Visualization cortical surface and ROIS

Background: http://web.stanford.edu/group/vista/cgi-bin/wiki/index.php/Visualization

These are notes about how to script the following calculation (rr_brainandreadingcircuitry) in CoverageReading/ForReadingReview repository. There are example scripts in there.

Take a mesh of the cortical surface (there are scripts for producing these meshes) or (a nifti T1) and an ROI (chosen from somewhere that is a nifti in the same coordinate frame) and render it. The mesh should probably be an obj file if possible. with the cortical ROIs shown as colored overlay on the cortical surface.

Logic is take a T1 file, run FreeSurfer to get the class file. Build the mesh (AFQ_RenderCorticalSurface) in the original T1 NIFTI coordinate frame. Add the ROI using, say, AFQ_meshAddRoi.

Ask JW/NB about standardizing formats and converting.

Output format

We would like to be able to write it out as an obj file, as well, so we can view it in Flywheel or any obj viewer.

We would like to be able to write it out show the vistasoft's mesh viewer (mrmViewer?) brings it up.