Old FreeSurfer color lookup table

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In older Slicer releases, there was a color map called “FreeSurfer Labels”. In more recent nightly releases, this color map is gone, and I see new ones called “SPL-BrainAtlas-2009-ColorFile”, “SPL-BrainAtlas-2012-ColorFile”, and “SPL-BrainAtlas-ColorFile”, none of which correspond exactly to the old colormap. The 2009 one seems very similar, but differs at least in that label 0 is called “unknown” and transparent in the old colormap, whereas label 0 is called “background” and is black in the SPL-BrainAtlas-2009-ColorFile. In addition, there seem to be some missing labels in the 2009 (for example 16 is listed as “none” (I think meaning no colormap entry) whereas it is “brainstem” in the old color map) and some changed labels (for example 24 is listed as “CSF” in the old color map and as “third ventricle” in the newer one).

Is there a currently a colormap which fully and accurately interprets the labels in the aparc+aseg volume generated by FreeSurfer? I know that there has been an effort to move FreeSurfer-related functionality out of the Slicer core and to the FreeSurferImporter module, but I have this extension and it did not come with the “FreeSurfer Labels” colormap as far as I can tell. Thanks for any help you can provide.

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The FreeSurfer labels were moved to the SlicerFreeSurfer extension, however it appears that there is currently an issue when loading the color node. I’ll fix it and let you know when it’s available.

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The lookup table should be available from the SlicerFreeSurfer extension in the preview release tomorrow.

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Hi @Sunderlandkyl, I tried putting the file here:

Slicer-4.11.20200930-linux-amd64/share/Slicer-4.11/ColorFiles/FreeSurferColorLUT.txt

but then no color shows up in my loaded wmparc.mgz. As you can see, I am trying to get away without installing your extension. Would that be at all possible?

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@tbillah Do you have issues that prevent you from installing SlicerFreeSurfer? Maybe those issues could be addressed directly. SlicerFreeSurfer offers many more features than just a lookup table, such as importing of images and surfaces in a consistent coordinate system.

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