Summary of what happened:
I am trying to pre-process my fMRI data using fMRIprep. However, when I do so, I see floating voxels outside the brain when I visually inspect my GLM, and when I pull peak MNI coordinates for different contrasts, I get voxels in unlabelled regions.
Command used (and if a helper script was used, a link to the helper script or the command generated):
echo "RUNNING FMRIPREP"
# Make sure FS_LICENSE is defined in the container
export SINGULARITYENV_FS_LICENSE=/home/groups/glc/freesurferlicense.txt
singularity run --cleanenv /home/groups/glc/simg/fmriprep-25.2.4.simg \
/home/groups/glc/TBD_study/data/BIDS/sourcedata/ \
/home/groups/glc/TBD_study/data/BIDS/derivatives/fmriprep \
participant --participant-label sub-$SLURM_ARRAY_TASK_ID \
-w /scratch/groups/glc/fmriprep_wrk \
--slice-time-ref 0 \
--output-spaces anat MNI152NLin2009cAsym \
--dummy-scans 6
# --ignore sbref \
# --skip-bids-validation \
# --skull-strip-t1w skip \
# --output-layout legacy
Version:
25.2.4
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity image
Data formatted according to a validatable standard? Please provide the output of the validator:
BIDS validator. The validator only provides warnings that our README files are too small.
Screenshots / relevant information:
Thank you all in advance for your time and expertise.