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

---

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.

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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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; dchinapp@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-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

---

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