Summary of what happened:
Hi! I have processed the MRI/fMRI data of my participants with different versions of fmriprep, normalizing it to MNI space, and I found the functional images’ dimensions to be in a mismatch. With fMRI v23.1.3, the func images’ dimensions are [121, 144, 121], but with v24.1.0 the dimensions are [95,118,101]. Can someone help me understand why? I’m pretty new to using FMRIprep. 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 p0006
and
docker run -ti --rm \
-v /DATAPOOL/SOMATOMAP/BIDS:/data:ro \
-v /DATAPOOL/SOMATOMAP/BIDS/derivatives/fmriprep_boldheader:/out \
-v /SCRATCH/users/user1/fmriprep-work_S1Map_boldheader:/work \
-v /SCRATCH/software/freesurfer/license.txt:/license \
nipreps/fmriprep:23.1.3 \
/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 p0006
Version:
v23.1.3 and v24.1.1
Environment (Docker, Singularity / Apptainer, custom installation):
docker
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
PASTE LOG OUTPUT HERE