FSaverage fMRI data

Software Support
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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

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A post was merged into an existing topic: fMRIPrep in Compute Canada

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