afni.nimh.nih.gov

The aspect I'm trying to understand is what file format to recommend for people doing neuroimaging research in our lab. There are a few of aspects about the default afni file format that are intimidating to non-experts (two-part file packages and functionally significant filenames, for example) that seem more friendly with NIfTI files.

If we were to use, by default, .nii files, what kind of limitations might we see, and what would workarounds look like?

Thanks!
-Nate