afni.nimh.nih.gov

No, you do not need to align a mask to a cardinal epi (I'm not sure what you mean by aligning a mask here).

If you would like to combine alignment with obliquity handling, I would recommend using align_epi_anat.py (for anat2epi) and then apply the same transformation with 3dAllineate -1D_matrix_apply. The transformation will include both the obliquity transformation together with the alignment.

If you assume alignment of epi with anat data to start, just use the 3dWarp command I recommended.



Edited 1 time(s). Last edit at 03/25/2015 10:47PM by Daniel Glen.