Hi all,

I’ve been spending a lot of time in python manipulating nifti files in nibabel and have been running into some trouble with afni extensions. The only one that’s really causing me grief is the template space specification, i.e. suppose that I load a nifti file that has bee processed by AFNI and marked as TLRC and then compute some function on it and write it back out again, I lose the AFNI extensions get lost, and then when I load it back into AFNI it’s treated as being in ORIG.

Is there a doc somewhere, or some example code, that creates/modifies AFNI extensions so that I can make my python code produce sensible output?

3drefit works fine, but I’d rather avoid that step if possible.

Thanks,
Souheil