thanks. So there looks to be a pretty dramatic failure in the aseg which is the root of man of your problems. If you upload one of your datasets I'll take a look Bruce

On Mon, 7 May 2012, Zixuan Yang wrote:

Sorry Bruce! Please find the attachment here.

Many thanks! Kind regards,

Zixuan

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Friday, 4 May 2012 10:28 PM To: Zixuan Yang Subject: RE: [Freesurfer] Difficulties in processing cortical thickness with 2 atrophic brains

Hi Zixuan

there was no attachment. Also, can you cc the list so others can answer?

thanks Bruce On Fri, 4 May 2012, Zixuan Yang wrote:

...

Hi Bruce,

Please find the attached aseg images of participant A and B. Many thanks!!!

Kind regards,

Zixuan

From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Friday, 4 May 2012 12:40 PM To: Zixuan Yang Cc: freesurfer@nmr.mgh.harvard.edu; mailman-owner@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Difficulties in processing cortical thickness with 2 atrophic brains

What do the asegs look like?

On May 2, 2012, at 8:18 PM, Zixuan Yang zixuan.yang1@student.unsw.edu.au wrote:

  Dear Freesurfer experts,

   

  I am processing some atrophic brains with Freesurfer. However
  considerable part of 2 participants? brains (WM+GM) is not
  recognized (especially for participant B, the posterior part is
  not processed at all). I have checked the Talairach registration
  of both, only the borderlines of the posterior brain regions
   are not exactly accurate. Then I have tried to add thousands of
  control points and run the <recon-all ?autorecon2-cp ?ssubject name>
  but that doesn?t help.

   

  Please find the attached slides of 2 participants. Could you
  please give me some suggestions for better processing or further
  editing? Many thanks!!

   

  Kind regards,

  Zixuan

   

  --

  Zixuan YANG

   

  Ph.D student
  UNSW School of Psychiatry
  NPI - Euroa Centre, Prince of Wales Hospital Barker Street,
  RANDWICK NSW
  2031 Australia
  Tel: 0405256313

  Email: zixuan.yang1@unsw.edu.au

   

  <Participant A and B for cortical thickness.docx>

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