External Email - Use Caution There is no such flag in mri_segstats to calculate gray matter cortical parcels. There is a flag for total gray matter rather. Nevertheless, I think there is a file in recon-all output that has white matter to gray matter ratio : lh.w-g.pct and rh.w-g.pct and I have a file for the white matter so I think I may be able to create a code to calculate the gray matter.
On Wed, Feb 21, 2024 at 7:21 PM Fischl, Bruce R.,PHD < bfis...@mgh.harvard.edu> wrote: > I think that is exactly one of the outputs of mri_segstats. Check the help > on it and see if it does what you want. I believe it is also run by default > during recon-all and the values placed into one of the stats output files > > > > Cheers > > Bruce > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *ERNEST KISSI > *Sent:* Wednesday, February 21, 2024 11:14 AM > *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] Grey Matter Intensities > > > > * External Email - Use Caution * > > Yes, please > > That's exactly what I mean. > > > > On Wed, Feb 21, 2024, 6:44 PM Fischl, Bruce R.,PHD < > bfis...@mgh.harvard.edu> wrote: > > Can you clarify what you mean by “measure the intensities for the grey > matter regions”? You could for example compute the mean gray matter > intensity within each cortical parcel and each subcortical structure. Is > that what you want? > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *ERNEST KISSI > *Sent:* Wednesday, February 21, 2024 9:45 AM > *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] Grey Matter Intensities > > > > * External Email - Use Caution * > > I think these are not grey matter but cortical parcellation. > > FSL can output grey matter segmentation but I do not think freesurfer has > such an output. > > In aparc.stats (rh.aparc or lh.aparc), there is only GrayVol and no > intensity measure. I want to know how I can measure the intensities for the > grey matter regions. > > > > On Wed, Feb 21, 2024, 5:25 PM Huang, Yujing <yhuan...@mgh.harvard.edu> > wrote: > > Recon-all outputs these 3 aparc aseg volumes: > > > > aparc.DKTatlas+aseg.mgz > > aparc.a2009s+aseg.mgz > > aparc+aseg.mgz > > > > > > Are these what you are looking for? They should work the same way as aseg > volume. > > > > Best, > > > > Yujing > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *ERNEST KISSI > *Sent:* Tuesday, February 20, 2024 3:22 PM > *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject:* [Freesurfer] Grey Matter Intensities > > > > * External Email - Use Caution * > > Hi Freesurfer team, > > > > Recon-all output shows the white matter volumes and white matter > intensities of different brain regions but only shows grey matter volumes. > I want to know if there is a function or a flag to also get information on > the regional grey matter intensities. > > > > Thank you. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1Sbu0XwqsrtArIBltcesEisgJnMS5nFCWJdyBtCb-QILCiqW7f35wAO4FtzRrF1YR6-k85oQ5nK1G_KW_7_V8VIPm73c-KJQN6ADAmuL_MzyjSqtWHV1YnyzHGJVWnky1jhUc4kqEUwAmavWy0UQlegqqdKLCXG6gS7yGY30GNOI7VDoSc2m34M2kK3CGsu9sYMk5zHPefPzAovVhijm598_Sc7TsGy76NLiLEfCM4OqMMJoud7RfB_ICfOvqHug0Gq0mcc_iClMjwK9as4GCGd2wYD-959uoQbsreV8PoUkxlqdIy5pQL1tmbTr2SBJI/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > <https://secure-web.cisco.com/16ifYTsux0iUNjv1oYt9Hv-c1-WpEkOHYOrBq7h3PWyvvS76iScX_WZ2o8lNEaIpa7qoiyDGPhAqI6bC1dHM7bd_Vk_eG55Dj2LfAA0w8W1JH8Gxa-FPjNttxVj00sCJD7OFiTODAbS8thnuOjDATFw5xNSzFI49sqFFsPcZvcQxUGdb7i6Ug8FwqPnD1lh7oyCqLgB_SKeSCqspHSLCW3-OInKWuEem9SSGwzsb96fKTAIdbRUvkhjdxzPv1EG32Xp7e3DkEiGrk6rTPtRmfUU3pz19N6hdnDR6ZEF4Gacf-Gg6hHit5L3yfilTeIqwI_OsthS_zeC-UAbknjzsMcw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > The information in this e-mail is intended only for the person to whom it > is addressed. 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