Hi,
I've just reconstructed AFNI files from anatomical and EPI DICOMs. AFNI is giving me a lot of fuss about the datasets being oblique. Specifically, it says,
"If you are performing spatial transformations on an oblique dataset, or viewing/combining it with volumes of differing obliquity, you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session."
Aside from this issue, the anatomical scan has orientation ASR, and the EPIs have orientation RAI.
I plan to run my anatomical dataset and my EPI datasets together through the script afni_proc.py generates. Do I need to do anything to prepare them for this processing? I'm afraid that running 3dWarp as AFNI recommends or running 3dresample to reorient the datasets before I run the proc script will mess with the slice-timing information -- screwing up my eventual call to 3dTshift. But if I leave them as is, I'm afraid they'll be too different from each other for the calls in the proc script to handle.
I know I can try a bunch of different options and see which one seems to produce the best results, but artifacts in fMRI data can be very subtle, and so I'd really like to do something that I know a priori is the sensible thing to do -- based on the experience of the many AFNI users out there. What is the standard way people have been dealing with this issue?
Many thanks,
Dan
