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:[EMAIL PROTECTED]
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:[EMAIL PROTECTED]
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
[EMAIL PROTECTED]
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