Hi, Just had a couple of questions re: the -pvvol flag in mri_segstats: How does it take account of partial voluming? Is there anyway to visualize what the partial volume-corrected volume would look like? Would you recmmoned using this falg routinely to obtain subcortical volumes?
Finally, on a completely unrelated question, is there any reason to think that surfaces created using the same freesurfer distribution on a Mac would be incompatible with those created using a Linux machine (ie., would you be able to pool them for one study without any problems, and could you start creating surfaces on one, and then re-run afdter manual edits on the other?)
Thanks, Alex
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thu 9/15/2005 10:11 AM To: Bruce Fischl Cc: Fornito, Alexander; freesurfer@nmr.mgh.harvard.edu; Tracy Wang Subject: RE: [Freesurfer] intensity normalization failure
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
Hi Alex,
the -pvol flag assumes ever border voxel is a linear combination of the class that it is labeled as and another class that it borders. The local class means are computed by as the sample mean in a local window of all non border voxels of that class.
The mac and linux version should be compatible, as long as you make sure they are the same version of the software.
cheers, Bruce
On Fri, 16 Sep 2005, Fornito, Alexander wrote:
Hi, Just had a couple of questions re: the -pvvol flag in mri_segstats: How does it take account of partial voluming? Is there anyway to visualize what the partial volume-corrected volume would look like? Would you recmmoned using this falg routinely to obtain subcortical volumes?
Finally, on a completely unrelated question, is there any reason to think that surfaces created using the same freesurfer distribution on a Mac would be incompatible with those created using a Linux machine (ie., would you be able to pool them for one study without any problems, and could you start creating surfaces on one, and then re-run afdter manual edits on the other?)
Thanks, Alex
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thu 9/15/2005 10:11 AM To: Bruce Fischl Cc: Fornito, Alexander; freesurfer@nmr.mgh.harvard.edu; Tracy Wang Subject: RE: [Freesurfer] intensity normalization failure
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 -
Fornito, Alexander