Update,
I actually still have the problem (a few co-registration misalignments) of macaques anatomical T1 to the template (out of 90 success, not bad!)
to resume:

- something not normal with aff_move_opt. It seems that you can only use one option and not combine multiple ones.
- _shft.nii.gz = far from the BASE. The orientation (mostly in SI axis in my case) is not correct (not sure actually what is the command is producing this image).
The mistake seems to happen when to orientation in the SI axis is far from the base despite that the two images are centred.
- _shft_aff.nii.gz is almost well aligned to BASE but the little mistake generates big misalignments in the end.
- in my case, the misalignment is in the occipital areas

I can provide images if needed

Tks!



Edited 1 time(s). Last edit at 10/29/2021 08:50PM by Doughboys.