Hi, Misho-

Sorry to hear that you are having to spend so much time with alignment, rather than being out in the (fleeting) London sun...

It might be useful to see your afni_proc.py command, for starters--could you please copy+paste that here?

The default cost function for EPI-anatomical alignment is lpc (or lpc+ZZ, a modified version for when things are potentially wonky). This usually works well, assuming that the EPI and anatomical start out with good overlap and that the EPI has appropriate tissue contrast. To focus on alignment, one wants to check that sulcal and gyral features line up well, that ventricles overlap well, etc. Namely, that interior and boundary brain regions line up well.

In the image above, the tissue contrast does look a bit low. Can you post the images from the afni_proc.py-generated QC HTML? Namely, the ones from the "vorig" block and the "ve2a" block? That will help diagnose by displaying the raw EPI volume used for alignment, as well as the EPI underlaying the edges of the aligned anatomical.

thanks,
pt



Edited 1 time(s). Last edit at 05/10/2021 01:17PM by ptaylor.