I am trying to align my anatomical to my functional however I am getting very poor results for some participants (see attached images). After alignment the anatomical looks very wonky and this was happening on quite a few participants. I have tried using different cost functions such as lpa and nmi but have had no luck. When I try the alignment on another computer with an older version of afni the alignment looks good.
Computer 1 (mis-aligned): Afni version: 19.2, AMD chipset, Ubuntu 18.04
Computer 2 (well-aligned): Afni version 18.3, Intel Chipset, MacOS High Sierra
Here is the command I was using:
align_epi_anat.py -overwrite -anat2epi -anat MPRAGE1.nii
-epi vr_base_min_outlier+orig -epi_base 0
-volreg off -tshift off
Thanks for any help,