Re: [Freesurfer] CORRECTING DEFECT 1 problem

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Dear Freesurfer experts,

I frequently get correcting defect error. It seems freezing the recon-all after the defect and it won't run thereafter. Due to this error, I can not use most of the data for connectome analysis. Can you please tell me how to get rid of this?

I have attached a picture FYI.

Best regards, Ruwan

On Mon, Apr 22, 2019 at 11:10 AM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

sorry, I've been traveling On Mon, 22 Apr 2019, Abby tang wrote:

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Hi BruceI did't get your reply message yet. I have send the subject

file to you. Could you give me

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your advises? Thank you for your help. Abby

Abby tang abbytang0925@gmail.com 于2019年4月19日周五 上午8:32写道： Hello，BruceI attached my subjects. Please help me. Thank you. Abby [icon_10_generic_list.png] 2851A_T1_w4.nii[IMAGE]

Bruce Fischl fischl@nmr.mgh.harvard.edu 于2019年4月18日周四 下午10:53写道： Hi Abby

  it's hard to tell from the image, but it looks like there is a big

I/S

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  bias field as well as large amounts of pathology.

  If you upload the subject to our ftp site we will take a look

  cheers
  Bruce
  On Thu, 18 Apr
  2019, Abby
  tang wrote:

  >
  >         External Email - Use Caution
  >
  > Hello FreeSurfer Developers,
  >
  > I'm attempting to recon_all my subjects which is .nii file. But

I usually meet

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  this error.
  >
  > CORRECTING DEFECT 0 (vertices=67, convex hull=73, v0=950)
  > After retessellation of defect 0 (v0=950), euler #=20

(87340,255044,167724) :

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  difference with theory
  >  (-32) = -52
  >
  > CORRECTING DEFECT 1 (vertices=46367, convex hull=8524, v0=962)
  > Segmentation fault (core dumped)
  > Linux abby-virtual-machine 4.15.0-47-generic #50-Ubuntu SMP Wed

Mar 13 10:44:52

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  UTC 2019 x86_64 x86_
  > 64 x86_64 GNU/Linux
  >
  > recon-all -s 2851A_T1_w4 exited with ERRORS at Thu Apr 18

20:25:16 CST 2019

...

  >
  > To report a problem, see

http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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  >
  > I check files in blow command and attached picture.
  >
  > freeview -v 2851A_T1_w4/mri/norm.mgz -f

2851A_T1_w4/surf/lh.orig.nofix

...

  2851A_T1_w4/surf/lh.inflated.
  > nofix
  >
  > almost all of subjects go wrong. I need your help.
  >
  > please give some advises with program statements in detail.
  >
  > I really appreciate your help
  >
  > 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev.tar.gz
  > 2) Platform: ubuntu 18
  > 3) recon-all.log:see attached
  >
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