help > Outlining Overlays
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Sep 24, 2020  05:09 PM | Joseph Taylor
Outlining Overlays
Hello! I am trying to show where a brain lesion (overlay) hits a brain network (overlay) on a template brain. I am unhappy with the results despite trying several colors schemes and opacity settings. Is there a way to outline the lesion overlay rather than fill it with color? It would be helpful to learn how to do this in MRIcroGL and Surfice. Thanks!
Sep 24, 2020  07:09 PM | Chris Rorden
RE: Outlining Overlays
To make an outline I would use the Matlab script "nii_dilate_outlines". For example,
  nii_dilate_outlines('les.nii', [-2 0])
will create an outline that goes from 2 voxels inside the region to the outer border. You can even make different outline shells like a Russian Matryoshka doll
  nii_dilate_outlines('les.nii', [-2 0 2 4])
You can get the script here:
  https://github.com/rordenlab/spmScripts
Unlike iterating typical dilation and erosion, this creates nice smooth shapes rather than diamond-like patterns. It uses distance fields as described here. Grigori Yourganov deserves credit for this script.
Sep 25, 2020  02:09 PM | Joseph Taylor
RE: Outlining Overlays
Thank you!