Thanks, that's useful for getting the ROI volumes and a list of all that's been found for a particular data set.

I would still like to have a way to identify a listed region as gray matter or not so that I can parse the file for only GM regions that have been returned, particularly as different numbers of ROIs are typically returned in an aparc+aseg file.

I see in the aseg.stats file that there are volumetric summations for GM quantities, such as:
# Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 238183.759207, mm^3
# Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 240824.502797, mm^3
# Measure Cortex, CortexVol, Total cortical gray matter volume, 479008.262004, mm^3
....
# Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 57815.000000, mm^3
# Measure TotalGray, TotalGrayVol, Total gray matter volume, 643956.262004, mm^3

Are these calculated by summing individual ROI volumes, so that a list of all possible GM volumes does already exist somewhere?

Thanks,

On Mon, Nov 7, 2016 at 3:39 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

I don't know that we have a complete list in one place of just the
aparc+aseg ROIs, but you can get one by running

mri_segstats --seg aparc+aseg.mgz --ctab-default --sum sum.dat

then look in the sum.dat file

On 11/03/2016 04:32 PM, P Taylor wrote:
> 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
>
>
>

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