✨ Surface-based Derivatives

[tergeorge]

Related problem

1. The DCAN labs postfreesurfer bash script that is called by CPAC often fails to run to completion while running CPAC abcd-options pipeline. The error messages are often too vague and it is difficult to identify where the crash occurs.
2. Currently CPAC does generates derivatives such as falff, alff, reho, connectivity matrix only in the volume space and not in the surface space.

Proposed feature

1. Break down the DACN labs postfreesurfer bash script into smaller bash scripts and call each one separately so that any crashes that occur can be identified, generate the postfreesurfer outputs in the output directory and rename the surface generated files to a BIDS compatible format.
2. Use surface based files to generate derivatives such as falff, alff, reho and connectivity matrix.

Acceptance criteria

1. The postfreesurfer bash should run to completion without any errors and generate all the required outputs in the working and output directory.
2. The name of surface files generated should be BIDS compliant.
3. CPAC should be able to generate the derivatives (falff, alff, reho and connectivity matrix) in the surface space if specified by the user.

Current Status (04/02/2023)

1. DCAN lab Post freesurfer bash scripts run to completion without errors. All outputs are generated to the output directory with compatible BIDS naming format.
2. Surface derivatives node blocks falff, alff, Reho and connectivity matrix completed and tested.

Current issues:
The surface derivatives node blocks crash for certain configs.

Next steps

1. Plan and design the configs for each of the surface based derivatives node block.
2. BIDS compliant naming for surface derived output files.
3. Perform regression test.

Additional context

No response