Hello,

I'm analyzing a few datasets, one of which has an oblique anat and epi and a diff dataset w/non-oblique anat and oblique epi. Trying to understand how 3dWarp figures into the afni.proc script generation and had a few questions:

1. Prior to generating the afni proc scripts with a diff script, I'm running a FS subcortical parcellation (recon-all -autorecon1) which generates anat.nii.gz file, which is what I'm using as anatomical input for the afni proc script. My understanding is that it doesn't matter with that script if the image is oblique going in and that it gets resliced and diced and comes out as non-oblique. Just want to confirm that this is the case.

2. If #1 is true above then I have an anat that's no longer oblique, but my epi in one of the studies is still oblique at the point - hence I get errors suggesting I run 3dWarp -deoblique as I generate the afni proc script. My questions about this are:

a) If I put in the oblique epi and then add the 3dWarp -deoblique into my model afni proc script that is used to generate the afni proc for multiple subs, where does it go in the order of commands?

b) If I also do nonlinear warping during the single sub afni proc script does that become affected at all by 3dWarp? Just trying to understand how 3dWarp "warps" the data, or if it's more of an affine transformation.

c) If I stick this command (3dWarp) in the script will it use the output of the script (which I think is tagged as "warped" by my having run it in command line) to feed into the rest of the afni proc script?

Thanks in advance for any help that you might be able to give me in this matter.

Best Regards,

Aviva Olsavsky