I see. So, to be clear, when you asked:
" I’m confused on how to take the lh/rh.1D.roi files which define the rois drawn in native space and project those to atlas space. I’ve also tried saving as .niml.roi. "
… you meant an “atlas space” of a surface, not of a volume?
One thing to note: I mentioned checking out the scripts in the Bootcamp subdirectory suma_demo/afni; actually, those are a bit out of date, and as Rick reminded me, the more uptodate ones are in the same Bootcamp download, but in the subdirectory: AFNI_data6/FT_analysis/FT/SUMA/. That will help out a bit with the subsequent description/explanation here:
The std.141* and std.60* meshes created by @SUMA_Make_Spec_FS are standardized meshes; you can read more about these here:
and in Ziad & Rick’s paper:
In the volumetric case, we geometrically warp a dataset to line up “voxel-by-voxel” with a reference template-- the output lies on the same grid, having mushed (in a technical sense) the brain around. In the surface case, Ziad+Rick worked out an equivalent way to perform alignment on the mesh so that every given node ID should correspond to the same anatomical location across meshes; this is done by default in SUMA, as noted above.
So, if you draw your ROI on, say, your subject’s std.60lh dset, then you can convert your ROI to a *.niml.dset with the ROI2dataset command, like this (from the aforementioned “tuna.lh” Bootcamp example):
ROI2dataset -prefix $prefix.lh.niml.dset -input $prefix.lh.niml.roi
… and those node numbers should produce the equivalent ROI on any std.60lh dset. (The same is true is you drew on a std.141lh dset-- it would apply to any std.141lh dset-- and equivalently for “rh” dsets-- too; std.60 dsets are a coarser mesh than the std.141 ones.)
I did this using the data+scripts in the AFNI_data6/FT_analysis/FT/SUMA/ directory:
- first I ran run.suma.01.lh.141
- then I drew an ROI on a nicely flattened surface there (can draw on any surface, but soooo much easier on one of those balloony-flat representations)
- I saved the ROI with the name “tuna.lh”, to be able to use another script in the directory easily; the ROI’s full name on the disk was tuna.lh.niml.roi
- then I ran run.roi2dset, which converted the tuna.lh ROI into a surface dataset “tuna.lh.niml.dset” (and also made the volumetric representation, but you said you only care about the surface stuff here)
- then I copied the surface data set tuna.lh.niml.dset (which was drawn on a std.141lh mesh) to a directory where I had a standard space MNI152 FS mesh, and loaded that file there.
Attached is the image of the original ROI drawn in the individual subject space (upper left, SUMA window, purple surface ROI), the ROI loaded on the MNI dset mesh (upper right, SUMA window, red surface ROI), and the volumetric version of the file created by the 3dSurf2Vol command in run.roi2dset, just because it’s cool (the AFNI volumetric viewers along the bottom, purple ROI overlay because the volume is that of the individual subject).
NB: there is nothing special or particularly standard about the MNI152 dset mesh; it was just another subject’s mesh that I had available to show the ROI dset on.