University of Oxford dataset - inquiries about epi-2-anat alignment

[nutty-bunny]

Dear all,

Over the last few months I've been actively preprocessing MRI data from various datasets. I have been using animal warper for structural processing, and this has been working great! However, throughout all datasets, I have encountered issues with epi-2-anat alignment. I have been using afni_proc.py for this step, but regardless of how many times I'd tweak the command, my results are still sub-optimal. For anyone that has succeeded doing functional analyses on University of Oxford, is there a different tool or particular tweaks you would recommend for processing this particular dataset?

For reference, I have attached the best results of afni_proc so far:

As well as the relevant command to achieve this:
ap.cmd.pdf

I am relatively new to MRI preprocessing, so I would appreciate any and all input, particularly on how to achieve good multi-modal alignment. Many thanks in advance!

Sincerely,
Simona Vaitekunaite

[afni-dglen]

That doesn't look too bad to me. afni_proc.py and align_epi_anat.py do not handle EPI distortion without some extra datasets. Still, I can try to tweak it too if you send me an example dataset.