Thanks Doug. And good question that I've wondered about myself Jeff. The part about the high-resolution volume that is created "under the hood" explains why mris_wm_volume takes substantially longer to complete than would be expected relative to just running `mris_volume Xh.white` and then subtracting off some values from the aseg.stats
cheers, -MH On Fri, 2011-12-02 at 12:07 -0500, Douglas N Greve wrote: > Hi Jeff, it's going to be tricker than that to get the exact value. For > the WM volume computation, there's yet another routine that is used. > This one creates a high-resolution volume to determine which voxels are > withing the WM surface. It then loops through the voxels within the WM > surface and counts the ones that have the following labels in the aseg: > case Left_Cerebral_Cortex: > case Right_Cerebral_Cortex: > case Left_Cerebral_White_Matter: > case Right_Cerebral_White_Matter: > case Left_WM_hypointensities: > case Right_WM_hypointensities: > case CC_Posterior: > case CC_Mid_Posterior: > case CC_Central: > case CC_Mid_Anterior: > case CC_Anterior: > Note that the cortical labels are there to catch the partially volumed > voxels. > hope this helps > doug > > > > Jeff Sadino wrote: > > Thank you Doug for your answer. After reading the wiki more, it has > > led me to another question. > > > > I am trying to duplicate the White Matter value from aseg.stats using > > FreeSurfer 5.0.0. The value from aseg.stats is 220804 (as it is also > > when running mris_wm_volume). By hand, when I run mris_volume subject > > lh.white, I get 239035. From this, I subtract: > > Left-Lateral-Ventricle > > Left-Inf-Lat-Vent > > Left-vessel > > Left-Thalamus-Proper > > Left-Caudate > > Left-Putamen > > Left-Pallidum > > Left-Accumbens-area > > Left-VentralDC > > Left-choroid-plexus > > and then I am left with 209832. Can someone please give more detail > > about how or which areas mris_wm_volume excludes? > > > > Thank you very much, > > Jeff > > > > On Wed, Nov 30, 2011 at 7:46 AM, Douglas N Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > Hi Jeff, the total cortical gray matter is based on the volume > > between the white and pial surfaces. The other structures you > > mention below are based on the automatic volume segmentation. > > doug > > > > Jeff Sadino wrote: > > > > Hello, > > > > Thank you Bruce and Doug for your answers to my previous > > question about a bad talairach.lta file. I am now grabbing > > volumes using fs5.0.0 and would like to ask for clarification. > > On the Morphometry Stats page at > > http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats, it > > says that the cortex is based on the pial surface. I am > > wondering what this includes. I loaded up the pial surface in > > tkmedit along with aseg.mgz. It looks like the following > > regions are completely outside the pial surface: cerebellum, > > 4th ventricle, Brain-Stem, optic chiasm. Is it correct that > > these regions are excluded? And then it looks like the > > hippocampus, amygdala, and inferior-lateral-ventricle are only > > halfway outside the pial surface. Is that correct? If it is, > > then is there a recommended way to exclude the hippocampus, > > amygdala, and inferior-lateral-ventricle regions in the > > cortical gray matter? Do these regions get properly accounted > > for in the subcortical gray calculation? > > > > And then for the white matter, the webpage says that it is > > based on the white surface. Looking at the white surface > > (lh.white), all of the subcortical gray matter and ventricles > > are enclosed in the surface. Can someone explain how the > > subcortical gray gets excluded? > > > > Finally, for the SubCortGray reported in aseg.stats file, does > > that exclude the following areas: > > Left-Lateral-Ventricle > > Left-Inf-Lat-Vent > > 3rd-Ventricle > > 4th-Ventricle > > CSF > > Left-vessel > > Right-Lateral-Ventricle > > Right-Inf-Lat-Vent > > Right-vessel > > 5th-Ventricle > > Left-Cerebellum-White-Matter > > Right-Cerebellum-White-Matter > > WM-hypointensities > > > > What about the brain stem? Why is the cerebellum Gray Matter > > included? I ask because the only way I can get close to the > > SubCortGray by using the aseg file is by excluding those regions. > > > > Once again, thank you for your invaluable help! > > Jeff Sadino > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > > > > 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 . 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
