Add ability to skip tractography

[jhauneuro]

Summary

Hello,
Thank you for creating and continuing to develop the QSI tool family. They have been very useful in my work. I would like to run --recon-spec mrtrix_singleshell_ss3t_ACT-hsvs to create my FOD maps and then perform tractography with specific ROIs using mrtrix. The tck.gz files take time to compute and take up quite a bit of space (~9GB per participant). I saw there was a --notrack option and tried it but it still runs and outputs the tracks.

Here is the command I ran:

docker run -it --rm \
    -v $fs_license:/opt/freesurfer/license.txt \
    -v $qsiprep_dir:/data:ro \
    -v $qsirecon_dir:/out \
    -v $qsirecon_dir:/scratch \
    -v $fs_subjects_dir:/freesurfer \
    pennlinc/qsirecon:1.0.0rc3 \
    /data /out participant \
    -w /scratch \
 	--fs-license-file /opt/freesurfer/license.txt \
	--input-type qsiprep \
 	--fs-subjects-dir /freesurfer \
    --recon-spec mrtrix_singleshell_ss3t_ACT-hsvs \
    --notrack \
    --atlases Brainnetome246Ext \
 	--participant-label 0001

Additional details

• QSIRecon version: 1.0.0rc3
• Docker version: 27.3.1

[tsalo]

--notrack refers to opting out of sending reports to the developers through Sentry. Those reports are useful for us to identify common failure points in the workflow, but there are times when people don't want to send them (protected information, running on servers without internet access, etc.).

[jhauneuro]

Yes, my bad, I just read that. In that case, this would be a feature request.