Dear AFNI users,

When I deal with Anat/EPI alignment via align_epi_anat.py,

I was confused to set up the option -epi_base.

Prior to this process, I did other pre-processing protocols including slice timing correction, and discarding the first TRs etc.

When setting the base volume for the alignment, should I set the base volume for the same volume I have used in the slice timing correction process?

And, reading through the cases notes in the afni_proc.py script, I had a problem understanding the following sentences.

The typical cases is to align EPI to one of volumes used in pre-processing (where dataset is provided by -dsets and where particular TR is not removed by tcat_remove_first_trs). If base volume is first or third (TR 0 or 2) from first run, or is last TR of last run, then -volreg_align _to can be used.
To specify TR that is not one of 3 just stated (first, third or last), -volreg_base_ind can be used.
To specify volume that is NOT one of those used in preprocessing (such as first presteady state volume, which would be excluded by the option -tcat_remove_first_trs), use -volreg_base_dset.


--> If I used the first volume as the base in the preprocessing, do I just use the same volume in the alignment?
(If I used the middle volume in the preprocessing, can I use the specific # of volume in the alignment via -volreg_base_ind? or -epi_base #?)
--> Should the base volume be the same between the preprocessing and the alignment processes?

I will look forward to the answer.

Thank you.