Hi Matt,
you could use mri_binarize to extract a gray matter binarization then go from there, although we've never put together scripts to do it since the biological intepretation is always hard. Are you interested in subcortical volumes or just cortical? If cortical, why not look at surface area and thickness independently?
cheers Bruce On Wed, 23 Jun 2010, Matthew Ku wrote:
Dear Professor Fischl,
Thanks a lot for your prompt response.
We are trying to compute the grey matter density because we are analyzing the maturation of grey matter, as referred to by N. Gogtay et al. (Dynamic mapping of human cortical development during childhood though early adulthood).
From Freesurfer's output, we have only noticed grey matter volume. However, would there be a way to obtain the grey matter mass through an ROI mask without having to use SPM or FSL?
Thanks again, Matt
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, June 23, 2010 3:20 PM To: Matthew Ku Cc: dchinapp@seas.upenn.edu; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Grey Matter Density?
Hi Matt,
density is really just average gray matter per unit volume. Why would you want to compute such a thing? I think the way SPM/FSL does it is to take a binary segmentation and smooth it, but you can check with them.
cheers Bruce On Wed, 23 Jun 2010, Matthew Ku wrote:
Hi Freesurfer Experts,
I have been running Freesurfer to calculate the grey matter volume of pediatric brains but I was wondering if there was a method to determine grey matter density using Freesurfer? I have read a question previously posted asking a similar question, but there had been no replies or answers. If there is no command to calculate the density of grey matter, is there any alternate method to determine the density from
the volume data?
Thanks,
Matt
Matthew Ku
University of Pennsylvania
School of Engineering Class of 2013
(845) 596-3840
mattku@seas.upenn.edu
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