I'll help Bruce out here :) See Panizzon et al, Cerebral Cortex, 2009, 19:2728-35 http://www.ncbi.nlm.nih.gov/pubmed/19299253
and Winkler et al, Neuroimage, 2009 (in press) http://www.ncbi.nlm.nih.gov/pubmed/20006715 cheers, -MH On Wed, 2010-06-23 at 17:06 -0400, Matthew Ku wrote: > Dear Professor Fischl, > > Thank you for your suggestions. We have used mri_binarize before with > success and we are interested with both the cortical and subcortical > volumes. > > However, we would appreciate it if you could clarify why you suggested for > us to consider surface area and thickness independently, and how we should > use those values in a reportable method. If possible, could you direct us to > any relevant literature that would help us understand why we should use > these values independently? > > Thanks for all the help. > > Best, > Matt > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Wednesday, June 23, 2010 3:47 PM > To: Matthew Ku > Cc: freesurfer@nmr.mgh.harvard.edu; dchin...@seas.upenn.edu > Subject: Re: [Freesurfer] Grey Matter Density? > > 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-boun...@nmr.mgh.harvard.edu > > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce > > Fischl > > Sent: Wednesday, June 23, 2010 3:20 PM > > To: Matthew Ku > > Cc: dchin...@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 > >> > >> mat...@seas.upenn.edu > >> > >> > >> > >> > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the person to whom > > it is addressed. If you believe this e-mail was sent to you in error > > and the e-mail contains patient information, please contact the > > Partners Compliance HelpLine at http://www.partners.org/complianceline > > . If the e-mail was sent to you in error but does not contain patient > > information, please contact the sender and properly dispose of the e-mail. > > > > > > > > > _______________________________________________ > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
