Optional pre-processing

[kaitj]

Optionally perform pre-processing for workflow if not already run.

• brain extraction (Synthseg)
• Freesurfer / Fastsurfer
• DWI Preprocessing (Snakedwi)

[kaitj]

Some notes from the SCATTR meetings:

• Probably want to set up some kind of severely downsampled source dataset.
• Maybe look into Snakemake unit testing facilities
• Potential issue for GH Actions: It would need the container.
• Can build the container on the GH actions runner and overwrite the config value.

[kaitj]

Additional thoughts / comments after last meeting:

• Preprocessing (of DWI and maybe all things considered here) may fall out-of-scope of SCATTR. The docker container would either need to include the software necessary to perform preprocessing or call snakedwi, the processing workflow of choice, which would download another larger container.
• Freesurfer / fastsurfer may be possible with an updated version of freesurfer used in the container.
• Brain extraction may also be possible (synthseg via Freesurfer or via mrtrix's brain extraction tool).

The gist of this is that anatomical processing is possible with existing container while diffusion pre-processing is likely out-of-scope.

[akhanf]

I think brain extraction (e.g. synthstrip) would be good to include directly in scattr, since we don't really have any BIDS apps that solely perform that step, and it is a really quick and easy rule to add in.