I am experiencing weird EPI to T1 registrations for some FMRI sessions:
(this ‘was’ a whole brain scan of a healthy subject)
After going through the working directory, I think this comes from
N4BiasFieldCorrection, because after this stage the output looks like the image above. Furthermore, calling
N4BiasFieldCorrection with the fmriprep arguments and additionally
–shrinkage-factor 3 seems to solve the problem.
This only happens for some of the MRI sessions, while others work fine.
I uploaded the
command.txt and the input and output files for the
N4BiasFieldCorrection call here.
I am happy to provide more information if needed,
EDIT: I am using fmriprep version v1.3.1 with call
singularity run -B /data/pt_01994,/data/pt_01756/tmp/fmriprep_wd:/wd
participant --participant-label 01 02 03 04
–output-space T1w template