Summary of what happened:
I successfully ran fmriprep on a dataset, but I noticed some streaks of missing datapoints (see attached screenshot) in certain volumes on the standard space nifti image (*_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz) and wanted to see if anyone had any thoughts on where the issue may be? I’ve looked at the unprocessed bold for the same volume and there aren’t any signal missing. Any feedback and ideas would be greatly appreciated!
Command used (and if a helper script was used, a link to the helper script or the command generated):
docker run --rm -it \
--platform linux/amd64 \
-v "$1:/data:ro" \
-v "$2:/out" \
-v "$3:/workdir" \
-v "$4:/opt/freesurfer/license.txt:ro" \
-v "/Users/chichichang/Desktop/PhD/DARPA/dicom_data/freesurfer:/fsdir" \
-e KMP_AFFINITY=disabled \
-e OMP_NUM_THREADS=4 \
--memory="50g" \
nipreps/fmriprep:latest \
/data /out participant \
--participant-label $5 \
--fs-license-file /opt/freesurfer/license.txt \
--fs-subjects-dir /fsdir \
--output-spaces MNI152NLin6Asym:res-2 \
--skip-bids-validation \
--work-dir /workdir \
--stop-on-first-crash
Version:
25.1.3
Environment (Docker, Singularity / Apptainer, custom installation):
Docker
BIDS validator output
PASTE VALIDATOR OUTPUT HERE
N/A
Relevant log outputs
PASTE LOG OUTPUT HERE
N/A
Screenshots / relevant information:
This volume has a lot of streaks (volume 12)
Volume 12 unprocessed bold
This volume has only one small streak on the bottom right (volume 28)
