Hello afni gurus,
I am using afni_proc for the first time, in particular for a subject that had some very misaligned data due to parallel imaging. I am trying to align all the epi’s to the anat in original space to conduct machine learning analyses in orig space, and am using -giant_move to account for the misalignment. The afni_proc documentation says: “To process in orig space, remove -volreg_tlrc_warp.” I have done this, yet the resulting anat is warped in some way, and the epi’s are aligned to this warped anat. It is also skullstripped, and I don’t necessarily need this unless it really helps with the alignment.
These are the commands I am using:
This is the command I’m running:
afni_proc.py -subj_id $subject
-blocks tcat despike tshift align volreg mask
-volreg_align_e2a -align_opts_aea -giant_move
If you have suggestions for the code to ensure alignment in orig space, please let me know.
Thanks very much,