Summary of what happened:
Hello everyone! I’m facing a normalization issue in one participant at the postcentral gyrus (see image below). Do you have any suggestions for alternative flags or preprocessing adjustments? I’m a new fmriprep user!
Command used (and if a helper script was used, a link to the helper script or the command generated):
docker run -ti --rm \
-v /DATAPOOL/SOMATOMAP/BIDS2025:/data:ro \
-v /DATAPOOL/SOMATOMAP/BIDS2025/derivatives/fmriprep_boldheader_2025:/out \
-v /SCRATCH/users/user1/fmriprep-work_S1Map_boldheader_2025:/work \
-v /DATAPOOL/SOMATOMAP/BIDS2025/freesurfer/license.txt:/license \
nipreps/fmriprep:24.1.1 \
/data /out/fmriprep \
participant \
-w /work \
--fs-license-file /license \
--bold2t1w-init header \
--nprocs 18 \
--skip_bids_validation \
--stop-on-first-crash \
--output-spaces T1w func MNI152NLin2009cAsym \
--participant-label p0003
Version:
24.1.1
Environment (Docker, Singularity / Apptainer, custom installation):
docker
Data formatted according to a validatable standard? Please provide the output of the validator:
yes
Relevant log outputs (up to 20 lines):
PASTE LOG OUTPUT HERE
Screenshots / relevant information:
Participant MNI image (space-MNI152NLim2009cAsym_desc_preproc_T1w) over a MNI template (mni_icbm152_t1_tal_nlin_sym_09c_brain.nii.gz) with a white rectangle highlighting the normalization issue at the postcentral gyrus:
