirely sure how we should create the grouping so that we definitely don't accidentally mix sessions.
• Sessions should be created automatically when importing scans.

The new interface for fMRIPrep is working as expected, but the outputs aren't being logged.

I used Scan.objects.import_path to import a subject's directory and got these messages (nothing was imported). @Aharonyn do you have an idea what might be causing this?

A download link should be displayed and a NIfTI version should be created on demand.

Give some kind of upload success or failure feedback when importing new scans.

The Session model needs to be registered in the admin site.

Outputs need to be added to the outputs.py module within the CAT12 segmentation interface's package so that they are copied to the run's destination directory, and also added to the analysis version's specification.

Sequence/modality deduction could be tidier and more comprehensive (?).

Exclude irrelevant definitions.

Compressed NIfTI scan tests raise an exception (not found in the expected location). Tests run successfully in the development environment.

Uses depracated NiftiInputDefinition.

Create a view to return a zipped archive containing one or more scans in a specific format.

Show some informative information about the session.

Querysets should be evaluated with qs.exists() rather than bool(qs).

Integrate first preprocessing pipeline to prepare scans for group-level analyses.

Adding a json field file for pipeline, sorting inputs to their designated nodes when initiating pipeline's run.

Due to the irregular DICOM header's ScanningSequence and SequenceVariant field values, the Bids class, which is used to determine the destination path for NIfTI format scan files, failes to determine a BIDS-compatible destination path.

Update tests to pass with maximal coverage.

The CAT12 interface needs to be updated to work with version 12.7. The batch template has gone some significant changes.

This will allow a lab manager to view all of the lab's sessions.

Move any visualization experiments to a dedicated branch, if required.

Different analyses represent scans in different ways (NIfTI path, DICOM directory, .mif path), and can receive these representations as either FileInput (e.g. BET, CAT12, FslAnat, etc.) or ListInput (e.g. ReconAll). It would be useful to have some utility method to easily query the runs in which a particular scan instance is represented.

get_instance_representation() is called in has_run() before the self._nifti condition is evaluated.

Creating a source distribution with sdist creates a package with missing modules (e.g. django_mri.analysis.matlab, django_mri.analysis.specifications).

It would be better to simply return the exception that was raised and display it instead of the plot.

NIfTI conversion currently raises an exception for non-BIDS compatible destinations. This is caused by Dcm2niix, which expects the file to be created at the returned_path, which is parsed from the process' output.

Duplicate sessions created when saving series instances.

• Option to download scan from admin list view.
• Option to download session from change view.
• Option to download session from list view.