Hi, I am interested in measuring the cortical thickness in entorhinal cortex. I can display the thickness measurement by " tkmedit AD1232 brain.mgz lh.white " to look at the measurement in entorhinal region, but I don't know the boundary of entorhinal cortex by this way. Is there any way that I can only display the measurement of cortical thckness in the entorhinal cortex? Thanks,
Antao
Hi Antao,
if you are using the new FreeSurfer, there will be a ?h.aparc.annot file for each hemi (from Rahul Desikan and Ron Killiany's recently accepted paper), and entorhinal is one of the parcellation units in it.
cheers, Bruce
On Wed, 18 Jan 2006, Antao Du wrote:
Hi, I am interested in measuring the cortical thickness in entorhinal cortex. I can display the thickness measurement by " tkmedit AD1232 brain.mgz lh.white " to look at the measurement in entorhinal region, but I don't know the boundary of entorhinal cortex by this way. Is there any way that I can only display the measurement of cortical thckness in the entorhinal cortex? Thanks,
Antao
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
Yes, I used new freesurfer and I can get the cortical thickness in entorhinal cortex. But one control subject had very small entorhinal volume, therefore, I want to check the bourdary of entorhinal cortex during the surface measurement. Do you know how to display it?
Thanks,
Antao
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, January 18, 2006 11:45 AM To: Antao Du Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Display of thickness measurement
Hi Antao,
if you are using the new FreeSurfer, there will be a ?h.aparc.annot file for each hemi (from Rahul Desikan and Ron Killiany's recently accepted paper), and entorhinal is one of the parcellation units in it.
cheers, Bruce
On Wed, 18 Jan 2006, Antao Du wrote:
Hi, I am interested in measuring the cortical thickness in
entorhinal
cortex. I can display the thickness measurement by " tkmedit AD1232 brain.mgz lh.white " to look at the measurement in
entorhinal region,
but I don't know the boundary of entorhinal cortex by this way. Is there any way that I can only display the measurement of cortical thckness in the entorhinal cortex? Thanks,
Antao
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
if you have the surfaces loaded you can load the annotation into tkmedit directly (or tksurfer for that matter)
On Wed, 18 Jan 2006, Antao Du wrote:
Hi Bruce,
Yes, I used new freesurfer and I can get the cortical thickness in entorhinal cortex. But one control subject had very small entorhinal volume, therefore, I want to check the bourdary of entorhinal cortex during the surface measurement. Do you know how to display it?
Thanks,
Antao
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, January 18, 2006 11:45 AM To: Antao Du Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Display of thickness measurement
Hi Antao,
if you are using the new FreeSurfer, there will be a ?h.aparc.annot file for each hemi (from Rahul Desikan and Ron Killiany's recently accepted paper), and entorhinal is one of the parcellation units in it.
cheers, Bruce
On Wed, 18 Jan 2006, Antao Du wrote:
Hi, I am interested in measuring the cortical thickness in
entorhinal
cortex. I can display the thickness measurement by " tkmedit AD1232 brain.mgz lh.white " to look at the measurement in
entorhinal region,
but I don't know the boundary of entorhinal cortex by this way. Is there any way that I can only display the measurement of cortical thckness in the entorhinal cortex? Thanks,
Antao
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, I've generally been successful in using control points to get the white surfaces into darker areas, where the white matter appears similar to grey matter. I'm wandering if it's possible to use control points (or any other remedy) to get make the white matter segmentation less 'harsh', i.e., for some of my images, the white surface seems to consistently eat into the grey matter, so I wonder if it's possible to lower the threshold of what it calls grey in some way. Thanks Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
can you send an image showing what you mean? On Wed, 1 Feb 2006, Fornito, Alexander wrote:
Hi, I've generally been successful in using control points to get the white surfaces into darker areas, where the white matter appears similar to grey matter. I'm wandering if it's possible to use control points (or any other remedy) to get make the white matter segmentation less 'harsh', i.e., for some of my images, the white surface seems to consistently eat into the grey matter, so I wonder if it's possible to lower the threshold of what it calls grey in some way. Thanks Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
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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Antao Du -
Bruce Fischl -
Fornito, Alexander