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 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer