using afni_proc in orig space

AFNI Message Board
1

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 $subject
-script preproc.$subject.orig.csh
-out_dir afniPreprocessed.orig
-blocks tcat despike tshift align volreg mask
-copy_anat t1+orig.HEAD
-dsets run?+orig.HEAD
-volreg_align_e2a -align_opts_aea -giant_move
-volreg_base_dset run5+orig’[0]’
-mask_apply epi

If you have suggestions for the code to ensure alignment in orig space, please let me know.

Thanks very much,
Helen

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Hi Helen,

If you are staying in orig space, maybe it would make
more sense to align the anat to the EPI.

With that afni_proc.py command, a warped anat will be
created, but it is garbage (and its name should include
“junk”). The original anat should be aligned with the
final EPI data.

To be specific, the junk anat gets aligned with the
EPI volreg base (which is aligned with the original
EPI, say), while the final EPI is aligned with the
original anat (due to -volreg_align_e2a).

Without -volreg_align_e2a, the EPI and final anat
would be aligned (to the original volreg base image).

But the only question here is which anatomical volume
you should be focusing on. Please ignore anything
with ‘junk’ in the name.

  • rick