How is image type automatically determined from the file name ? The logic failed to label sub-XXX_ses-YYY_run-01_T1w.nii as a T1-weighted MRI. This should work based on the help text, and also probably be good to support as it is a valid BIDS name, and will save computation when re-facing an entire session in one go as only the T1w will undergo non-linear registration, if I understand correctly.