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dutchconnectomelab / CATO

Toolbox for structural and functional brain connectivity reconstruction.
http://www.dutchconnectomelab.nl/CATO/
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Group mode #34

Open koenhelwegen opened 1 year ago

koenhelwegen commented 1 year ago

Adds a group mode to the structural and functional pipeline. To use the group mode, the user passes a file instead of a subject directory; the file should contain one subject directory per line.

This feature is useful when doing short computations in which starting up the MCR becomes a substantial overhead.

SiemondeLange commented 1 year ago

Great feature! This option would not only be helpful for reducing MATLAB Runtime (MCR) overhead, but simplify running multiple subjects by eliminating the need for a separate script.

In the current implementation, this PR would introduce a breaking change, as the --subjectDir option of the executable would be deprecated, requiring a new major CATO version (v4) that is not anticipated(?) in the near future. Maybe we can use both --subjectDir and --subjectListFile as input options for the executable? This approach would be similar to the pipeline functions in MATLAB that use structural_pipeline(SUBJECTDIR) and structural_pipeline(SUBJECTLISTFILE). This way, we can integrate these improvements much faster into CATO v3.X.

I would also recommend to try to implement test coverage for this newly introduced feature to ensure its proper functioning.

I will add more detailed comments to the code as well!