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?
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):
-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 \
Thank you, this is very helpful.