Hi, Dane-

When you think of an atlas, you can never think of it in isolation. It is *always* tied to a particular space, or more specifically template.

The standard Brainnetome and Glasser atlases can *only* be overlaid and used on the MNI template (probably specifically the MNI 2009c, as you note, because "MNI" has become a family of spaces, grids and templates).

The voxel dimensions and matrix dimensions of the Brainnetome and MNI_Glasser* atlases appear to be:

$ 3dinfo -ad3 -n4 -prefix BN_Atlas_246_1mm.nii.gz MNI_Glasser_HCP_v1.0.nii.gz 
1.000000	1.000000	1.000000	182	218	182	1	    BN_Atlas_246_1mm.nii.gz
1.000000	1.000000	1.000000	256	256	256	1	MNI_Glasser_HCP_v1.0.nii.gz

The Glasser atlas matches the MNI template well, but the grid dimensions are a bit different than MNI2009c. To make it match better the @SSwarper base volume MNI, I once ran:

3dZeropad -master MNI152_2009_template_SSW.nii.gz -prefix MNI_Glasser_HCP_v1.0_LPI_2009c.nii.gz MNI_Glasser_HCP_v1.0_LPI.nii.gz
3drefit -copytables MNI_Glasser_HCP_v1.0.nii.gz MNI_Glasser_HCP_v1.0_LPI_2009c.nii.gz
3drefit -cmap INT_CMAP MNI_Glasser_HCP_v1.0_LPI_2009c.nii.gz

... where the 3drefits are to copy of the labeltables and then to make the default colorbar be "integer"y, respectively.

The BN_Atlas_246_1mm.nii.gz appears to mostly match the MNI*2009c* well, but at the edges it seems a bit "rounded in", oddly.

Re. Q1) Yes.

Re. Q2) It would be non-optimal re warp all functionals from TT27 space to MNI space, because they have already been re-gridded once from their native space, and warping them all again would smooth them additionally. It would be better to use the appropriate MNI template as a reference base for the dsets directly (e.g., make it the template base in @SSwarper for skullstripping and nonlinear warping and then providing that info to afni_proc.py).

Re. Q3) One would want to have a good atlas in that TT27 template space. Offhand, I don't know of one (Daniel might?).
-> One *could* warp one of the MNI templates to TT27 space, and then use it there. One will have to do a bit of regridding and ROI smoothing; that might be better than warping the TT27 space EPI data to MNI, because the ROI voxels are smaller.

--pt