Hello, I've recently started a project that involves measuring the volume of the hippocampus and other subcortical structures, so I was also wondering whether aseg.stats was more accurate or wmparc.stats. So far the difference between them appears to be approximately a hundred voxels for each right/left hippocampus.
Thank you, Kathy Zhang '09
On Wed, Oct 8, 2008 at 12:08 PM, Nurunisa Neyzi nneyzi@gmail.com wrote:
Hi, for subcortical segmentations, is it then better to use the volumes in wmparc.stats than those in aseg.stats?
On Tue, Jul 22, 2008 at 2:54 PM, Doug Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote: > > Actually, the construction of aparc+aseg and wmparc do use info about where > the surface is to refine the aseg cortical boundaries. This information is > stored in ribbon.mgz (and it overrides the aseg definition). At some point, > we will use the surfaces to directly refine the aseg boundaries. > > doug > > > > > Michael Harms wrote: > > Hi Chris, > Doug, please correct me if I'm wrong, but the original gm/wm > segmentation contained in aseg.mgz is based on the 3D volume-based > tissue segmentation. This original segmentation then forms the basis > for all subsequent additional segmentations of either GM or WM in the 3D > volume. That is, aparc+aseg.mgz and wmparc.mgz make "use" of the > surface based parcellation, but only to decide the most appropriate > label to assign to GM/WM as defined in the already existing volume-based > segmentation that is contained in aseg.mgz. > > Thus, since the GM/WM in aparc+aseg.mgz and wmparc.mgz is still based on > the 3D volume segmentation, there is no apriori reason that their > spatial extent will correspond precisely to the more accurate gray and > white mattes surfaces that come out of the surface-based processing > stream. (Although certainly we would hope that the discrepancies don't > become too large). > > cheers, > Mike H. > > On Thu, 2008-07-17 at 12:00 -0500, bell0368@umn.edu mailto:bell0368@umn.edu wrote: > > > I have sent two images created with the following commands. > > tkmedit $subjid brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white > -segmentation (aparc+aseg.mgz and wmparc.mgz) > $FREESURFER_HOME/FreesurferColorLUT.txt > > The wm segmenations go through the "main surface" and the "orig surface" > into the gray matter, for example in the rh-supramarginal and > rh-postcentral. From your last response I am unsure as to which pipeline > creates the wm parcellations, the volume-based pipeline (.i.e aseg.mgz) or > the surface-based pipeline (i.e. ribbon.mgz) or some combination of the > two. It seems to me that the gm/wm parcellations are created using the > surface pipeline and then transferred to the closest class-matched voxels > from Left-Cerebral-Cortex and Left-Cerebral-White-Matter aseg > segmentations. I guess the question is how are we getting from the surface > parcellations back to volume space; is there a binary? > In a related vein, the value from aseg.stats "surface-based-volume mm3 > lh-cerebral-white-matter" seems to be created with mri_segstats or is it > from mris_wm_volume? Thanks for all your help! > > Chris Bell > > > > > > On Jul 17 2008, Doug Greve wrote: > > > > When the volume is created, a decision has to be made at each voxel as > to what to classify it as. This is used when the aseg.mgz and > ribbon.mgz are created. aparc+aseg.mgz inherit these decisions from > these files. When using mri_segstats with --pv, it will take the > volume of a 1mm3 voxel and divide it up so that it can contribute to > more than one region. But there's not a way to put the partial volume > information into the segmentation itself. Not sure why that do not > appear alingned, but we've been recently looking into this for other > reasons. Can you send a pic.? > > doug > > > > On Wed, 16 Jul 2008, bell0368@umn.edu mailto:bell0368@umn.edu wrote: > > > > I was wondering how the calculations of the wm volume were performed as > well. The six values below are volume values from aseg I believe. I > assume mris_wm_volume does more than sub-divide these regions into the > wm parcellations, but probably also includes partial volume estimations > along the wm/gm surface, is this correct? I basically have the same > question for the gm volume values in aparc.stats; do they include > partial volume calculations from the gm/pial and gm/white borders? Which > binary is used to create these values for gm in aparc.stats... is it > mri_segstats (with --pv)? I was assuming it would be an mris (surface) > calculation as well. I am asking because if you use tkmedit to view the > ?h.surface files and load the aparc+aseg or wmparc segmentation volumes > in also, the surfaces and the segmentations don't seem to line up. Is > there a way to create a segmentation volume that includes > partial-volumed voxels at the gray/white and gray/pial boundries? Thanks > for your help. > > Chris Bell > > > > > the interior voxels are only included in the volume if they are one of > the following in the aseg.mgz: > > 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: > > cheers, > Bruce > > > > On Tue, 15 Jul 2008, Marin Richardson wrote: > > OK, so aparc.stats is better for cortical gray matter. I want to look > at the > parcellated white matter volumes as well - is the only/best option to > use the > wm volumes from wmparc.stats? > > Also, when using mris_wm_volume to calculate total white matter, I > saw the > result defined as the volume within the white matter surface minus > non-WM > structures? Can you tell me which regions are and are not included? > > Marin > > > > > Doug Greve <[EMAIL PROTECTED]> 7/15/2008 12:02 PM >>> > > It is better to use the aparc as it is derived from surface > measurements, which have sub-voxel resolution. The wmparc.stats are > generated by counting 1mm^3 voxels. > > doug > > Marin Richardson wrote: > > > Hi all, > > I noticed that the gray volumes for parcellated cortical regions > in > wmparc.stats are different from those for the same region in > aparc.stats (e.g. > ctx-lh-middletemporal = 8419 in wmparc.stats, middletemporal = > 9466 in > lh.aparc.stats). Why are the values different and which one is a > better > measure to use? > > Thanks, > Marin > > > > > > > _______________________________________________ > 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 > > > > > > > > _______________________________________________ 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 > > > _______________________________________________ > 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 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > _______________________________________________ > 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 > _______________________________________________ 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
They should be exactly the same. If not, it's a bug. I just looked at a few of mine, and they are the same.
doug
Kathy Zhang wrote:
Hello, I've recently started a project that involves measuring the volume of the hippocampus and other subcortical structures, so I was also wondering whether aseg.stats was more accurate or wmparc.stats. So far the difference between them appears to be approximately a hundred voxels for each right/left hippocampus.
Thank you, Kathy Zhang '09
On Wed, Oct 8, 2008 at 12:08 PM, Nurunisa Neyzi nneyzi@gmail.com wrote:
Hi, for subcortical segmentations, is it then better to use the volumes in wmparc.stats than those in aseg.stats? On Tue, Jul 22, 2008 at 2:54 PM, Doug Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Actually, the construction of aparc+aseg and wmparc do use info about where > the surface is to refine the aseg cortical boundaries. This information is > stored in ribbon.mgz (and it overrides the aseg definition). At some point, > we will use the surfaces to directly refine the aseg boundaries. > > doug > > > > > Michael Harms wrote: > > Hi Chris, > Doug, please correct me if I'm wrong, but the original gm/wm > segmentation contained in aseg.mgz is based on the 3D volume-based > tissue segmentation. This original segmentation then forms the basis > for all subsequent additional segmentations of either GM or WM in the 3D > volume. That is, aparc+aseg.mgz and wmparc.mgz make "use" of the > surface based parcellation, but only to decide the most appropriate > label to assign to GM/WM as defined in the already existing volume-based > segmentation that is contained in aseg.mgz. > > Thus, since the GM/WM in aparc+aseg.mgz and wmparc.mgz is still based on > the 3D volume segmentation, there is no apriori reason that their > spatial extent will correspond precisely to the more accurate gray and > white mattes surfaces that come out of the surface-based processing > stream. (Although certainly we would hope that the discrepancies don't > become too large). > > cheers, > Mike H. > > On Thu, 2008-07-17 at 12:00 -0500, bell0368@umn.edu <mailto:bell0368@umn.edu> wrote: > > > I have sent two images created with the following commands. > > tkmedit $subjid brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white > -segmentation (aparc+aseg.mgz and wmparc.mgz) > $FREESURFER_HOME/FreesurferColorLUT.txt > > The wm segmenations go through the "main surface" and the "orig surface" > into the gray matter, for example in the rh-supramarginal and > rh-postcentral. From your last response I am unsure as to which pipeline > creates the wm parcellations, the volume-based pipeline (.i.e aseg.mgz) or > the surface-based pipeline (i.e. ribbon.mgz) or some combination of the > two. It seems to me that the gm/wm parcellations are created using the > surface pipeline and then transferred to the closest class-matched voxels > from Left-Cerebral-Cortex and Left-Cerebral-White-Matter aseg > segmentations. I guess the question is how are we getting from the surface > parcellations back to volume space; is there a binary? > In a related vein, the value from aseg.stats "surface-based-volume mm3 > lh-cerebral-white-matter" seems to be created with mri_segstats or is it > from mris_wm_volume? Thanks for all your help! > > Chris Bell > > > > > > On Jul 17 2008, Doug Greve wrote: > > > > When the volume is created, a decision has to be made at each voxel as > to what to classify it as. This is used when the aseg.mgz and > ribbon.mgz are created. aparc+aseg.mgz inherit these decisions from > these files. When using mri_segstats with --pv, it will take the > volume of a 1mm3 voxel and divide it up so that it can contribute to > more than one region. But there's not a way to put the partial volume > information into the segmentation itself. Not sure why that do not > appear alingned, but we've been recently looking into this for other > reasons. Can you send a pic.? > > doug > > > > On Wed, 16 Jul 2008, bell0368@umn.edu <mailto:bell0368@umn.edu> wrote: > > > > I was wondering how the calculations of the wm volume were performed as > well. The six values below are volume values from aseg I believe. I > assume mris_wm_volume does more than sub-divide these regions into the > wm parcellations, but probably also includes partial volume estimations > along the wm/gm surface, is this correct? I basically have the same > question for the gm volume values in aparc.stats; do they include > partial volume calculations from the gm/pial and gm/white borders? Which > binary is used to create these values for gm in aparc.stats... is it > mri_segstats (with --pv)? I was assuming it would be an mris (surface) > calculation as well. I am asking because if you use tkmedit to view the > ?h.surface files and load the aparc+aseg or wmparc segmentation volumes > in also, the surfaces and the segmentations don't seem to line up. Is > there a way to create a segmentation volume that includes > partial-volumed voxels at the gray/white and gray/pial boundries? Thanks > for your help. > > Chris Bell > > > > > the interior voxels are only included in the volume if they are one of > the following in the aseg.mgz: > > 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: > > cheers, > Bruce > > > > On Tue, 15 Jul 2008, Marin Richardson wrote: > > OK, so aparc.stats is better for cortical gray matter. I want to look > at the > parcellated white matter volumes as well - is the only/best option to > use the > wm volumes from wmparc.stats? > > Also, when using mris_wm_volume to calculate total white matter, I > saw the > result defined as the volume within the white matter surface minus > non-WM > structures? Can you tell me which regions are and are not included? > > Marin > > > > > Doug Greve <[EMAIL PROTECTED]> 7/15/2008 12:02 PM >>> > > It is better to use the aparc as it is derived from surface > measurements, which have sub-voxel resolution. The wmparc.stats are > generated by counting 1mm^3 voxels. > > doug > > Marin Richardson wrote: > > > Hi all, > > I noticed that the gray volumes for parcellated cortical regions > in > wmparc.stats are different from those for the same region in > aparc.stats (e.g. > ctx-lh-middletemporal = 8419 in wmparc.stats, middletemporal = > 9466 in > lh.aparc.stats). Why are the values different and which one is a > better > measure to use? > > Thanks, > Marin > > > > > > > _______________________________________________ > 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> > > > > > > > > _______________________________________________ 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> > > > _______________________________________________ > 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 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > _______________________________________________ > 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> > _______________________________________________ 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>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
Does anyone know how to run a glm with only one continous variable and without a class variable?
I would like to run mri_glmfit with age as the only variable, but I can't figure out how to do this without including and controlling for a class variable such as gender.
I have run the command: mri_glmfir --glmdir ../glm/dev_age_rh --y preproc/rh-thick15.mgz --fsgd fsgd_age.txt doss --surf average rh --C contrast_age
The fsgd file contains gender as a class variable (F or M) and age as a continous variable. The contrast is: 0 0 1
Any tips would be appreciated.
best regards, Christian
Christian,
The .fsgd file would look like this:
GroupDescriptorFile 1 Title Untitled MeasurementName thickness Class Main Variables age Input 030815_4882 Main 15.000000 Input 030713_1197 Main 18.000000 Input 000803_vc4829 Main 20.000000 Input 010728_vc7352 Main 20.000000 Input 010819_vc7505 Main 21.000000 . . .
and the contrast is: 0 1
The 'qdec' app might work well for you in this sort of analysis. At the very least it will generate the .fsgd and contrast matrices for you, which you can then manually input to mri_glmfit.
Nick
On Mon, 2008-10-27 at 09:17 +0100, c.k.tamnes@psykologi.uio.no wrote:
Hi,
Does anyone know how to run a glm with only one continous variable and without a class variable?
I would like to run mri_glmfit with age as the only variable, but I can't figure out how to do this without including and controlling for a class variable such as gender.
I have run the command: mri_glmfir --glmdir ../glm/dev_age_rh --y preproc/rh-thick15.mgz --fsgd fsgd_age.txt doss --surf average rh --C contrast_age
The fsgd file contains gender as a class variable (F or M) and age as a continous variable. The contrast is: 0 0 1
Any tips would be appreciated.
best regards, Christian
Doug, et al.,
We ran a few subjects through recon1, 2, and 3 in an effort to get the volume of the hippocampus bilaterally. We emailed the list to find out if we should use aseg.stats or wmparc.stats. Doug wrote back saying that the hippocampus volumes should be the same. We went back & ran more subjects and they all appear to have a discrepancy between the number of voxels in aseg.stats and wmparc.stats for the hippocampus. Some of the stats are the same-- just the NVoxels and Volume_mm3 differ between the two stat files. we've attached a set of these aseg.stats vs wmparc.stats files. Does anyone have any idea why we might be getting this bug and how we could fix it?
Thanks! Kathy & Margaret
On Fri, Oct 24, 2008 at 3:32 PM, Doug Greve greve@nmr.mgh.harvard.eduwrote:
They should be exactly the same. If not, it's a bug. I just looked at a few of mine, and they are the same.
doug
Kathy Zhang wrote:
Hello, I've recently started a project that involves measuring the volume of the hippocampus and other subcortical structures, so I was also wondering whether aseg.stats was more accurate or wmparc.stats. So far the difference between them appears to be approximately a hundred voxels for each right/left hippocampus.
Thank you, Kathy Zhang '09
On Wed, Oct 8, 2008 at 12:08 PM, Nurunisa Neyzi nneyzi@gmail.comnneyzi@gmail.comwrote:
Hi, for subcortical segmentations, is it then better to use the volumes in wmparc.stats than those in aseg.stats?
On Tue, Jul 22, 2008 at 2:54 PM, Doug Greve greve@nmr.mgh.harvard.edu wrote:
Actually, the construction of aparc+aseg and wmparc do use info about
where
the surface is to refine the aseg cortical boundaries. This information
is
stored in ribbon.mgz (and it overrides the aseg definition). At some
point,
we will use the surfaces to directly refine the aseg boundaries.
doug
Michael Harms wrote:
Hi Chris, Doug, please correct me if I'm wrong, but the original gm/wm segmentation contained in aseg.mgz is based on the 3D volume-based tissue segmentation. This original segmentation then forms the basis for all subsequent additional segmentations of either GM or WM in the 3D volume. That is, aparc+aseg.mgz and wmparc.mgz make "use" of the surface based parcellation, but only to decide the most appropriate label to assign to GM/WM as defined in the already existing volume-based segmentation that is contained in aseg.mgz.
Thus, since the GM/WM in aparc+aseg.mgz and wmparc.mgz is still based on the 3D volume segmentation, there is no apriori reason that their spatial extent will correspond precisely to the more accurate gray and white mattes surfaces that come out of the surface-based processing stream. (Although certainly we would hope that the discrepancies don't become too large).
cheers, Mike H.
On Thu, 2008-07-17 at 12:00 -0500, bell0368@umn.edu wrote:
I have sent two images created with the following commands.
tkmedit $subjid brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation (aparc+aseg.mgz and wmparc.mgz) $FREESURFER_HOME/FreesurferColorLUT.txt
The wm segmenations go through the "main surface" and the "orig surface" into the gray matter, for example in the rh-supramarginal and rh-postcentral. From your last response I am unsure as to which pipeline creates the wm parcellations, the volume-based pipeline (.i.e aseg.mgz)
or
the surface-based pipeline (i.e. ribbon.mgz) or some combination of the two. It seems to me that the gm/wm parcellations are created using the surface pipeline and then transferred to the closest class-matched
voxels
from Left-Cerebral-Cortex and Left-Cerebral-White-Matter aseg segmentations. I guess the question is how are we getting from the
surface
parcellations back to volume space; is there a binary? In a related vein, the value from aseg.stats "surface-based-volume mm3 lh-cerebral-white-matter" seems to be created with mri_segstats or is it from mris_wm_volume? Thanks for all your help!
Chris Bell
On Jul 17 2008, Doug Greve wrote:
When the volume is created, a decision has to be made at each voxel as to what to classify it as. This is used when the aseg.mgz and ribbon.mgz are created. aparc+aseg.mgz inherit these decisions from these files. When using mri_segstats with --pv, it will take the volume of a 1mm3 voxel and divide it up so that it can contribute to more than one region. But there's not a way to put the partial volume information into the segmentation itself. Not sure why that do not appear alingned, but we've been recently looking into this for other reasons. Can you send a pic.?
doug
On Wed, 16 Jul 2008, bell0368@umn.edu wrote:
I was wondering how the calculations of the wm volume were performed as well. The six values below are volume values from aseg I believe. I assume mris_wm_volume does more than sub-divide these regions into the wm parcellations, but probably also includes partial volume estimations along the wm/gm surface, is this correct? I basically have the same question for the gm volume values in aparc.stats; do they include partial volume calculations from the gm/pial and gm/white borders? Which binary is used to create these values for gm in aparc.stats... is it mri_segstats (with --pv)? I was assuming it would be an mris (surface) calculation as well. I am asking because if you use tkmedit to view the ?h.surface files and load the aparc+aseg or wmparc segmentation volumes in also, the surfaces and the segmentations don't seem to line up. Is there a way to create a segmentation volume that includes partial-volumed voxels at the gray/white and gray/pial boundries? Thanks for your help.
Chris Bell
the interior voxels are only included in the volume if they are one of the following in the aseg.mgz:
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:
cheers, Bruce
On Tue, 15 Jul 2008, Marin Richardson wrote:
OK, so aparc.stats is better for cortical gray matter. I want to look at the parcellated white matter volumes as well - is the only/best option to use the wm volumes from wmparc.stats?
Also, when using mris_wm_volume to calculate total white matter, I saw the result defined as the volume within the white matter surface minus non-WM structures? Can you tell me which regions are and are not included?
Marin
Doug Greve <[EMAIL PROTECTED]> 7/15/2008 12:02 PM >>>It is better to use the aparc as it is derived from surface measurements, which have sub-voxel resolution. The wmparc.stats are generated by counting 1mm^3 voxels.
doug
Marin Richardson wrote:
Hi all, I noticed that the gray volumes for parcellated cortical regionsin wmparc.stats are different from those for the same region in aparc.stats (e.g. ctx-lh-middletemporal = 8419 in wmparc.stats, middletemporal = 9466 in lh.aparc.stats). Why are the values different and which one is a better measure to use?
Thanks, Marin
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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Centergreve@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
Sorry! Files for this question are attached.
On Tue, Nov 11, 2008 at 3:25 PM, Margaret Sheridan < sheridan.margaret@gmail.com> wrote:
Doug, et al.,
We ran a few subjects through recon1, 2, and 3 in an effort to get the volume of the hippocampus bilaterally. We emailed the list to find out if we should use aseg.stats or wmparc.stats. Doug wrote back saying that the hippocampus volumes should be the same. We went back & ran more subjects and they all appear to have a discrepancy between the number of voxels in aseg.stats and wmparc.stats for the hippocampus. Some of the stats are the same-- just the NVoxels and Volume_mm3 differ between the two stat files. we've attached a set of these aseg.stats vs wmparc.stats files. Does anyone have any idea why we might be getting this bug and how we could fix it?
Thanks! Kathy & Margaret
On Fri, Oct 24, 2008 at 3:32 PM, Doug Greve greve@nmr.mgh.harvard.eduwrote:
They should be exactly the same. If not, it's a bug. I just looked at a few of mine, and they are the same.
doug
Kathy Zhang wrote:
Hello, I've recently started a project that involves measuring the volume of the hippocampus and other subcortical structures, so I was also wondering whether aseg.stats was more accurate or wmparc.stats. So far the difference between them appears to be approximately a hundred voxels for each right/left hippocampus.
Thank you, Kathy Zhang '09
On Wed, Oct 8, 2008 at 12:08 PM, Nurunisa Neyzi nneyzi@gmail.comnneyzi@gmail.comwrote:
Hi, for subcortical segmentations, is it then better to use the volumes in wmparc.stats than those in aseg.stats?
On Tue, Jul 22, 2008 at 2:54 PM, Doug Greve greve@nmr.mgh.harvard.edu wrote:
Actually, the construction of aparc+aseg and wmparc do use info about
where
the surface is to refine the aseg cortical boundaries. This information
is
stored in ribbon.mgz (and it overrides the aseg definition). At some
point,
we will use the surfaces to directly refine the aseg boundaries.
doug
Michael Harms wrote:
Hi Chris, Doug, please correct me if I'm wrong, but the original gm/wm segmentation contained in aseg.mgz is based on the 3D volume-based tissue segmentation. This original segmentation then forms the basis for all subsequent additional segmentations of either GM or WM in the
3D
volume. That is, aparc+aseg.mgz and wmparc.mgz make "use" of the surface based parcellation, but only to decide the most appropriate label to assign to GM/WM as defined in the already existing
volume-based
segmentation that is contained in aseg.mgz.
Thus, since the GM/WM in aparc+aseg.mgz and wmparc.mgz is still based
on
the 3D volume segmentation, there is no apriori reason that their spatial extent will correspond precisely to the more accurate gray and white mattes surfaces that come out of the surface-based processing stream. (Although certainly we would hope that the discrepancies don't become too large).
cheers, Mike H.
On Thu, 2008-07-17 at 12:00 -0500, bell0368@umn.edu wrote:
I have sent two images created with the following commands.
tkmedit $subjid brainmask.mgz lh.white -aux T1.mgz -aux-surface
rh.white
-segmentation (aparc+aseg.mgz and wmparc.mgz) $FREESURFER_HOME/FreesurferColorLUT.txt
The wm segmenations go through the "main surface" and the "orig
surface"
into the gray matter, for example in the rh-supramarginal and rh-postcentral. From your last response I am unsure as to which
pipeline
creates the wm parcellations, the volume-based pipeline (.i.e aseg.mgz)
or
the surface-based pipeline (i.e. ribbon.mgz) or some combination of the two. It seems to me that the gm/wm parcellations are created using the surface pipeline and then transferred to the closest class-matched
voxels
from Left-Cerebral-Cortex and Left-Cerebral-White-Matter aseg segmentations. I guess the question is how are we getting from the
surface
parcellations back to volume space; is there a binary? In a related vein, the value from aseg.stats "surface-based-volume
mm3
lh-cerebral-white-matter" seems to be created with mri_segstats or is
it
from mris_wm_volume? Thanks for all your help!
Chris Bell
On Jul 17 2008, Doug Greve wrote:
When the volume is created, a decision has to be made at each voxel as to what to classify it as. This is used when the aseg.mgz and ribbon.mgz are created. aparc+aseg.mgz inherit these decisions from these files. When using mri_segstats with --pv, it will take the volume of a 1mm3 voxel and divide it up so that it can contribute to more than one region. But there's not a way to put the partial volume information into the segmentation itself. Not sure why that do not appear alingned, but we've been recently looking into this for other reasons. Can you send a pic.?
doug
On Wed, 16 Jul 2008, bell0368@umn.edu wrote:
I was wondering how the calculations of the wm volume were performed as well. The six values below are volume values from aseg I believe. I assume mris_wm_volume does more than sub-divide these regions into the wm parcellations, but probably also includes partial volume estimations along the wm/gm surface, is this correct? I basically have the same question for the gm volume values in aparc.stats; do they include partial volume calculations from the gm/pial and gm/white borders?
Which
binary is used to create these values for gm in aparc.stats... is it mri_segstats (with --pv)? I was assuming it would be an mris (surface) calculation as well. I am asking because if you use tkmedit to view the ?h.surface files and load the aparc+aseg or wmparc segmentation volumes in also, the surfaces and the segmentations don't seem to line up. Is there a way to create a segmentation volume that includes partial-volumed voxels at the gray/white and gray/pial boundries?
Thanks
for your help.
Chris Bell
the interior voxels are only included in the volume if they are one of the following in the aseg.mgz:
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:
cheers, Bruce
On Tue, 15 Jul 2008, Marin Richardson wrote:
OK, so aparc.stats is better for cortical gray matter. I want to look at the parcellated white matter volumes as well - is the only/best option to use the wm volumes from wmparc.stats?
Also, when using mris_wm_volume to calculate total white matter, I saw the result defined as the volume within the white matter surface minus non-WM structures? Can you tell me which regions are and are not
included?
Marin
Doug Greve <[EMAIL PROTECTED]> 7/15/2008 12:02 PM >>>It is better to use the aparc as it is derived from surface measurements, which have sub-voxel resolution. The wmparc.stats are generated by counting 1mm^3 voxels.
doug
Marin Richardson wrote:
Hi all, I noticed that the gray volumes for parcellated cortical regionsin wmparc.stats are different from those for the same region in aparc.stats (e.g. ctx-lh-middletemporal = 8419 in wmparc.stats, middletemporal = 9466 in lh.aparc.stats). Why are the values different and which one is a better measure to use?
Thanks, Marin
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In order to help us help you, please follow the steps in:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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We ran a few subjects through recon1, 2, and 3 in an effort to get the volume of the hippocampus bilaterally. We emailed the list to find out if we should use aseg.stats or wmparc.stats. Doug wrote back saying that the hippocampus volumes should be the same. We went back & ran more subjects and they all appear to have a discrepancy between the number of voxels in aseg.stats and wmparc.stats for the hippocampus. Some of the stats are the same-- just the NVoxels and Volume_mm3 differ between the two stat files. we've attached a set of these aseg.stats vs wmparc.stats files. Does anyone have any idea why we might be getting this bug and how we could fix it?
Thanks! Kathy & Margaret
freesurfer@nmr.mgh.harvard.edu
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