Is it possible to change/eliminate the border between atlas scouts during a cortical parcellation?

raajc · January 3, 2020, 12:53am

Is it possible to eliminate the borders between atlas scouts as shown here?

It would be great to be able to generate figures that look more similar to those from FreeSurfer:
http://freesurfer.net/fswiki/CorticalParcellation

Thanks!

Francois · January 7, 2020, 5:26pm

The scouts in Brainstorm are subsets of the vertices rather than full anatomical parcellations of the cortical surfaces generated by FreeSurfer. The goal is not anatomical (each section of the cortex must be classified in an anatomical region) but functional (grouping a list of dipoles for ROI analysis of estimated source activity). Only the vertices/dipoles are colored, Brainstorm has no representation of what the faces between two vertices are, and hence no reason for painting the area between two scouts.

That said, it is true that it could be nice to have a way to represent the parcellations in Brainstorm without these gaps. It has no real meaning in the context of source analysis, therefore we will not make it a priority in our developments, but if you are interested in contributing solutions for improving the display of anatomical atlases in Brainstorm, we are welcoming external contributions.

The corresponding Matlab code:

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/gui/panel_scout.m#L4254


      
          

          % Loop on all the scouts to export

          sMri.Cube = 0 * sMri.Cube(:,:,:,1);

          for i = 1:length(sScouts)

              % Get vertices coordinates

              bst_progress('text', sprintf('Computing scout envelope... [%d/%d]', i, length(sScouts)));

              Vertices = GridLoc(sScouts(i).Vertices,:);

              % Extract envelope

              if exist('alphaShape', 'file') && exist('boundary', 'file')

                  Faces = boundary(Vertices, 0.7);

              else

                  Faces = convhulln(Vertices);

              end

              % Compute interpolation matrix from tessellation to MRI voxel grid

              bst_progress('text', sprintf('Computing interpolation... [%d/%d]', i, length(sScouts)));

              tess2mri_interp = tess_tri_interp(Vertices, Faces, size(sMri.Cube));

              % Compute scout mask

              bst_progress('text', sprintf('Computing scout mask... [%d/%d]', i, length(sScouts)));

              scoutMask = tess_mrimask(size(sMri.Cube), tess2mri_interp);

              % Get scout integer label

              maskValue = round(str2num(sScouts(i).Label));