Hi, Osman-
Hmm, something might have gone wrong with one of hte alignment steps? There should be an automatically-generated QC HTML in the output results directory.
Can you see if there is a directory there starting with "QC_", and then run:
afni_open -b QC_*/index.html &
? That should open the QC HTML in an available browser.
More description on the main QC sections are provided here (though this page is a bit out of date...):
[
afni.nimh.nih.gov]
But specifically, check the ve2a (volumetric EPI-to-anatomical alignment) and va2t (volumetric anatomical-to-template alignment), and see how each of those look. My guess is that the EPI-to-anatomical alignment might not have gone well?
Also, what version of AFNI are you using? What is "afni -ver"?
--pt
