I am using fmriprep v23.0.2 and I am not sure if the registration of my functional images to the MNI space worked properly. When I look at the brain mask or the desc-preproc-bold.nii.gz file, they do not really look like being in the shape of the MNI template. For the T1, this looks fine.
So, I am not sure if this is normal, or if something went wrong somewhere?
When I compare the T1w and the functional image and/or brain mask, they all say being normalized to the MNI152NLin2009cAsym template, which would suggest to me that these should have the same shape.
Thank you for your help!
Command used (and if a helper script was used, a link to the helper script or the command generated):
/opt/conda/bin/fmriprep /data /out participant --participant-label 01 02 03 04 05 06 07 08 09 10 --write-graph --me-output-echos --use-aroma --skull-strip-t1w force --skip-bids-validation --fs-license-file /freesurfer_license/freesurfer-license.txt --fd-spike-threshold 0.5 --verbose --nprocs 30 --omp-nthreads 4 -w /fmriprep_temp
Data in BIDS format. Validator showed no issues.