Using macaque D99 surface template

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Dear AFNI experts,

I'm new to AFNI/SUMA and I have trouble figuring out how to make use of the D99 surface template. I have macaque fMRI data registered to the D99 space, and now I'd like to map the 3D volumes to a surface template for visualization. The D99 space data downloaded from your official site includes a 3D atlas, a 3D template, and a folder of 365 ROIs surface files (.gii and .dset). From my understanding after reading the instructions, I need to create a surface model via e.g. FreeSurfer, then make the spec files for SUMA use. I could not find the D99 space brain tissue segmentations on your site, so should I do this step myself? If so, what should I do if the mesh I make differs from where the D99 ROIs are defined? If this is a noob question, could you direct me to the relevant information?

I'd really appreciate your help!

-Qiuhan

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The D99 v2 template and atlas was distributed with those ROI surface files and pial surfaces, but it was missing some of the earlier surfaces, generated with Caret. You can find those here:

https://afni.nimh.nih.gov/pub/dist/atlases/macaque/D99_Saleem/archive/macaqueatlas_1.2a/wholebrain_surfaces/

The data is segmented by the parcellation only in the distribution, but you can make a gray matter mask yourself by doing this:

3dcalc -a D99_atlas_v2.0.nii.gz'<300..1000>' -expr 'step(a)' -prefix D99_gm_mask.nii.gz

All the gray matter regions have values of 300 and above, so they can be extracted with that single command.

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Hi Daniel,

Thank you very much for your help!