Hi PPJ and all,
I found that the 5.2 – 5.1 difference is primarily seen in the cortical thickness, and much less so in the aseg.volume.
Here, I picked right-amygdala volume as an example of aseg.volume and rh_bankssts_thickness as an example of rh.aparc.thickness.
While the correlation between the two versions of right-amygdala is r = .92 (n = 161), that of the rh_bankssts_thickness is r = .45.
Presumably I believe the correlation should be > .90 for a strong continuity between the two versions?
Do you have anything in the cortical thickness?
Daniel
--Yung-Jui "Daniel" Yang, PhDPostdoctoral ResearcherYale Child Study CenterNew Haven, CT
Date: Wednesday, April 10, 2013 11:07 AM
To: Daniel Yang <yung-jui.yang@yale.edu>
Cc: Bruce Fischl <fischl@nmr.mgh.harvard.edu>, "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
Ok, I'll try to put together a stat from aparc too.
---------------------------------------------------------------------
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
On Wed, Apr 10, 2013 at 12:04 PM, Yang, Daniel <yung-jui.yang@yale.edu> wrote:
Hi PPJ,
Thanks! It looks interesting. I also found FS 5.2 is faster. Is there any chance you could also provide the cortical thickness of the 2009 atlas (e.g., rh)?
I will take a look into the aseg.volume in my data too.
Best,Daniel
--Yung-Jui "Daniel" Yang, PhDPostdoctoral ResearcherYale Child Study CenterNew Haven, CT
From: Pedro Paulo de Magalhães Oliveira Junior <ppj@netfilter.com.br>
Date: Wednesday, April 10, 2013 10:49 AM
To: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Cc: Daniel Yang <yung-jui.yang@yale.edu>, "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
You'll find attached some preliminary data of the comparison we did among versions.
---------------------------------------------------------------------
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
On Wed, Apr 10, 2013 at 10:42 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi PPJThat's exactly what we are doing. Good to hear its stable for youBruce
I have processed more that 600 brains with both versions in the last weeks and the only difference I'm seeing between version 5.2.0 and 5.1, besides the obvious new features, is processing time.
Version 5.2 is 10% faster than 5.1 in an Amazon EC2 instance.
Besides that there's no visible difference in terms of cortical thickness, volumes, etc.
If you have access to computer resources to spare you can run recon-all of both versions in some well known database of images and do a more formal test.
---------------------------------------------------------------------
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
On Wed, Apr 10, 2013 at 8:11 AM, Yang, Daniel <yung-jui.yang@yale.edu> wrote:
Dear FreeSurfer Experts and Users,
Did anyone find similar things using FS 5.2 (please see my previous post
below)? That is, FS 5.2 is including more non-cortical "black spaces"
within pial surfaces, compared to FS 5.1?
I'm not interested in nitpicking but I feel this is a rather serious
issue, so I would like to raise it again before it's completely forgotten.
At the meantime I keep receiving Emails from people asking me this issue.
Thanks!
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
On 3/19/13 7:07 AM, "Yang, Daniel" <yung-jui.yang@yale.edu> wrote:
>
>Posting one of the brains.
>
>https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn
>
>
>It seems to me that neither version is perfect; however, 5.2.0 is
>capturing more "black spaces" in the region I'm looking at.
>
>It's in the right hemisphere, TAL coordinate about ~ (44, -46, 20).
>
>Given that the correlation between 5.1.0 and 5.2.0 is r = .33 in the
>region I examined with my samples, it's not a systematic "predictable"
>bias.
>
>Any solution?
>
>--
>Yung-Jui "Daniel" Yang, PhD
>Postdoctoral Researcher
>Yale Child Study Center
>New Haven, CT
>(203) 737-5454
>
>
>
>
>
>
>On 3/18/13 6:27 PM, "Matt Glasser" <matt@ma-tea.com> wrote:
>
>>Do the surfaces look correct in these regions? You might post some
>>screenshots of subjects who have a big difference between 5.1 and 5.2
>>with
>>the 5.1 and 5.2 white and pial surfaces on volume slices that highlight
>>the difference. Without this kind of info, its hard to know which was
>>more correct, 5.1 or 5.2.
>>
>>Peace,
>>
>>Matt.
>>
>>On 3/18/13 5:13 PM, "Ritobrato Datta" <ridatta@mail.med.upenn.edu> wrote:
>>
>>>I concur. I have seen similar results in primary visual cortex from ~40
>>>subjects. While fs 5.1 estimated mean thickness in the range of 1.5 to
>>>1.9 in V1, fs 5.2 is giving me V1 thickness in the range of 2 to 2.3.
>>>
>>>Ritobrato Datta, Ph.D.
>>>Post Doctoral Researcher
>>>Department of Neurology
>>>University of Pennsylvania School of Medicine
>>>3rd Floor, Room 312
>>>3710 Hamilton Walk (Goddard Laboratories)
>>>Philadelphia, PA 19104-6241
>>>email - ridatta@mail.med.upenn.edu
>>>
>>>
>>>----- Original Message -----
>>>From: Daniel Yang <yung-jui.yang@yale.edu>
>>>To: freesurfer@nmr.mgh.harvard.edu
>>>Sent: Mon, 18 Mar 2013 17:44:44 -0400 (EDT)
>>>Subject: [Freesurfer] Very different results between 5.1.0 and 5.2.0
>>>
>>>Dear FreeSurfer Experts,
>>>
>>>I ran FreeSurfer 5.1.0 and FreeSurfer 5.2.0 on identical set of 161
>>>subjects, and I'm interested in rh_superior_temporal_sulcus_thickness in
>>>particular.
>>>
>>>Previously, the mean thickness is 2.24 mm in 5.1.0; now it is 3.28 mm in
>>>5.2.0. They are significantly different, t(160) = 56.71.
>>>
>>>The correlation between the two versions is r = .33
>>>
>>>Is this something possible?? I can't see what went wrong in my
>>>procedures.
>>>
>>>Thanks!
>>>Daniel
>>>
>>>--
>>>Yung-Jui "Daniel" Yang, PhD
>>>Postdoctoral Researcher
>>>Yale Child Study Center
>>>New Haven, CT
>>>(203) 737-5454
>>>
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>>>
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>>>it
>>>is
>>>addressed. If you believe this e-mail was sent to you in error and the
>>>contains patient information, please contact the Partners Compliance
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>>>
>>
>>
>
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