Dear AFNI/SUMA experts,
Is there any way in SUMA to display only the border outline of a region from an atlas? I’m thinking of something like the attached image from Johns et al. figure 3 (https://doi.org/10.1080/23273798.2018.1476727), but they used FreeSurfer. Apologies if I’m missing something obvious. I’ve searched the helps and tutorials but haven’t found anything addressing this particular issue.
In suma, you can load other datasets including masks or atlases. You can either extract these from a dataset already mapped to the surface or map a new dataset to the surface. In the surface controller (ctrl-s), select “Load Dset”. If the dataset is named with the current hemisphere, you will likely see it in the list; otherwise, change the filter at the top to be more liberal - like *.niml.dset. Change the coloring method from “Col” to “Con” to use contours instead. “C&C” is to do both. Combine other datasets with “1” turned off.
extract an ROI by itself, and give the voxels a value of 1
3dcalc -a myatlas.nii.gz’’ -expr ‘step(a)’ -prefix myROI.nii.gz
map the ROI to the surface from segment connecting smoothwm and pial surfaces
use mode or nzmode here for statistic
3dVol2Surf -spec std.141.myspec.spec -surf_A std.141.rh.smoothwm.gii -surf_B std.141.rh.pial.gii
-sv myanatvol.nii.gz -grid_parent myROI.nii.gz -gp_index -1 -map_func nzmode
-f_steps 10 -f_index nodes -out_niml mymask.niml.dset
optional cleanup irregular regular regions on smoothwm surface (should use one of the “anatomical” surfaces here)
SurfLocalstat -prefix ROI_cluster2mm -input mymask.niml.dset -stat mode -nbhd_rad 2 -i std.141.lh.smoothwm.gii
inside suma, select mymask.niml.dset to color the surface (Ctrl-s), Dsp to set Colors/Contour/Both.
Thank you very much for spelling that out so clearly. It worked exactly as advertised!
And you might also find these related AFNI Academy videos useful: