Macaque atlas (D99 v2.0) in NMT v2 template

AFNI version info (afni -ver): linux_ubuntu_16_64, AFNI_21.0.12 'Titus'

Hi, AFNI experts,

I am planning to use the D99 v2.0 atlas (Saleem et al., 2021) (10.1.1. Macaque Atlas: D99 v2.0 (current) — AFNI, SUMA and FATCAT: v23.1.10) for macaque fMRI analysis. However, I have discovered that the D99 v2.0 atlas has not been wrapped to the macaque template NMT v2.1. I have found an older version of the atlas (Reveley et al., 2017) that has been wrapped in NMT v2.1 (for example, D99_atlas_in_NMT_v2.1_sysm_05mm.nii.gz). Can you please tell me how to wrap the D99 v2.0 in the NMT v2 space? Alternatively, do you know if there is a version of the D99 v2.0 atlas already wrapped in NMT v2?

Thank you

I've put various warps among various macaque template spaces here, including D99 space and NMT:

You can download these and apply them with

3dNwarpApply -master template.nii.gz -source atlas.nii.gz \
   -nwarp 'my_WARP.nii.gz my_AFF.1D' \
   -prefix atlas_on_new_template.nii.gz -ainterp NN
3drefit -cmap INT_CMAP -copytables atlas.nii.gz atlas_on_new_template.nii.gz

Copy the warp dataset and the 1D affine transformation to the current directory. The transformations are defined in a particular order - A->B. If you want B->A, then reverse the order and use the inverse warps or just add the -iwarp option to invert the original warp list.

Here's an example to transform the D99v2 atlas to NMT2.1 space (the inverse is computed here):

3dNwarpApply \
   -master ~/NMT_v2.1_sym/NMT_v2.1_sym_05mm/NMT_v2.1_sym_05mm.nii.gz \
   -source D99_atlas_v2.0.nii.gz \
   -nwarp 'NMTv2sym_shft_WARP.nii.gz NMTv2sym_composite_linear_to_template.1D' \
   -prefix D99v2atlas_in_NMT.nii.gz -ainterp NN -iwarp

3drefit -cmap INT_CMAP -copytables \
  D99_atlas_v2.0.nii.gz  D99v2atlas_in_NMT.nii.gz

Thank you, this is very helpful.