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):
singularity run --cleanenv -B $BIDSDIR -B $OUTDIR -B $WORKDIR -B $FS_LICENSE -B $FSDIR -B $BIDS_CONFIG_FPREP $FPREP_IMG \ $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
N/A; fMRIPrep finishes without errors
Initial aseg.mgz after running recon-all-clinical
aseg.mgz after running fMRIPrep
fMRIPrep T1w brain mask & tissue segmentation