freeview will show the coords of the white surface for the inflated surface since those of the inflated surface are not meaningful. why not just get the vertex no and reference that in matlab? Note that matlab will use 1-based indexing vs freeview uses 0-based
On 12/3/2022 12:27 PM, Sarah Lavelle wrote:
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Dear freesurfer,
I am trying to import surface files into MATLAB and highlight a selected vertex on it. I am getting the coordinates from FreeView and then trying to find the same position in my matlab plot using the RAS surface coordinates.
My code works perfectly for lh.pial but not for lh.inflated. Is lh.inflated transformed in FreeView? Why doesn't my method work the same for the inflated surface? How can I fix this? HIGHLIGHT vertex '80609' on INFLATED SURFACE in matlab %Vertex 80609 on /subject/bert/surf/lh.inflated; % FROM FREEVIEW : %lh.pial = [-39.45, 8.55, 50.40] = Surface RAS %lh.inflated = [-37.02, 8.26, 48.41] = Surface RAS [vertices, faces] = freesurfer_read_surf('/Applications/freesurfer/7.3.2/subjects/bert/surf/lh.inflated'); % Plot the rotated surface data patch('Faces', faces, 'Vertices', vertices, 'FaceColor', [0.5 0.5 0.5], 'EdgeColor', 'none'); % Hp = patch('vertices',vertices,'faces',faces(:,[1 3 2])); camlight('headlight','infinite'); title('Left hemisphere of the cortex (file = lh.pial) with a point overlayed in FreeSurfer Surface RAS Coordinate System') xlabel('R') ylabel('A') zlabel('S') hold on; str=sprintf('Vertex A'); label1=str; vertexA=[-37.02, 8.26, 48.41]; plot3(vertexA(1), vertexA(2), vertexA(3), '*r'); text(vertexA(1),vertexA(2), vertexA(3),label1,'Color','r', 'FontSize',20,'VerticalAlignment','bottom','HorizontalAlignment','left'); Any help would be greatly appreciated, Thanks! Sarah
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