I would like to calculate total brain volume (defined as: total white, gray, and subcortical altogether). Should I take the BrainSegVol and minus out cerebellum and ventricles, or add the white and gray matter volumes from mris_anatomical_stats (it seems I remember hearing that white matter from mris_anatomical_stats is not reliable)? Thanks.
-Derin
Hi Derin,
the aseg labeling of cortical gm is not that accurate - the surfaces are quiet a bit more so. We have a new tool for generating the estimate of the gm and wm volume from the surfaces called mris_volume and mris_wm_volume. I think Doug or Nick has integrated it into the dev version of recon-all.
cheers, Bruce
On Fri, 2 Feb 2007, Derin Cobia wrote:
I would like to calculate total brain volume (defined as: total white, gray, and subcortical altogether). Should I take the BrainSegVol and minus out cerebellum and ventricles, or add the white and gray matter volumes from mris_anatomical_stats (it seems I remember hearing that white matter from mris_anatomical_stats is not reliable)? Thanks.
-Derin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Bruce,
So if I downloaded the dev version of the program I could use it to get the volumes from subjects processed with 3.0.3? And would adding these volumes together generate the total volume I'm looking for (including subcoritical)? Thanks!
-Derin
Hi Derin,
the aseg labeling of cortical gm is not that accurate - the surfaces are quiet a bit more so. We have a new tool for generating the estimate of the gm and wm volume from the surfaces called mris_volume and mris_wm_volume. I think Doug or Nick has integrated it into the dev version of recon-all.
cheers, Bruce
On Fri, 2 Feb 2007, Derin Cobia wrote:
I would like to calculate total brain volume (defined as: total white, gray, and subcortical altogether). Should I take the BrainSegVol and minus out cerebellum and ventricles, or add the white and gray matter volumes from mris_anatomical_stats (it seems I remember hearing that white matter from mris_anatomical_stats is not reliable)? Thanks.
-Derin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
you would need to add in whatever subcortical components you wanted to include, as they are excluded from the wm volume On Fri, 2 Feb 2007, Derin Cobia wrote:
Bruce,
So if I downloaded the dev version of the program I could use it to get the volumes from subjects processed with 3.0.3? And would adding these volumes together generate the total volume I'm looking for (including subcoritical)? Thanks!
-Derin
Hi Derin,
the aseg labeling of cortical gm is not that accurate - the surfaces are quiet a bit more so. We have a new tool for generating the estimate of the gm and wm volume from the surfaces called mris_volume and mris_wm_volume. I think Doug or Nick has integrated it into the dev version of recon-all.
cheers, Bruce
On Fri, 2 Feb 2007, Derin Cobia wrote:
I would like to calculate total brain volume (defined as: total white, gray, and subcortical altogether). Should I take the BrainSegVol and minus out cerebellum and ventricles, or add the white and gray matter volumes from mris_anatomical_stats (it seems I remember hearing that white matter from mris_anatomical_stats is not reliable)? Thanks.
-Derin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I have not implemented it in recon-all yet.
doug
On Fri, 2 Feb 2007, Bruce Fischl wrote:
you would need to add in whatever subcortical components you wanted to include, as they are excluded from the wm volume On Fri, 2 Feb 2007, Derin Cobia wrote:
Bruce,
So if I downloaded the dev version of the program I could use it to get the volumes from subjects processed with 3.0.3? And would adding these volumes together generate the total volume I'm looking for (including subcoritical)? Thanks!
-Derin
Hi Derin,
the aseg labeling of cortical gm is not that accurate - the surfaces are quiet a bit more so. We have a new tool for generating the estimate of the gm and wm volume from the surfaces called mris_volume and mris_wm_volume. I think Doug or Nick has integrated it into the dev version of recon-all.
cheers, Bruce
On Fri, 2 Feb 2007, Derin Cobia wrote:
I would like to calculate total brain volume (defined as: total white, gray, and subcortical altogether). Should I take the BrainSegVol and minus out cerebellum and ventricles, or add the white and gray matter volumes from mris_anatomical_stats (it seems I remember hearing that white matter from mris_anatomical_stats is not reliable)? Thanks.
-Derin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Is there any way I can get mris_wm_volume? If not, what's the next best thing? Can I use the aseg.stats estimates?
-Derin
I have not implemented it in recon-all yet.
doug
On Fri, 2 Feb 2007, Bruce Fischl wrote:
you would need to add in whatever subcortical components you wanted to include, as they are excluded from the wm volume On Fri, 2 Feb 2007, Derin Cobia wrote:
Bruce,
So if I downloaded the dev version of the program I could use it to get the volumes from subjects processed with 3.0.3? And would adding these volumes together generate the total volume I'm looking for (including subcoritical)? Thanks!
-Derin
Hi Derin,
the aseg labeling of cortical gm is not that accurate - the surfaces are quiet a bit more so. We have a new tool for generating the estimate of the gm and wm volume from the surfaces called mris_volume and mris_wm_volume. I think Doug or Nick has integrated it into the dev version of recon-all.
cheers, Bruce
On Fri, 2 Feb 2007, Derin Cobia wrote:
I would like to calculate total brain volume (defined as: total white, gray, and subcortical altogether). Should I take the BrainSegVol and minus out cerebellum and ventricles, or add the white and gray matter volumes from mris_anatomical_stats (it seems I remember hearing that white matter from mris_anatomical_stats is not reliable)? Thanks.
-Derin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
sure. Tell us what platform and Nick can post it for you On Mon, 5 Feb 2007, Derin Cobia wrote:
Is there any way I can get mris_wm_volume? If not, what's the next best thing? Can I use the aseg.stats estimates?
-Derin
I have not implemented it in recon-all yet.
doug
On Fri, 2 Feb 2007, Bruce Fischl wrote:
you would need to add in whatever subcortical components you wanted to include, as they are excluded from the wm volume On Fri, 2 Feb 2007, Derin Cobia wrote:
Bruce,
So if I downloaded the dev version of the program I could use it to get the volumes from subjects processed with 3.0.3? And would adding these volumes together generate the total volume I'm looking for (including subcoritical)? Thanks!
-Derin
Hi Derin,
the aseg labeling of cortical gm is not that accurate - the surfaces are quiet a bit more so. We have a new tool for generating the estimate of the gm and wm volume from the surfaces called mris_volume and mris_wm_volume. I think Doug or Nick has integrated it into the dev version of recon-all.
cheers, Bruce
On Fri, 2 Feb 2007, Derin Cobia wrote:
I would like to calculate total brain volume (defined as: total white, gray, and subcortical altogether). Should I take the BrainSegVol and minus out cerebellum and ventricles, or add the white and gray matter volumes from mris_anatomical_stats (it seems I remember hearing that white matter from mris_anatomical_stats is not reliable)? Thanks.
-Derin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
CentOS 4 (32-bit). Thanks!
-Derin
sure. Tell us what platform and Nick can post it for you On Mon, 5 Feb 2007, Derin Cobia wrote:
Is there any way I can get mris_wm_volume? If not, what's the next best thing? Can I use the aseg.stats estimates?
-Derin
I have not implemented it in recon-all yet.
doug
On Fri, 2 Feb 2007, Bruce Fischl wrote:
you would need to add in whatever subcortical components you wanted to include, as they are excluded from the wm volume On Fri, 2 Feb 2007, Derin Cobia wrote:
Bruce,
So if I downloaded the dev version of the program I could use it to get the volumes from subjects processed with 3.0.3? And would adding these volumes together generate the total volume I'm looking for (including subcoritical)? Thanks!
-Derin
Hi Derin,
the aseg labeling of cortical gm is not that accurate - the surfaces are quiet a bit more so. We have a new tool for generating the estimate of the gm and wm volume from the surfaces called mris_volume and mris_wm_volume. I think Doug or Nick has integrated it into the dev version of recon-all.
cheers, Bruce
On Fri, 2 Feb 2007, Derin Cobia wrote:
> I would like to calculate total brain volume (defined as: total > white, > gray, and subcortical altogether). Should I take the BrainSegVol > and > minus out cerebellum and ventricles, or add the white and gray > matter > volumes from mris_anatomical_stats (it seems I remember hearing > that > white > matter from mris_anatomical_stats is not reliable)? Thanks. > > -Derin > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Derin,
mris_wm_volume for 32bit centos is on the website:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist
It's gzipped, so to install, after downloading and copying to your $FREESURFER_HOME/bin, type:
gunzip mris_wm_volume.gz chmod a+z mris_wm_volume
Typing 'mris_wm_volume' without args gives some usage text.
Nick
On Mon, 2007-02-05 at 13:08 -0600, Derin Cobia wrote:
CentOS 4 (32-bit). Thanks!
-Derin
sure. Tell us what platform and Nick can post it for you On Mon, 5 Feb 2007, Derin Cobia wrote:
Is there any way I can get mris_wm_volume? If not, what's the next best thing? Can I use the aseg.stats estimates?
-Derin
I have not implemented it in recon-all yet.
doug
On Fri, 2 Feb 2007, Bruce Fischl wrote:
you would need to add in whatever subcortical components you wanted to include, as they are excluded from the wm volume On Fri, 2 Feb 2007, Derin Cobia wrote:
Bruce,
So if I downloaded the dev version of the program I could use it to get the volumes from subjects processed with 3.0.3? And would adding these volumes together generate the total volume I'm looking for (including subcoritical)? Thanks!
-Derin
> Hi Derin, > > the aseg labeling of cortical gm is not that accurate - the surfaces > are > quiet a bit more so. We have a new tool for generating the estimate > of > the > gm and wm volume from the surfaces called mris_volume and > mris_wm_volume. > I > think Doug or Nick has integrated it into the dev version of > recon-all. > > cheers, > Bruce > > > On Fri, 2 Feb 2007, Derin Cobia wrote: > >> I would like to calculate total brain volume (defined as: total >> white, >> gray, and subcortical altogether). Should I take the BrainSegVol >> and >> minus out cerebellum and ventricles, or add the white and gray >> matter >> volumes from mris_anatomical_stats (it seems I remember hearing >> that >> white >> matter from mris_anatomical_stats is not reliable)? Thanks. >> >> -Derin >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I've noticed that the gray matter volume output from mris_anatomical_stats (lh) vs. mris_volume (lh.pial) differs. Am I missing something? Do I need to run mris_volume for a different surface? Thanks.
-Derin
sure. Tell us what platform and Nick can post it for you On Mon, 5 Feb 2007, Derin Cobia wrote:
Is there any way I can get mris_wm_volume? If not, what's the next best thing? Can I use the aseg.stats estimates?
-Derin
I have not implemented it in recon-all yet.
doug
On Fri, 2 Feb 2007, Bruce Fischl wrote:
you would need to add in whatever subcortical components you wanted to include, as they are excluded from the wm volume On Fri, 2 Feb 2007, Derin Cobia wrote:
Bruce,
So if I downloaded the dev version of the program I could use it to get the volumes from subjects processed with 3.0.3? And would adding these volumes together generate the total volume I'm looking for (including subcoritical)? Thanks!
-Derin
Hi Derin,
the aseg labeling of cortical gm is not that accurate - the surfaces are quiet a bit more so. We have a new tool for generating the estimate of the gm and wm volume from the surfaces called mris_volume and mris_wm_volume. I think Doug or Nick has integrated it into the dev version of recon-all.
cheers, Bruce
On Fri, 2 Feb 2007, Derin Cobia wrote:
> I would like to calculate total brain volume (defined as: total > white, > gray, and subcortical altogether). Should I take the BrainSegVol > and > minus out cerebellum and ventricles, or add the white and gray > matter > volumes from mris_anatomical_stats (it seems I remember hearing > that > white > matter from mris_anatomical_stats is not reliable)? Thanks. > > -Derin > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Derin Cobia -
Doug Greve -
Nick Schmansky