afni.nimh.nih.gov

Hi Ajay,

1) No, that alignment should work fine.

2) No, 3dAllineate will apply that xyz to xyz transformation
correctly, regardless of the orientaion. You can verify
this by bouncing between the anat and EPI in orig space
(e.g. with 'u') at some location, and then doing the same
thing in standard space, and seeing that they align in a
similar way in each view (of course, at the same brain
location the coordinates will differ).

- rick