Dear Professor Fischl,
Thank you for your support and the support from everyone else. It has been a really pleasant experience so far using Freesurfer and it’s great to know that such a great program has comparatively great support!
We have accessed the NIH repository for normal pediatric brains, and have run the normative data through Freesurfer, then compared it to data outputted from the contracted NIH program, MINC.
These are the results we have obtained so far:
Left
Right
Calculated Total
Frontal
Occipital
Parietal
Temporal
Frontal
Occipital
Parietal
Temporal
Freesurfer
108531
27381
80714
60177
106584
23498
85577
61030
553492
MINC
136241
35980
71381.4
84373.5
133588
32558.9
72250.5
86489.7
652863
By any chance, would you happen to know of any discrepancies between MINC and Freesurfer? In addition, since the NIH website reports their total through MINC as 820,000 while we summed it to be 652,863, do you know what MINC considers grey matter in comparison to what Freesurfer considers grey matter?
Best,
Matt
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, June 23, 2010 5:40 PM To: Schwartz, Carl R.E. Cc: mattku@seas.upenn.edu Subject: Re: [Freesurfer] Grey Matter Density?
Sure, that would be great
On Jun 23, 2010, at 5:21 PM, "Schwartz, Carl R.E." carl_schwartz@hms.harvard.edu wrote:
Bruce, if you want I can answer this with a reference tonight and share a thread between you, me and Kagan re VBM vs. freesurfer that may help.
Carl
On 6/23/10 5:06 PM, "Matthew Ku" mattku@seas.upenn.edu 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
Hi Matt,
I don't know what the MNI considers and whether it includes things we don't, sorry. Bruce On Wed, 30 Jun 2010, Matthew Ku wrote:
Dear Professor Fischl,
Thank you for your support and the support from everyone else. It has been a really pleasant experience so far using Freesurfer and itÿÿs great to know that such a great program has comparatively great support!
We have accessed the NIH repository for normal pediatric brains, and have run the normative data through Freesurfer, then compared it to data outputted from the contracted NIH program, MINC.
These are the results we have obtained so far:
Left
Right Calculated TotalFrontal
Occipital
Parietal
Temporal
Frontal
Occipital
Parietal
Temporal
Freesurfer
108531
27381
80714
60177
106584
23498
85577
61030
553492
MINC
136241
35980
71381.4
84373.5
133588
32558.9
72250.5
86489.7
652863
By any chance, would you happen to know of any discrepancies between MINC and Freesurfer? In addition, since the NIH website reports their total through MINC as 820,000 while we summed it to be 652,863, do you know what MINC considers grey matter in comparison to what Freesurfer considers grey matter?
Best,
Matt
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, June 23, 2010 5:40 PM To: Schwartz, Carl R.E. Cc: mattku@seas.upenn.edu Subject: Re: [Freesurfer] Grey Matter Density?
Sure, that would be great
On Jun 23, 2010, at 5:21 PM, "Schwartz, Carl R.E." carl_schwartz@hms.harvard.edu wrote:
Bruce, if you want I can answer this with a reference tonight and share a thread between you, me and Kagan re VBM vs. freesurfer that may help.
Carl
On 6/23/10 5:06 PM, "Matthew Ku" mattku@seas.upenn.edu 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
Thanks for your prompt response! We'll continue to investigate this discrepancy, but we really appreciate all the help that has been given.
Matt -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, June 30, 2010 5:22 PM To: Matthew Ku Cc: dchinapp@seas.upenn.edu; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Grey Matter Density?
Hi Matt,
I don't know what the MNI considers and whether it includes things we don't, sorry. Bruce On Wed, 30 Jun 2010, Matthew Ku wrote:
Dear Professor Fischl,
Thank you for your support and the support from everyone else. It has been
a really pleasant experience so far using Freesurfer and itÿÿs great to know that such a great program has comparatively great support!
We have accessed the NIH repository for normal pediatric brains, and have
run the normative data through Freesurfer, then compared it to data outputted from the contracted NIH program, MINC.
These are the results we have obtained so far:
Left
Right Calculated TotalFrontal
Occipital
Parietal
Temporal
Frontal
Occipital
Parietal
Temporal
Freesurfer
108531
27381
80714
60177
106584
23498
85577
61030
553492
MINC
136241
35980
71381.4
84373.5
133588
32558.9
72250.5
86489.7
652863
By any chance, would you happen to know of any discrepancies between MINC
and Freesurfer? In addition, since the NIH website reports their total through MINC as 820,000 while we summed it to be 652,863, do you know what MINC considers grey matter in comparison to what Freesurfer considers grey matter?
Best,
Matt
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, June 23, 2010 5:40 PM To: Schwartz, Carl R.E. Cc: mattku@seas.upenn.edu Subject: Re: [Freesurfer] Grey Matter Density?
Sure, that would be great
On Jun 23, 2010, at 5:21 PM, "Schwartz, Carl R.E."
carl_schwartz@hms.harvard.edu wrote:
Bruce, if you want I can answer this with a reference tonight and share a
thread between you, me and Kagan re VBM vs. freesurfer that may help.
Carl
On 6/23/10 5:06 PM, "Matthew Ku" mattku@seas.upenn.edu 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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Matthew Ku