Re: [Freesurfer] GM ROI list?

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 mailto: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 <mailto: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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