Using fmriprep (v.1.1.2 & v.1.1.3.) I get these strange misalignments between tissue contours and the actual anatomical scan in the visual reports on “Brain mask and brain tissue segmentation of the T1w” and “Susceptibility distortion correction” steps. Also, I see that the brainmasks is actually misdefined as part of my EPI-scans are cut off in preprocessing (so it is not just an error in the visual report, but seems to actually affect preprocessing. Ive done fmriprep in the following configurations.
-fmriprep 1.1.2 and fmriprep 1.1.3
-with and without running freesurfer (either by flagging freesurfer on and off, or using previously run freesurfer files on the same anatomical scans but in a different study).
all of these configurations give the same error. Any idea what seems to be going wrong here?
My next step is to run in fmriprep 1.3.1, but no idea if this problem is familiar.