I am writing because I have some (hopefully simple) questions about AFNI software and the latest NIMH macaque atlas. I was wondering if there is a way to change the D99 NIMH atlas files to the macaque 112 atlas space. Is there a function for this in AFNI? And if so how would I do it? Basically I am trying to do this because I want to be able to use the atlas for ROI analysis (outside of AFNI, I use SPM12) but all of my data has already been pre-processed through SPM12 using an atlas that is in 112 space. I tried co-registering one template to the other and doing some other things, but the D99 atlas brain just turns out kind of squished afterwards, so I worry that whatever I am doing is incorect/unreliable. Also, I am not super familiar with AFNI since I just recently started using it…
I haven’t heard of the 112 space, but we do have a couple tools that may be applicable. @animal_warper can be used to align the macaque subject brain to a template and also transform atlas datasets to the individual subject space. If you are doing most of the standard FMRI processing for task or resting state , then you can use the warps from @animal_warper as part of your input for afni_proc.py. These are described in the AFNI class documentation here, particularly the afni14 and afni15 presentations on alignment and atlases. There is also a demo you can install to see the results of both these tools with @Install_MACAQUE_DEMO. The README.txt file it installs provides more info.
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National Institute of Mental Health (NIMH) is part of the National Institutes of
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