Optional pre-processing - Githubissues

khanlab / scattr

BIDS app for structural connectivity between targeted regions

https://scattr.readthedocs.io/en/stable/

MIT License

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Optional pre-processing #29

Open kaitj opened 1 year ago

kaitj commented 1 year ago

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

[ ] brain extraction (Synthseg)
[ ] Freesurfer / Fastsurfer
[ ] ~DWI Preprocessing (Snakedwi)~

kaitj commented 1 year ago

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 commented 5 months ago

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.