Hi Daniel,
I had one additional question. If I have 1 T1 image and 2 EPI datasets and all with different oblique angles I wanted to find out the best way to use 3dWarp -card2oblique. I would not be able to use it on the original T1 image as this would force me to run freesurfer twice (since i'd need 2 copies of T1 to match the different oblique angles of the 2 EPI datasets). I had the following ideas:

1)One thought is just take the original T1 and make it cardinal (it is isotropic but 256x256x208 matrix size) using 3dWarp -oblique2card and then run the freesurfer pipeline once. Then use bbregister or 3dAllineate on it to have it match for each EPI scan.

2) Would it be possible to run 3dWarp -card2oblique on the freesurfer result file brain.mgz, and have aseg.mgz match the same transform (apply same change vs redoing 3dWarp -card2oblique with aseg file instead of brain) after i convert both images to nifti format? From here I would then run 3dAllineate for each EPI dataset.

3) Another way to work around the issues I was having is to see if you know how freesurfer bbregister writes to the nifti file header compared with how AFNI looks for this transform information:
#Calculate alignment
bbregister --s ${sub}_FS --mov $bbrest_file --reg ${sub}_RS_register.dat --init-header --bold --frame $NP_last --nearest --template-out ${sub}.RS.template.nii
#Apply alignment
mri_vol2vol --mov $loc_dir/spm/m${sub}.T1.nii --targ $SUBJECTS_DIR/${sub}_FS/mri/brain.mgz --o $out_dir/__brain_FS2spm.nii --inv --no-save-reg --reg $out_dir/${sub}_RS_register.dat

The images looked overlayed in freesurfer, but I was not able to get the images overlayed properly in afni for the oblique datasets. They only looked perfectly aligned when the T1 and EPI were acquired with no oblique angles. I have a feeling that because the original T1 and EPI images were of different obllique angles this may contribute to the mismatch. Additionally, I'm guessing that freesurfer's mri_vol2vol may store the transform differently in the header than where AFNI looks to read it. Are you aware of how freesurfer stores these transforms, as well as where afni looks (sform, qform etc)...

Thanks,
Ajay