Lesion masks not being used in fmriprep anat_norm_wf

I’m using fmriprep 1.4.1 to do multi-session preprocessing on lesioned brains. After checking the normalisation logs for fmriprep_wf.single_subject_xxx_wf.anat_preproc_wf.anat_norm_wf.registration, in execution inputs lesion mask is undefined.

The lesion mask is in the subject’s anat directory with the naming convention specified (sub-xxx_T1w_label-lesion_roi.nii.gz).

I’ve attached a copy of the report.

Thanks. report.txt (4.5 KB)

Hi @petergoodin - thanks for the report. There have been numerous updates since 1.4.1, could you try rerunning using the latest version (20.0.2) and see if the problem still persists?