Questions about antsBrainExtraction


I just finished running the anat_only portion of fmriprep version 1.1.4 and while the skull stripping looks good, I have two lingering questions:

1). The full brain extraction command was -a /N/dc2/scratch/dlevitas/fMRI_data/ADM5/1032/sub-1032/anat/sub-1032_T1w.nii.gz -m /N/dc2/scratch/dlevitas/fMRI_data/ADM5/1032/fmriprep_wf/single_subject_1032_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/T_template0_BrainCerebellumProbabilityMask.nii.gz -e /niworkflows_data/ants_oasis_template_ras/T_template0.nii.gz -d 3 -f /niworkflows_data/ants_oasis_template_ras/T_template0_BrainCerebellumRegistrationMask.nii.gz -s nii.gz -k 1 -o highres001_ -q 1 -u 1 however, the file in the -m argument doesn’t exist; I can only find that file in the container. I don’t see an error message, so I’m not sure how this commands was able to run.

2). I understand that the template (OASIS) is a defaced file, but my original T1 is not. Is it okay to to use template that has been defaced even if the original T1 isn’t?

Again, these questions may be non-consequential since the extraction looks fine, but I just wanted to clarify.