Hi Daniel,

Thanks for your answers to the first two questions; I'd just like to ask you for a few clarifications on the third. You wrote:

"The final output combines transformations for obliquity, motion correction and alignment."

1. Which file actually is the final output? I understand it to be filestem_vr+orig. Relatedly, is that file identical to filestem_tsh_vr+orig? I see that one is created from the other using 3dcopy.

2. If I am using the default anat2epi procedure, wouldn't the final epi output only combine transformations for obliquity and motion correction (and slice-timing correction)? I thought the alignment would be represented only in the mprage_al+orig file.

3. When you say the final output "combines transformations", do you mean that the sequentially-computed (but not applied) transformations are simultaneously applied in the final step? I understood that the benefit of using align_epi_anat.py was that all transforms were applied together, reducing data changes caused by multiple interpolations. If, on the other hand, the final output is produced by sequentially applying each transformation, it seems that align_epi_anat.py works the same as if I scripted 3dTshift, 3dvolreg, and 3dAllineate on my own.

Sorry to be a pest--I just want to be clear about what is happening to the data.

Jeff