Right, but is there a way I can fix the subcortical structures so that I can get accurate measures of them?
-Eric -----Original Message----- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wed 8/9/2006 12:29 PM To: Faden, Eric (NIH/NIMH) [F] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Non Human Primate (Macaque) Subcortical Hi Eric, that's what it's supposed to do. It's really not a bias correction in the way N3 is - it's more of a filtering for the purpose of cortical segmentation. cheers, Bruce On Wed, 9 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote: > I am working on running some scans through FreeSurfer. I have scans at both > 0.5mm and 0.8mm that have all been skull stripped and N3 corrected. The > images have good contrast in general and specifically are fairly good in the > subcortical regions. I am skipping a bunch of the FreeSurfer pipeline and > bringing my scans directly into the mri_normalize step. I have been running > it with the -monkey option and a set of about 25 to 50 control points in > various areas of white matter. The normalization yields very good contrast > in cortex, but basically removes any sign of gray matter in the sub cortical > region (e.g. it basically all winds up with a value of 110). Is there any > way to combat this problem? > > -Eric > > _______________________________________________ > 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
