On Tue, Nov 8, 2016 at 12:29 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

Yes. It just uses a rule on the numbers that it expects to be GM. At some point, I'll add both tissue type and laterality info to the ROIs, but not for version 6
On 11/8/16 12:03 PM, P Taylor wrote:
And a final question, which might be a silly one--
This GM map applies to both the aparc.a2009s+aseg.mgz and aparc+aseg.mgz files, right?

Running "mri_binarize --gm ..." on each of those files separately gave the same mask-- I believe this should be a general property?

Thanks,

pt
On Tue, Nov 8, 2016 at 11:57 AM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:
yes
On 11/8/16 11:51 AM, P Taylor wrote:
Ah, cool, that looks like it does the trick-- thanks much.

Will that version of mri_binarize be in the next release of FS?

Thanks,

pt
On Tue, Nov 8, 2016 at 11:35 AM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:
Try this one https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize
On 11/8/16 11:26 AM, P Taylor wrote:
Thanks, I'd like to try that. However, my mri_binarize doesn't show that option, and when I try running it, that option isn't recognized:

$ mri_binarize --gm --o map_gm.nii --i aparc+aseg.mgz
ERROR: Option --gm unknown

Looking at the mri_binarize help, I see '--wm' exists, and that does, indeed, produce a WM-looking volume. I also see an option "--wm+vcsf"; would subtracting that resulting map leave only GM?

My version of FS is:

----------------------------------------------------------------------
You are running this version of FreeSurfer:

freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
----------------------------------------------------------------------

In the online description of mri_binarize:

https://surfer.nmr.mgh.harvard.edu/fswiki/mri_binarize
I see a "--subcort-gm" option that doesn't appear to work for me, but I guess that isn't full WM.

So, am I somehow behind the times? From the download page:
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

it looks like my v5.3 is the most currently available?

... and, in case it's useful, the explicit version of my mri_binarize (bottom line of the help) is:
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $

Thanks,

pt
On Tue, Nov 8, 2016 at 11:08 AM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:
We don't currently have that information (ie, tissue type) stored with the ROI. One thing you can do is to run mri_binarize with the --gm option on aparc+aseg.mgz This uses some rules to determine what is GM and creates a mask of GM. You can then feed this into mri_segstats with --mask, and it should only return ROIs that are in the GM mask.
On 11/7/16 8:10 PM, P Taylor wrote:
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,

pt

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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greve@nmr.mgh.harvard.edu
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