I am trying to understand what exactly is happening with the data in the long script generated by and I have a question regarding the align block.
I used to generate an afni proc command. I chose among other blocks: align and volreg.

I don t understand a couple things:

  1. Why does the afni_proc command (generated by uber_subject) include the option ‘-volreg_align_e2a’ ?
    I thought that by default aligns the anatomical to the epi? And I did not have any additional option in uber_subject except of choosing a different cost function.

Then, when running this command I get for the alignment block in the long tcsh script:

for e2a: compute anat alignment transformation to EPI registration base

(new anat will be current anat_ns+orig) -anat2epi -anat anat_ns+orig
-suffix _al_junk
-epi vr_base_min_outlier+orig -epi_base 0
-epi_strip 3dAutomask
-volreg off -tshift off

here is my confusion: Is it going to align the anatomical image to the min_outlier volume? If so, why is there the "-epi_base 0? The min_outlier volume is not the volume no. 0. If I change in uber_subject that I want the volume registration base to be the third volume. It still says -epi_base 0? So what does this expression mean?

Thank you very much