Dear Freesurfers, Reading the surface segmentation paper, Dale et al 1999, it says that in freesurfer the grey/white matter boundary is detected first based on voxel intensity, and then by fitting locally a plane of list variance. Is there a way to use that data to assess how clear cut the grey/white border is? For example, to distinguish the superior temporal gyrus, which has often a very distinct GM/WM border, from the precentral gyrus, which is often more blurry? thank you in advance! roberto
Hi Roberto, you are probably better off using the surfaces for this. You can sample inside and outside the gray/white surface and compute the contrast that way using mri_vol2surf.
cheers, Bruce
On Mon, 1 Jun 2009, roberto toro wrote:
Dear Freesurfers, Reading the surface segmentation paper, Dale et al 1999, it says that in freesurfer the grey/white matter boundary is detected first based on voxel intensity, and then by fitting locally a plane of list variance. Is there a way to use that data to assess how clear cut the grey/white border is? For example, to distinguish the superior temporal gyrus, which has often a very distinct GM/WM border, from the precentral gyrus, which is often more blurry? thank you in advance! roberto _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
There's a script called pctsurfcon which will compute the percent gray/white contrast at each vertex on the surface.
doug
Bruce Fischl wrote:
Hi Roberto, you are probably better off using the surfaces for this. You can sample inside and outside the gray/white surface and compute the contrast that way using mri_vol2surf.
cheers, Bruce
On Mon, 1 Jun 2009, roberto toro wrote:
Dear Freesurfers, Reading the surface segmentation paper, Dale et al 1999, it says that in freesurfer the grey/white matter boundary is detected first based on voxel intensity, and then by fitting locally a plane of list variance. Is there a way to use that data to assess how clear cut the grey/white border is? For example, to distinguish the superior temporal gyrus, which has often a very distinct GM/WM border, from the precentral gyrus, which is often more blurry? thank you in advance! roberto _______________________________________________ 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 Doug,
I can't find the script in my version of freesurfer (freesurfer-Darwin-leopard-i686-stable-pub-v4.2.0).... does it also work by sampling above and below the white matter surface?
thanks, roberto
On Mon, Jun 1, 2009 at 6:00 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
There's a script called pctsurfcon which will compute the percent gray/white contrast at each vertex on the surface.
doug
Bruce Fischl wrote:
Hi Roberto, you are probably better off using the surfaces for this. You can sample inside and outside the gray/white surface and compute the contrast that way using mri_vol2surf.
cheers, Bruce
On Mon, 1 Jun 2009, roberto toro wrote:
Dear Freesurfers, Reading the surface segmentation paper, Dale et al 1999, it says that in freesurfer the grey/white matter boundary is detected first based on voxel intensity, and then by fitting locally a plane of list variance. Is there a way to use that data to assess how clear cut the grey/white border is? For example, to distinguish the superior temporal gyrus, which has often a very distinct GM/WM border, from the precentral gyrus, which is often more blurry? thank you in advance! roberto _______________________________________________ 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
Thank you Bruce!
I will try sampling 1mm above and bellow the surface using mri_vol2surf --projdist mmdist -1 and --projdist mmdist 1, and trilinear interpolation. Should also check that I'm not sampling beyond the grey matter... roberto
On Mon, Jun 1, 2009 at 5:49 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Roberto, you are probably better off using the surfaces for this. You can sample inside and outside the gray/white surface and compute the contrast that way using mri_vol2surf.
cheers, Bruce
On Mon, 1 Jun 2009, roberto toro wrote:
Dear Freesurfers, Reading the surface segmentation paper, Dale et al 1999, it says that in freesurfer the grey/white matter boundary is detected first based on voxel intensity, and then by fitting locally a plane of list variance. Is there a way to use that data to assess how clear cut the grey/white border is? For example, to distinguish the superior temporal gyrus, which has often a very distinct GM/WM border, from the precentral gyrus, which is often more blurry? thank you in advance! roberto _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
roberto toro