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To: freesurfer@nmr.mgh.harvard.edu
Sent: Thu, July 1, 2010 12:20:58 AM
Subject: Freesurfer Digest, Vol 76, Issue 58
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Today's Topics:
1. tksurfer bus error (Nai Ding)
2. Re: Grey Matter Density? (Matthew Ku)
----------------------------------------------------------------------
Message: 1
Date: Wed, 30 Jun 2010 15:37:47 -0400
From: Nai Ding <
gahding@gmail.com>
Subject: [Freesurfer] tksurfer bus error
To:
freesurfer@nmr.mgh.harvard.eduCc: ccamero2-contact ~ <
sepranagw@yahoo.com>
Message-ID:
<
AANLkTimFZf6O12yqCEGu6lscO0kYhXZ-Lo2roomwRQor@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi everyone,
We installed Freesurfer on our Mac system.
freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0-full
Everything works except tksurfer.
When we try
> tksurfer bert rh pial
Freesurfer returns
> surfer: current subjects dir: /Applications/freesurfer/subjects
> Bus error
How could we fix the problem?
Thanks a lot,
Nai
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Message: 2
Date: Wed, 30 Jun 2010 17:20:49 -0400
From: "Matthew Ku" <
mattku@seas.upenn.edu>
Subject: Re: [Freesurfer] Grey Matter Density?
To: "'Bruce Fischl'" <
fischl@nmr.mgh.harvard.edu>
Cc:
freesurfer@nmr.mgh.harvard.edu,
dchinapp@seas.upenn.eduMessage-ID: <001501cb189a$1fbde540$5f39afc0$@seas.upenn.edu>
Content-Type: text/plain; charset="utf-8"
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.eduSubject: 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.eduSubject: 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>>
>>
>>
>>
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