Summary of what happened:
Hi everyone!
I’m processing fMRI data using fMRIPrep (new user!), where I acquired a functional slab (27 slices) focused on S1. Coregistration has been the biggest challenge, but I achieved good results for most participants using --bold2t1w-init header. However, for one participant, two out of four runs are poorly coregistered, while the other two look fine. This happens both in T1w and MNI space. This misaligned may be caused by participant movement between runs because it is pretty notorious on raw data.
I’ve already tried:
--fs-no-reconall--bold2t1w-init header--bold2t1w-dof 6- Running the pipeline without field maps (Spin Echoes)
None of these improved the misalignment. Has anyone faced similar issues with partial-brain acquisitions? Any suggestions for alternative flags or preprocessing adjustments?
Thanks in advance!
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 p0011
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):
Screenshots / relevant information:
Functional raw data: one run is in gray, and the other is in orange.
Example of misalignment at MNI space (func file: desc-preproc_bold):
Example of good alignment at MNI space (func file: desc-preproc_bold):
