Howdy-

I'm a little confused. Did you first run afni_proc.py, and now you are separately running align_epi_anat.py in the same directory? If so, I was wondering why you are running this separately, after the analysis is complete?

Separately, in this line of the afni_proc.py command:

-align_opts_aea -cost lpa -cost lpa+ZZ -giant_move \

... "-cost .." should not be specified twice. Also, generally neither lpa or lpa+ZZ should be used for EPI-anatomical alignment, because those two volumes have opposite tissue contrasts (NB: if a subject has an injection, sometimes that can change the relative EPI contrast, but such cases are rare). We would generally recommend using "lpc" or "lpc+ZZ" there, instead.

For your FreeSurfer follower ROIs, please check out this helpful page:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/fs/fs_makespec.html
In general, the *REN* datasets would be preferred to the "aparc.a2009s+aseg.nii.gz" ones. Also, there are WM and ventricle maps created for users in the output SUMA/ directory.

It is a little odd not to see a 'volreg' block, for motion estimation and reduction. I am not sure what this line:

-regress_apply_mot_types demean deriv \

... will do then, since there aren't motion regressors to demean or derivatize?

-pt



Edited 1 time(s). Last edit at 10/25/2022 10:07AM by ptaylor.