Hello,
I have been trying to allineate the anatomical to the EPI. Originally, only my EPI datasets were oblique. I obliqued the anatomical and seem to have some alignment. 3dAllineating these oblique sets caused the anatomical to shift very little and doesn't seem as well aligned anymore. I am new to 3dAllineate. Can anyone suggest a proper syntax so I may know where in my code I am going wrong or why this may have happened? The syntax I used to 3dAllineate is as follows:
3dAllineate \
-base epi+orig \
-input anat+orig \
-mi \
-prefix anat_aln+orig \
-warp shift_only
Thank you!
