fMRIPrep & recon-all-clinical

Summary of what happened:

I’m working with glioma patient data, on which FreeSurfer normally doesn’t work very well; but thanks to recon-all-clinical, using FreeSurfer on our data is now possible.

However, providing the outputs of recon-all-clinical to fMRIPrep yields some strange results: fMRIPrep seems to redo/alter FreeSurfer’s aseg.mgz, ignoring a large chunk of brain, and the brain mask used by fMRIPrep is equally bad-- please see the screenshots included below.

Is this a known issue with the relatively new recon-all-clinical, and is there any way to get this to work?

Any help would be greatly appreciated!

Command used (and if a helper script was used, a link to the helper script or the command generated):

    $BIDSDIR $OUTDIR participant \
    --participant-label $SUBJ_ID \
    --use-aroma \
    --output-spaces func T1w fsnative fsaverage5 MNI152NLin6Asym:res-2 \
    --skip-bids-validation \
    --fs-license-file $FS_LICENSE \
    --fs-subjects-dir $FSDIR \
    --bids-filter-file $BIDS_CONFIG_FPREP \
    --ignore fieldmaps slicetiming \
    --use-syn-sdc \
    --stop-on-first-crash \
    --omp-nthreads 8 \
    --nthreads 16 \
    --mem-mb 32000 \
    --work-dir $WORKDIR



Environment (Docker, Singularity, custom installation):


Data formatted according to a validatable standard? Please provide the output of the validator:


Relevant log outputs (up to 20 lines):

N/A; fMRIPrep finishes without errors

Screenshots / relevant information:

Initial aseg.mgz after running recon-all-clinical

aseg.mgz after running fMRIPrep

fMRIPrep T1w brain mask & tissue segmentation


Just to give this thread a quick kick: I still haven’t been able to figure this out. Would anyone have any ideas? :sweat_smile: