In freesurfer, is there any way to run a gray/white matter segmentation within the cortex? Thanks, Sasha
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what does that mean? On Mon, 26 Feb 2007, Sasha Wolosin wrote:
In freesurfer, is there any way to run a gray/white matter segmentation within the cortex? Thanks, Sasha
Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Well, since at the neuronal level there is some degree of white matter present in the cortex, in whole brain segmentation cortical gray matter is often reported (plus subcortical gray), which is different from the freesurfer output of cortical "gray matter volume" because it may exclude small amounts of white matter embedded within the cortex. We would like to know if there is any way to obtain a comparable measure in freesurfer.
Bruce Fischl fischl@nmr.mgh.harvard.edu 2/26/2007 3:49 PM >>>
what does that mean? On Mon, 26 Feb 2007, Sasha Wolosin wrote:
In freesurfer, is there any way to run a gray/white matter
segmentation
within the cortex? Thanks, Sasha
Disclaimer: The materials in this e-mail are private and may contain Protected
Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
you can certainly get cortical gray by using the ?h.cortex.label that's generated automatically by the new mris_make_surfaces. The whole notion of a gray/white boundary is a myth. There's about 1/2mm of slack in which there are gradually more and more cell bodies (moving up from the wm) until it's only cell bodies and no wm.
On Mon, 26 Feb 2007, Sasha Wolosin wrote:
Well, since at the neuronal level there is some degree of white matter present in the cortex, in whole brain segmentation cortical gray matter is often reported (plus subcortical gray), which is different from the freesurfer output of cortical "gray matter volume" because it may exclude small amounts of white matter embedded within the cortex. We would like to know if there is any way to obtain a comparable measure in freesurfer.
Bruce Fischl fischl@nmr.mgh.harvard.edu 2/26/2007 3:49 PM >>>
what does that mean? On Mon, 26 Feb 2007, Sasha Wolosin wrote:
In freesurfer, is there any way to run a gray/white matter
segmentation
within the cortex? Thanks, Sasha
Disclaimer: The materials in this e-mail are private and may contain Protected
Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Ok, thanks. Is the new mris_make_surfaces included with the latest release?
Bruce Fischl fischl@nmr.mgh.harvard.edu 2/26/2007 5:29 PM >>>
you can certainly get cortical gray by using the ?h.cortex.label that's
generated automatically by the new mris_make_surfaces. The whole notion of a gray/white boundary is a myth. There's about 1/2mm of slack in which
there are gradually more and more cell bodies (moving up from the wm) until it's only cell bodies and no wm.
On Mon, 26 Feb 2007, Sasha Wolosin wrote:
Well, since at the neuronal level there is some degree of white
matter
present in the cortex, in whole brain segmentation cortical gray
matter
is often reported (plus subcortical gray), which is different from
the
freesurfer output of cortical "gray matter volume" because it may exclude small amounts of white matter embedded within the cortex.
We
would like to know if there is any way to obtain a comparable measure
in
freesurfer.
Bruce Fischl fischl@nmr.mgh.harvard.edu 2/26/2007 3:49 PM >>>
what does that mean? On Mon, 26 Feb 2007, Sasha Wolosin wrote:
In freesurfer, is there any way to run a gray/white matter
segmentation
within the cortex? Thanks, Sasha
Disclaimer: The materials in this e-mail are private and may contain Protected
Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If
you
are not the intended recipient, be advised that any unauthorized
use,
disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited.
If
you have received this e-mail in error, please immediately notify
the
sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sasha,
Freesurfer v3.0.4 (and 3.0.5) has the new mris_make_surfaces which generates the ?h.cortex.label file stored in the subject's label directory.
Nick
On Mon, 2007-02-26 at 17:53 -0500, Sasha Wolosin wrote:
Ok, thanks. Is the new mris_make_surfaces included with the latest release?
Bruce Fischl fischl@nmr.mgh.harvard.edu 2/26/2007 5:29 PM >>>
you can certainly get cortical gray by using the ?h.cortex.label that's
generated automatically by the new mris_make_surfaces. The whole notion of a gray/white boundary is a myth. There's about 1/2mm of slack in which
there are gradually more and more cell bodies (moving up from the wm) until it's only cell bodies and no wm.
On Mon, 26 Feb 2007, Sasha Wolosin wrote:
Well, since at the neuronal level there is some degree of white
matter
present in the cortex, in whole brain segmentation cortical gray
matter
is often reported (plus subcortical gray), which is different from
the
freesurfer output of cortical "gray matter volume" because it may exclude small amounts of white matter embedded within the cortex.
We
would like to know if there is any way to obtain a comparable measure
in
freesurfer.
Bruce Fischl fischl@nmr.mgh.harvard.edu 2/26/2007 3:49 PM >>>
what does that mean? On Mon, 26 Feb 2007, Sasha Wolosin wrote:
In freesurfer, is there any way to run a gray/white matter
segmentation
within the cortex? Thanks, Sasha
Disclaimer: The materials in this e-mail are private and may contain Protected
Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If
you
are not the intended recipient, be advised that any unauthorized
use,
disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited.
If
you have received this e-mail in error, please immediately notify
the
sender via telephone or return e-mail.
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
it should be in the current stable (check to see if your subjects' label dir has it) On Mon, 26 Feb 2007, Sasha Wolosin wrote:
Ok, thanks. Is the new mris_make_surfaces included with the latest release?
Bruce Fischl fischl@nmr.mgh.harvard.edu 2/26/2007 5:29 PM >>>
you can certainly get cortical gray by using the ?h.cortex.label that's
generated automatically by the new mris_make_surfaces. The whole notion of a gray/white boundary is a myth. There's about 1/2mm of slack in which
there are gradually more and more cell bodies (moving up from the wm) until it's only cell bodies and no wm.
On Mon, 26 Feb 2007, Sasha Wolosin wrote:
Well, since at the neuronal level there is some degree of white
matter
present in the cortex, in whole brain segmentation cortical gray
matter
is often reported (plus subcortical gray), which is different from
the
freesurfer output of cortical "gray matter volume" because it may exclude small amounts of white matter embedded within the cortex.
We
would like to know if there is any way to obtain a comparable measure
in
freesurfer.
Bruce Fischl fischl@nmr.mgh.harvard.edu 2/26/2007 3:49 PM >>>
what does that mean? On Mon, 26 Feb 2007, Sasha Wolosin wrote:
In freesurfer, is there any way to run a gray/white matter
segmentation
within the cortex? Thanks, Sasha
Disclaimer: The materials in this e-mail are private and may contain Protected
Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If
you
are not the intended recipient, be advised that any unauthorized
use,
disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited.
If
you have received this e-mail in error, please immediately notify
the
sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Nick Schmansky -
Sasha Wolosin