Is it possible to obtain and intensity histogram of the wm voxels, or descriptive stats (eg., Mean, SD) as a quick check?
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 15, 2005 3:33 AM To: Tracy Wang Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] intensity normalization failure
if it succeeds then the intensity in the wm should be exactly 110 over much of the brain, and 90<wm<120 pretty much everywhere
Bruce
On Wed, 14 Sep 2005, Tracy Wang wrote:
Hi
What is a typical example of when the intensity normalization process
fails?
Does the over-all image seem brighter? What is a good indicator of
success
or failure?
Thanks, Tracy
Tracy Wang Research Assistant Cognitive Neuroscience Laboratory
Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang@artsci.wustl.edu
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
should be easy enough to do in matlab. Just load the wm volume, then find all the T1 voxels that are nonzero in it.
Bruce On Thu, 15 Sep 2005, Fornito, Alexander wrote:
Is it possible to obtain and intensity histogram of the wm voxels, or descriptive stats (eg., Mean, SD) as a quick check?
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 15, 2005 3:33 AM To: Tracy Wang Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] intensity normalization failure
if it succeeds then the intensity in the wm should be exactly 110 over much of the brain, and 90<wm<120 pretty much everywhere
Bruce
On Wed, 14 Sep 2005, Tracy Wang wrote:
Hi
What is a typical example of when the intensity normalization process
fails?
Does the over-all image seem brighter? What is a good indicator of
success
or failure?
Thanks, Tracy
Tracy Wang Research Assistant Cognitive Neuroscience Laboratory
Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang@artsci.wustl.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You should be able to use mri_segstats somehow. You'll need a segmentation, though. You could tell it to report on the aseg wm values. You could also use the fill volume (127 and 255?). Check out the --help
doug
On Wed, 14 Sep 2005, Bruce Fischl wrote:
should be easy enough to do in matlab. Just load the wm volume, then find all the T1 voxels that are nonzero in it.
Bruce On Thu, 15 Sep 2005, Fornito, Alexander wrote:
Is it possible to obtain and intensity histogram of the wm voxels, or descriptive stats (eg., Mean, SD) as a quick check?
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 15, 2005 3:33 AM To: Tracy Wang Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] intensity normalization failure
if it succeeds then the intensity in the wm should be exactly 110 over much of the brain, and 90<wm<120 pretty much everywhere
Bruce
On Wed, 14 Sep 2005, Tracy Wang wrote:
Hi
What is a typical example of when the intensity normalization process
fails?
Does the over-all image seem brighter? What is a good indicator of
success
or failure?
Thanks, Tracy
Tracy Wang Research Assistant Cognitive Neuroscience Laboratory
Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang@artsci.wustl.edu
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 -
Doug Greve -
Fornito, Alexander