Re: [Freesurfer] volumes in wmparc.stats vs. aparc.stats

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