thanks, looking at the 0th volume def helped and it took 2 min to complete.
However, the top is still cut off for me. I've attached what I see when I view t1_aligned_NEW in freeview and also when I align it with data.nii.gz using @djunct_overlap_check.
The t1_aligned_NEW didn't seem to be cut off for you if I saw/understood correctly... or were you suggesting that the EPI distortion at the anterior part is what could be causing it to be cut out?
also, what command did you use to view all those slices and the alignment?
best, E
Edited 1 time(s). Last edit at 01/09/2021 07:36AM by eji.