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SCIL Nextflow Toolbox
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[WIP][Module] Fastsurfer #151

Closed arnaudbore closed 3 weeks ago

arnaudbore commented 4 months ago

Fastsurfer

Draft and need some love but we'll get there !

gagnonanthony commented 3 months ago

When I added FastSurfer to my pediatric pipeline, I had to compute the registration from the subject's space to the fsaverage of reference to have the transform file I could use to recreate the brainnetome parcellations in the subject's space (as it is done in freesurferflow). Maybe it would be worth adding this after the fastsurfer run? Here is the command I used for reference:

    mri_ca_register -align-after -nobigventricles -mask $sid/mri/brainmask.mgz \
        -T $sid/mri/transforms/talairach.lta -threads $params.nb_threads $sid/mri/norm.mgz \
        \${FREESURFER_HOME}/average/RB_all_2020-01-02.gca $sid/mri/transforms/talairach.m3z

It could also be a different process, but I am not sure it would be used in any other case. Could also potentially be an optional thing.

arnaudbore commented 3 weeks ago

replace with #198