Is there an available list of GM regions within the list of regions in the FreeSurferColorLUT.txt?
(In particular, I am interested in a list of GM regions output in a default run of recon-all, which seems to have a maximum regionnumber of 2035. But a full list is great, too-- I'm not sure which might be already available or easier to generate.)
I had thought of using the segmentation volumes to help me differentiate ROIs. For example, I could get rid of regions that overlap with the WM volume, but I think that the segmentation might come from a slightly different bit of information than the sum of segmented regions. As shown in the attached slice image, if I underlay the WM segmentation volume (color = white), and overlay a "recon-all" parcellation+segmentation map (color = red for GM on right, yellow for GM on left, and green for non-GM) to look for overlap, I see that some of the WM seg volume overlaps with GM ROIs (overlaps are isolated pink-ish voxels and light yellow voxels; one highlighted in cross hairs). I guess this difference occurs because the segmentation volume comes from the surfaces themselves?
Anyways, this makes me think that I can't automate finding the GM, and I would rather go from LUT numbers, and hence the above question.
Thanks, pt
