Continuing the discussion from fMRIPrep in Compute Canada:
Hi Steven!
I’ve finally gotten the script to run through completely (it took a while for the hob to be accepted into Compute Canada queue.
I have a question that I hope will be quick for you to answer.
I’d like to have all my subjects fMRI data preprocessed into fsaverage space, and I see that is not now (I can only find data in the volume space). Will adding --output-space fsaverage to my job submission solve this? My job submission would then be this:
singularity run --cleanenv \
-B /project \
-B $SINGULARITYENV_TEMPLATEFLOW_HOME \
/project/6001995/coopapap/downloads/fmriprep/fmriprep-23.2.0.simg \
/project/6001995/coopapap/data/garrison/BIDS/meditators \
/project/6001995/coopapap/data/garrison/BIDS/out/ \
participant \
--participant-label $subject \
--fs-license-file $license \
--output-space fsaverage
I just want to make sure whether this is or is not possible as I see some other forum threads suggesting that I will need to run the volume to surface transformation manually.
Warm regards,
Austin