Re: [Freesurfer] sum of WM and GM coming out to be bigger than ICV after recon-all

Hi Sue, mri_segstats does not compute the eTIV itself, it just gets it from the transform matrix. doug

On 07/18/2012 09:33 AM, Susan Ruiz wrote:

Hi Bruce, Nick, Muhammad et al.,

I noticed that there is an updated mri_segstats for download in the release notes on the wiki, but that appears to be for the SupraTentorial Volume rather than the eTIV. If the patch is available, that would be greatly appreciated (and preferable to running everyone through 5.0). Muhammad--thanks for your question about this since we had not noticed!

Thanks all, ~Sue

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Susan M. M. Ruiz, Ph.D. Boston University School of Medicine Laboratory for Neuropsychology VA Boston Healthcare System smosher@bu.edu mailto:smosher@bu.edu

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On Jul 17, 2012, at 9:50 AM, Bruce Fischl wrote:

...

Hi Sue

you could take the eTIV from 5.0 and the aparc stats from 5.1.0. I believe we already distribute the updated template but it's not used. Nick: do you want to send around a patch to recon-all that people can use before 5.2 comes out?

thanks Bruce

On Tue, 17 Jul 2012, Susan Ruiz wrote:

...

Hi all, Using previous versions of FreeSurfer, we have used the eTIV as a covariate for our volumetric analyses. We have been using the eTIV numbers from 5.1.0 for new studies. What would you recommend using for subjects who have been run with 5.1.0? Can you make the template available publicly, or would it be legitimate to take the eTIV from 5.0 and the aparc stats from 5.1.0? Thanks, ~Sue

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Susan M. M. Ruiz, Ph.D. Boston University School of Medicine Laboratory for Neuropsychology VA Boston Healthcare System smosher@bu.edu mailto:smosher@bu.edu

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On Jul 16, 2012, at 4:17 PM, Bruce Fischl wrote:

 can you send us an example? In the ones we've looked at the 

older versions were more stable. Alternatively, we can send you a new template that Avi Snyder generated that you could try out

 cheers
 Bruce

 On Mon, 16 Jul 2012, Ayaz, Muhammad wrote:

       Well, I am using version 5.1.0. I have had same issue in 

fewer subjects when I used the older version as well. Any comments about that?

       -----Original Message-----

       From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu]

       Sent: Monday, July 16, 2012 3:04 PM

       To: Ayaz, Muhammad

       Cc: freesurfer@nmr.mgh.harvard.edu 

mailto:freesurfer@nmr.mgh.harvard.edu

       Subject: Re: [Freesurfer] sum of WM and GM coming out to 

be bigger than ICV after recon-all

       Hi Ayaz

       what version are you running? There appears to be an 

instability in the

       eTIV calculation in just version 5.1 (not before or in 

the upcoming 5.2)

       cheers

       Bruce

       On

       Mon, 16 Jul 2012, Ayaz, Muhammad wrote:

             Dear All,



             After running recon-all, I noticed several subjects 

that sum of WM and GM is

             bigger  than ICV. I have re-run these subjects and 

the results is the same

             sum of GM and WM is coming out to be bigger than ICV.

             Any suggestions? I need to calculate normalized 

volumes.

             Regards

             Ayaz

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