I tried to generate a 5tt image for HCP 3T data. I tested it with the T1w_acpc_dc.nii.gz and with the T1w_acpc_dc_restore_brain.nii.gz file and the -premasked option.
Unfortunately the command ends with a warning: “[WARNING] Generated image does not perfectly conform to 5TT format:”
The _restore_brain run looks a lot better but I’m still wondering whether I should use the result or if I can tweak the generation somehow.
This is a slice of 5ttvis.mif from the _restore_brain input: