Hello folks,

I hope you can answer a few questions about align_epi_anat.py, which I haven't been able to figure out from the documentation.

The help for the script gives the following example:

# align anat to sub-brick 5 of epi+orig. In addition, do slice timing
# correction on epi+orig and register all sub-bricks to sub-brick 5
# (Sample data files are in AFNI_data4/sb23 in sample class data)
# Note the intermediate file, the volume registered EPI dataset,
# is **not** saved unless the -save_vr option is also used.
# See the -save_xxx option section of this help for more information.

align_epi_anat.py -anat sb23_mpra+orig -epi epi_r03+orig \
-epi_base 5

1) Even if none of the -save_xxx flags are used, will epi_r03+orig have been slice-time and motion-corrected after running the script? That is implied, since the help says the -save_xxx flags are only necessary for saving out intermediate steps, not the results of the script's operations.

2) Assuming that the answer to 1) is yes, will align_epi_anat.py update the history of epi_r03+orig to indicate that it has been slice-time and motion corrected (possibly also de-obliqued and co-registered to anatomical)?

3) Can you confirm which transformations are applied simultaneously, and which are performed sequentially by the script? From reading the help, I conclude that slice-time correction is first, and that a second step combines motion correction, obliquity correction (if needed), and co-registration (if using -epi2anat). Is that accurate?

Thanks,

Jeff