Dear AFNI team,

Apologies if this is a silly question, I have not used AFNI before.

I would like to register a native space T1w macaque image to the D99 v2 atlas using the @animal_warper function. However, it seems that the D99_template.nii.gz is in a different space to the D99_atlas_v2.0.nii.gz. I have probably misunderstood but I was under the impression that @animal_warper uses the template image for registration with a native T1w, and then applies this transformation to the atlas image. I have run it nonetheless (command pasted below) and the atlas results actually seem okay at first glance, however I did notice that the old atlas and the macaque tutorial have the templates and atlas in the same space. Therefore I am wondering if this is making the script work harder than it needs to/ could affect the precision of the results?

The command I have run is:

@animal_warper -input my_T1.nii.gz -base ../Monkey_brains/D99_v2.0_dist/D99_template.nii.gz -atlas ../Monkey_brains/D99_v2.0_dist/D99_atlas_v2.0.nii.gz -outdir test_dir

Many thanks!
Sam



Edited 2 time(s). Last edit at 02/15/2023 10:43AM by El_suri.