Hi All,
Upon reviewing subortical segmentations I see that often a mismatch exists between what appears on the wm.mgz and the color-coded segmented maps.
Precisely - as an example - in the attached figure you can see that in the case of left insula WM, part of the tissue was classified as GM (in brown) in the color-coded segmented map and as WM in the wm.mgz. Contrariwise, the right temporal-parietal GM cortex part of the tissue is classified as WM (in green) the color-coded segmented map and as non-WM in the wm.mgz. The latter occurs in many regions of the brain without a clear anatomical pattern.
I was wondering if this is just a display issue or it rather reflects some mismatch in actual tissue classification with consequential errors in the generated values of thickness and volumes as well?
If so, is there any way I can correct for this?
Thank you in advance,
Antonio
Antonio Gallo, MD
NIB-NINDS-NIH
10 Center Drive
Building 10, Room 5B16
Bethesda, MD, 20892 - USA
ph #: 001-301-402.6391
fax #: 001-301-402.0373
***********************
Hi Antonio,
I wouldn't use the wm.mgz for much of anything. It's really just an intermediate step in the creation of the surfaces. In general we trust the ?h.white and ?h.pial surfaces first, then the aseg.mgz for things like hippocampus, ventricles, etc...
Bruce
On Mon, 25 Jun 2007, Gallo, Antonio (NIH/NINDS) [F] wrote:
Hi All,
Upon reviewing subortical segmentations I see that often a mismatch exists between what appears on the wm.mgz and the color-coded segmented maps.
Precisely - as an example - in the attached figure you can see that in the case of left insula WM, part of the tissue was classified as GM (in brown) in the color-coded segmented map and as WM in the wm.mgz. Contrariwise, the right temporal-parietal GM cortex part of the tissue is classified as WM (in green) the color-coded segmented map and as non-WM in the wm.mgz. The latter occurs in many regions of the brain without a clear anatomical pattern.
I was wondering if this is just a display issue or it rather reflects some mismatch in actual tissue classification with consequential errors in the generated values of thickness and volumes as well?
If so, is there any way I can correct for this?
Thank you in advance,
Antonio
Antonio Gallo, MD
NIB-NINDS-NIH
10 Center Drive
Building 10, Room 5B16
Bethesda, MD, 20892 - USA
ph #: 001-301-402.6391
fax #: 001-301-402.0373
Hi Bruce, Thank you for your quick response.
Our problem, actually, is that when we visualize the aseg.mgz volume (with color-coded subcortical structures) we see that WM is classified as GM (left circle around insula in the figure) and GM is classified as WM (right lower circle in the figure). So, even if the surfaces look good, we are worried about the effects of this misclassification on volume measurements in aseg.mgz.
Thanks,
Antonio
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, June 25, 2007 4:10 PM To: Gallo, Antonio (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation
Hi Antonio,
I wouldn't use the wm.mgz for much of anything. It's really just an intermediate step in the creation of the surfaces. In general we trust
the
?h.white and ?h.pial surfaces first, then the aseg.mgz for things like hippocampus, ventricles, etc...
Bruce
On Mon, 25 Jun 2007, Gallo, Antonio (NIH/NINDS) [F] wrote:
Hi All,
Upon reviewing subortical segmentations I see that often a mismatch exists between what appears on the wm.mgz and the color-coded
segmented
maps.
Precisely - as an example - in the attached figure you can see that
in
the case of left insula WM, part of the tissue was classified as GM
(in
brown) in the color-coded segmented map and as WM in the wm.mgz. Contrariwise, the right temporal-parietal GM cortex part of the
tissue
is classified as WM (in green) the color-coded segmented map and as non-WM in the wm.mgz. The latter occurs in many regions of the brain without a clear anatomical pattern.
I was wondering if this is just a display issue or it rather reflects some mismatch in actual tissue classification with consequential
errors
in the generated values of thickness and volumes as well?
If so, is there any way I can correct for this?
Thank you in advance,
Antonio
Antonio Gallo, MD
NIB-NINDS-NIH
10 Center Drive
Building 10, Room 5B16
Bethesda, MD, 20892 - USA
ph #: 001-301-402.6391
fax #: 001-301-402.0373
Hi Antonio,
that's why we we use the surfaces for white matter and cortical gray matter volume.
cheers, Bruce On Mon, 25 Jun 2007, Gallo, Antonio (NIH/NINDS) [F] wrote:
Hi Bruce, Thank you for your quick response.
Our problem, actually, is that when we visualize the aseg.mgz volume (with color-coded subcortical structures) we see that WM is classified as GM (left circle around insula in the figure) and GM is classified as WM (right lower circle in the figure). So, even if the surfaces look good, we are worried about the effects of this misclassification on volume measurements in aseg.mgz.
Thanks,
Antonio
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, June 25, 2007 4:10 PM To: Gallo, Antonio (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation
Hi Antonio,
I wouldn't use the wm.mgz for much of anything. It's really just an intermediate step in the creation of the surfaces. In general we trust
the
?h.white and ?h.pial surfaces first, then the aseg.mgz for things like hippocampus, ventricles, etc...
Bruce
On Mon, 25 Jun 2007, Gallo, Antonio (NIH/NINDS) [F] wrote:
Hi All,
Upon reviewing subortical segmentations I see that often a mismatch exists between what appears on the wm.mgz and the color-coded
segmented
maps.
Precisely - as an example - in the attached figure you can see that
in
the case of left insula WM, part of the tissue was classified as GM
(in
brown) in the color-coded segmented map and as WM in the wm.mgz. Contrariwise, the right temporal-parietal GM cortex part of the
tissue
is classified as WM (in green) the color-coded segmented map and as non-WM in the wm.mgz. The latter occurs in many regions of the brain without a clear anatomical pattern.
I was wondering if this is just a display issue or it rather reflects some mismatch in actual tissue classification with consequential
errors
in the generated values of thickness and volumes as well?
If so, is there any way I can correct for this?
Thank you in advance,
Antonio
Antonio Gallo, MD
NIB-NINDS-NIH
10 Center Drive
Building 10, Room 5B16
Bethesda, MD, 20892 - USA
ph #: 001-301-402.6391
fax #: 001-301-402.0373
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi
I am interested in measuring the Brain Parenchymal Fraction (BPF) which is defined as follows:
BPF = (total White Matter (WM) Volume + total Gray Matter (GM) Volume) / (total White Matter Volume (WM) + total Gray Matter Volume (GM)+ total CSF volume)
I think I get the White and Gray Matter Volumes for each hemisphere from the command: mris_anatomical_stats. I think the denominator in the BPF equation is just the Intracranial Volume, reported in the aseg.stats file
Would this be an appropriate way to measure these volumes ? Thanks Mehul p.s: For the subject bert the BPF = 1661478/1799364 = 0.92
On 6/25/07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Antonio,
that's why we we use the surfaces for white matter and cortical gray matter volume.
cheers, Bruce On Mon, 25 Jun 2007, Gallo, Antonio (NIH/NINDS) [F] wrote:
Hi Bruce, Thank you for your quick response.
Our problem, actually, is that when we visualize the aseg.mgz volume (with color-coded subcortical structures) we see that WM is classified as GM (left circle around insula in the figure) and GM is classified as WM (right lower circle in the figure). So, even if the surfaces look good, we are worried about the effects of this misclassification on volume measurements in aseg.mgz.
Thanks,
Antonio
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, June 25, 2007 4:10 PM To: Gallo, Antonio (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation
Hi Antonio,
I wouldn't use the wm.mgz for much of anything. It's really just an intermediate step in the creation of the surfaces. In general we trust
the
?h.white and ?h.pial surfaces first, then the aseg.mgz for things like hippocampus, ventricles, etc...
Bruce
On Mon, 25 Jun 2007, Gallo, Antonio (NIH/NINDS) [F] wrote:
Hi All,
Upon reviewing subortical segmentations I see that often a mismatch exists between what appears on the wm.mgz and the color-coded
segmented
maps.
Precisely - as an example - in the attached figure you can see that
in
the case of left insula WM, part of the tissue was classified as GM
(in
brown) in the color-coded segmented map and as WM in the wm.mgz. Contrariwise, the right temporal-parietal GM cortex part of the
tissue
is classified as WM (in green) the color-coded segmented map and as non-WM in the wm.mgz. The latter occurs in many regions of the brain without a clear anatomical pattern.
I was wondering if this is just a display issue or it rather reflects some mismatch in actual tissue classification with consequential
errors
in the generated values of thickness and volumes as well?
If so, is there any way I can correct for this?
Thank you in advance,
Antonio
Antonio Gallo, MD
NIB-NINDS-NIH
10 Center Drive
Building 10, Room 5B16
Bethesda, MD, 20892 - USA
ph #: 001-301-402.6391
fax #: 001-301-402.0373
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
Hi Mehul,
We explicitly label ventricular CSF, but not sulcal CSF (which you pretty much can't do from only a T1 volume). The ICV would give you an approximation of the sum of it all, so yes I think what you are doing is a reasonable approach.
cheers, Bruce
On Thu, 19 Jul 2007, Mehul Sampat wrote:
Hi
I am interested in measuring the Brain Parenchymal Fraction (BPF) which is defined as follows:
BPF = (total White Matter (WM) Volume + total Gray Matter (GM) Volume) / (total White Matter Volume (WM) + total Gray Matter Volume (GM)+ total CSF volume)
I think I get the White and Gray Matter Volumes for each hemisphere from the command: mris_anatomical_stats. I think the denominator in the BPF equation is just the Intracranial Volume, reported in the aseg.stats file
Would this be an appropriate way to measure these volumes ? Thanks Mehul p.s: For the subject bert the BPF = 1661478/1799364 = 0.92
On 6/25/07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Antonio,
that's why we we use the surfaces for white matter and cortical gray matter volume.
cheers, Bruce On Mon, 25 Jun 2007, Gallo, Antonio (NIH/NINDS) [F] wrote:
Hi Bruce, Thank you for your quick response.
Our problem, actually, is that when we visualize the aseg.mgz volume (with color-coded subcortical structures) we see that WM is classified as GM (left circle around insula in the figure) and GM is classified as WM (right lower circle in the figure). So, even if the surfaces look good, we are worried about the effects of this misclassification on volume measurements in aseg.mgz.
Thanks,
Antonio
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, June 25, 2007 4:10 PM To: Gallo, Antonio (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation
Hi Antonio,
I wouldn't use the wm.mgz for much of anything. It's really just an intermediate step in the creation of the surfaces. In general we trust
the
?h.white and ?h.pial surfaces first, then the aseg.mgz for things like hippocampus, ventricles, etc...
Bruce
On Mon, 25 Jun 2007, Gallo, Antonio (NIH/NINDS) [F] wrote:
Hi All,
Upon reviewing subortical segmentations I see that often a mismatch exists between what appears on the wm.mgz and the color-coded
segmented
maps.
Precisely - as an example - in the attached figure you can see that
in
the case of left insula WM, part of the tissue was classified as GM
(in
brown) in the color-coded segmented map and as WM in the wm.mgz. Contrariwise, the right temporal-parietal GM cortex part of the
tissue
is classified as WM (in green) the color-coded segmented map and as non-WM in the wm.mgz. The latter occurs in many regions of the brain without a clear anatomical pattern.
I was wondering if this is just a display issue or it rather reflects some mismatch in actual tissue classification with consequential
errors
in the generated values of thickness and volumes as well?
If so, is there any way I can correct for this?
Thank you in advance,
Antonio
Antonio Gallo, MD
NIB-NINDS-NIH
10 Center Drive
Building 10, Room 5B16
Bethesda, MD, 20892 - USA
ph #: 001-301-402.6391
fax #: 001-301-402.0373
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
Hi Bruce,
Thanks for the quick response. Are there plans to add functionality to label sulcal CSF from T2 images? (Or can I do this easily using some existing script ?) My intuition is that this would be helpful since as brain tissue atrophy occurs in a given neurological disorder (Multiple Sclerosis, aging), one would expect both the ventricular and the sulcal CSF volumes to increase and that we would get a lower estimate of atrophy by measuring only the ventricular CSF ?
Regards, Mehul On 7/19/07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Mehul,
We explicitly label ventricular CSF, but not sulcal CSF (which you pretty much can't do from only a T1 volume). The ICV would give you an approximation of the sum of it all, so yes I think what you are doing is a
reasonable approach.
cheers, Bruce
On Thu, 19 Jul 2007, Mehul Sampat wrote:
Hi
I am interested in measuring the Brain Parenchymal Fraction (BPF) which
is
defined as follows:
BPF = (total White Matter (WM) Volume + total Gray Matter (GM) Volume) / (total White Matter Volume (WM) + total Gray Matter Volume (GM)+ total
CSF
volume)
I think I get the White and Gray Matter Volumes for each hemisphere from
the
command: mris_anatomical_stats. I think the denominator in the BPF equation is just the Intracranial Volume, reported in the aseg.stats file
Would this be an appropriate way to measure these volumes ? Thanks Mehul p.s: For the subject bert the BPF = 1661478/1799364 = 0.92
On 6/25/07, Bruce Fischl <fischl@nmr.mgh.harvard.edu > wrote:
Hi Antonio,
that's why we we use the surfaces for white matter and cortical gray matter volume.
cheers, Bruce On Mon, 25 Jun 2007, Gallo, Antonio (NIH/NINDS) [F] wrote:
Hi Bruce, Thank you for your quick response.
Our problem, actually, is that when we visualize the aseg.mgz volume (with color-coded subcortical structures) we see that WM is
classified
as GM (left circle around insula in the figure) and GM is classified
as
WM (right lower circle in the figure). So, even if the surfaces look good, we are worried about the effects
of
this misclassification on volume measurements in aseg.mgz.
Thanks,
Antonio
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu ] Sent: Monday, June 25, 2007 4:10 PM To: Gallo, Antonio (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation
Hi Antonio,
I wouldn't use the wm.mgz for much of anything. It's really just an intermediate step in the creation of the surfaces. In general we
trust
the
?h.white and ?h.pial surfaces first, then the aseg.mgz for things
like
hippocampus, ventricles, etc...
Bruce
On Mon, 25 Jun 2007, Gallo, Antonio (NIH/NINDS) [F] wrote:
Hi All,
Upon reviewing subortical segmentations I see that often a mismatch exists between what appears on the wm.mgz and the color-coded
segmented
maps.
Precisely - as an example - in the attached figure you can see that
in
the case of left insula WM, part of the tissue was classified as GM
(in
brown) in the color-coded segmented map and as WM in the wm.mgz. Contrariwise, the right temporal-parietal GM cortex part of the
tissue
is classified as WM (in green) the color-coded segmented map and as non-WM in the wm.mgz. The latter occurs in many regions of the
brain
without a clear anatomical pattern.
I was wondering if this is just a display issue or it rather
reflects
some mismatch in actual tissue classification with consequential
errors
in the generated values of thickness and volumes as well?
If so, is there any way I can correct for this?
Thank you in advance,
Antonio
Antonio Gallo, MD
NIB-NINDS-NIH
10 Center Drive
Building 10, Room 5B16
Bethesda, MD, 20892 - USA
ph #: 001-301-402.6391
fax #: 001-301-402.0373
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
we have some prototypes for this, but nothing ready for distribution On Thu, 19 Jul 2007, Mehul Sampat wrote:
Hi Bruce,
Thanks for the quick response. Are there plans to add functionality to label sulcal CSF from T2 images? (Or can I do this easily using some existing script ?) My intuition is that this would be helpful since as brain tissue atrophy occurs in a given neurological disorder (Multiple Sclerosis, aging), one would expect both the ventricular and the sulcal CSF volumes to increase and that we would get a lower estimate of atrophy by measuring only the ventricular CSF ?
Regards, Mehul On 7/19/07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Mehul,
We explicitly label ventricular CSF, but not sulcal CSF (which you pretty much can't do from only a T1 volume). The ICV would give you an approximation of the sum of it all, so yes I think what you are doing is a
reasonable approach.
cheers, Bruce
On Thu, 19 Jul 2007, Mehul Sampat wrote:
Hi
I am interested in measuring the Brain Parenchymal Fraction (BPF) which
is
defined as follows:
BPF = (total White Matter (WM) Volume + total Gray Matter (GM) Volume) / (total White Matter Volume (WM) + total Gray Matter Volume (GM)+ total
CSF
volume)
I think I get the White and Gray Matter Volumes for each hemisphere from
the
command: mris_anatomical_stats. I think the denominator in the BPF equation is just the Intracranial Volume, reported in the aseg.stats file
Would this be an appropriate way to measure these volumes ? Thanks Mehul p.s: For the subject bert the BPF = 1661478/1799364 = 0.92
On 6/25/07, Bruce Fischl <fischl@nmr.mgh.harvard.edu > wrote:
Hi Antonio,
that's why we we use the surfaces for white matter and cortical gray matter volume.
cheers, Bruce On Mon, 25 Jun 2007, Gallo, Antonio (NIH/NINDS) [F] wrote:
Hi Bruce, Thank you for your quick response.
Our problem, actually, is that when we visualize the aseg.mgz volume (with color-coded subcortical structures) we see that WM is
classified
as GM (left circle around insula in the figure) and GM is classified
as
WM (right lower circle in the figure). So, even if the surfaces look good, we are worried about the effects
of
this misclassification on volume measurements in aseg.mgz.
Thanks,
Antonio
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu ] Sent: Monday, June 25, 2007 4:10 PM To: Gallo, Antonio (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation
Hi Antonio,
I wouldn't use the wm.mgz for much of anything. It's really just an intermediate step in the creation of the surfaces. In general we
trust
the
?h.white and ?h.pial surfaces first, then the aseg.mgz for things
like
hippocampus, ventricles, etc...
Bruce
On Mon, 25 Jun 2007, Gallo, Antonio (NIH/NINDS) [F] wrote:
> Hi All, > > Upon reviewing subortical segmentations I see that often a mismatch > exists between what appears on the wm.mgz and the color-coded
segmented
> maps. > > Precisely - as an example - in the attached figure you can see that
in
> the case of left insula WM, part of the tissue was classified as GM
(in
> brown) in the color-coded segmented map and as WM in the wm.mgz. > Contrariwise, the right temporal-parietal GM cortex part of the
tissue
> is classified as WM (in green) the color-coded segmented map and as > non-WM in the wm.mgz. The latter occurs in many regions of the
brain
> without a clear anatomical pattern. > > > > I was wondering if this is just a display issue or it rather
reflects
> some mismatch in actual tissue classification with consequential
errors
> in the generated values of thickness and volumes as well? > > If so, is there any way I can correct for this? > > > > Thank you in advance, > > > > Antonio > > > > > > Antonio Gallo, MD > > NIB-NINDS-NIH > > 10 Center Drive > > Building 10, Room 5B16 > > Bethesda, MD, 20892 - USA > > ph #: 001-301-402.6391 > > fax #: 001-301-402.0373 > > *********************** > > > >
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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Gallo, Antonio (NIH/NINDS) [F] -
Mehul Sampat