don't T1_tmp_1_brain and altinput=T1_orig_ud have different dimensions at this stage?
T1_tmp_1_brain
has been previously roi'd by fslmaths to remove empty slices, but T1_orig_ud
has not right?
T1_tmp_1_brain
has been previously roi'd by fslmaths to remove empty slices, but T1_orig_ud
has not right?