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] >>> >> _______________________________________________ >> 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
