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'<myROI>' -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.



Edited 1 time(s). Last edit at 03/04/2022 02:08PM by Daniel Glen.