How do you want to measure them? For example when we generate (human) subcortical segmentations we do *not* use the output of mri_normalize - it is only for cortical.
On Wed, 9 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote:
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:fischl@nmr.mgh.harvard.edu] 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
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