Hi Daniel,
Thanks for the link and info. The reason why I was asking is that the MNI template is LPI, the anatomical for this study is RAI (oblique angle after some preprocessing), and the resting state for this study is RAI (different oblique angle). I have also had analyses where the anatomical and functional are not in the same orientation as well as different oblique angles so I wanted to make sure my pipeline is flexible to handle all cases of orientations and oblique angle differences when moving to using afni_proc.py. I wanted my resting state and my aligned2EPI anatomical scan to be in LPI format to match the MNI template, although this may be unnecessary based on how AFNI handles things internally.

Overall I align the anatomical to a resting state EPI reference volume (3dresample -orient LPI for single reference) and then warp the anatomical to MNI. I was looking to test afni_proc.py. My question is I do not think there is a block where I can do despike, slice time, 3dresample (orient to LPI) and then volreg, smoothing regress. The reason why I want to orient to LPI is that down the line I may want to incorporate a fieldmap or other distortion correction and then simultaneously combine my motion correction, distortion correction and warp to MNI in one step (minimize interpolation). If volreg or the volume is in RAI (assuming no 3dresample/3dWarp/3drefit -deoblique -orient), the filedmap is RAI (collected same as EPI), the warp to MNI is LPI (anatomical after alignment to LPI reference EPI volume) to LPI (MNIj template), would this all be handled within AFNI or would it be better to make sure they are all in LPI space to ensure no issues of concatenation for all options down the line. Since each study has a different orientation, and oblique vs axial cut, I want this to be as flexible as possible to handle all cases.

Is this unnecessary to deal with the various orientation and obliquity differences between anatomical/EPI and MNI templates because this is all natively handled by AFNI in all of these cases or if it is better the way I proposed of using 3dresample -orient LPI after slicetiming?

Is there an easy way to introduce 3dresample into afni_proc.py after slice timing or just use an empty block and then after the script is generated, fix that block?

Thanks,
Ajay