help > ROI visualization with desikan/freesurfer/boggle atlas
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Jul 10, 2018  12:07 PM | drobinv
ROI visualization with desikan/freesurfer/boggle atlas
Hi, love the software for the rendering and visualization options. However, can't figure out how to treat the boggle.annot / Desikan/ freesurfer atlas as an atlas.

For example, how do you use the AtlasStatMap, AtlasHide, AtlasGray commands to selectively grey out, and hide certain ROIs while displaying others. This works with the built-in atlases really well as the example wiki shows. But the boggle.annot on the pial surface is not an "atlas" and I can't find a way to interact with it in a similar fashion to highlight certain ROIs.
Jul 10, 2018  01:07 PM | Chris Rorden
RE: ROI visualization with desikan/freesurfer/boggle atlas
 Surfice can load a large number of formats. Different formats have different properties: for example fiber tracks can be sorted based on fiber lengths, while connectomes can have their node size increased or decreased. The issue is that the boggle.annot files and freesurfer images only show the surface of a single, inflated brain. In contrast, the atlas format expects that each region is a self-contained volume. In other words, the boggle.annot file only maps the external surface of each region, and each region is just a 2D surface without any interior volume. Naive conversion of the annot files to an atlas would cause seams where the regions join and when you hide individual regions you would see the facade of the rest of the brain, rather than the other regions. 

One solution is you could write some code that would extrude each region of the annot files between the pial surface and the white matter boundary. This web page suggests a useful method to achieve this.