Summary of what happened:
Hi everyone!
I’m fairly new to fMRIPrep and have been using it to process data of an fMRI experiment where I acquired a functional slab (27 slices) of the brain. As you might expect, my biggest challenge so far has been the coregistration step. I finally achieved some good results using the --bold2t1w-init header flag. HOWEVER, I’ve noticed that some func brain mask (file: sub-p0002_ses-01_task1_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz) appears very strange in some participants/runs (as if parts of the mask are missing).
Does anyone know where this file is used within the fmriprep pipeline? I’d like to understand the potential consequences of these “damaged” masks in my analysis.
Thanks in advance for your help!
Command used (and if a helper script was used, a link to the helper script or the command generated):
docker run -ti --rm \
(...)
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 p0005
Version:
Environment (Docker, Singularity / Apptainer, custom installation):
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