Re: [Freesurfer] CORRECTING DEFECT 1 problem

[Bruce Fischl]

Hi Abby

it's hard to tell from the image, but it looks like there is a big I/S 
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 
this error.

CORRECTING DEFECT 0 (vertices=67, convex hull=73, v0=950)
After retessellation of defect 0 (v0=950), euler #=20 (87340,255044,167724) : 
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 
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

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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Re: [Freesurfer] CORRECTING DEFECT 1 problem

[Abby tang]

External Email - Use Caution

Hello，Bruce
I attached my subjects. Please help me.
Thank you.
Abby
 2851A_T1_w4.nii


Bruce Fischl  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
> 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 this error.
> >
> > CORRECTING DEFECT 0 (vertices=67, convex hull=73, v0=950)
> > After retessellation of defect 0 (v0=950), euler #=20
> (87340,255044,167724) : 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 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
> >
> > 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
> >
> >___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] CORRECTING DEFECT 1 problem

[Abby tang]

External Email - Use Caution

Hi Bruce
I did't get your reply message  yet. I have send the subject file to you.
Could you give me your advises?
Thank you for your help.
Abby

Abby tang  于2019年4月19日周五 上午8:32写道：

> Hello，Bruce
> I attached my subjects. Please help me.
> Thank you.
> Abby
>  2851A_T1_w4.nii
> 
>
> Bruce Fischl  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
>> 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 this error.
>> >
>> > CORRECTING DEFECT 0 (vertices=67, convex hull=73, v0=950)
>> > After retessellation of defect 0 (v0=950), euler #=20
>> (87340,255044,167724) : 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 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
>> >
>> > 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
>> >
>> >___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] CORRECTING DEFECT 1 problem

[Bruce Fischl]

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



External Email - Use Caution

Hi BruceI did't get your reply message  yet. I have send the subject file to 
you. Could you give me
your advises?
Thank you for your help.
Abby

Abby tang  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  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
  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
  this error.
  >
  > CORRECTING DEFECT 0 (vertices=67, convex hull=73, v0=950)
  > After retessellation of defect 0 (v0=950), euler #=20 
(87340,255044,167724) :
  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
  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
  >
  > 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
  >
  >___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] CORRECTING DEFECT 1 problem

[Pradeepa Ruwan]

External Email - Use Caution

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 
wrote:

> sorry, I've been traveling
> On Mon, 22 Apr 2019, Abby tang wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi BruceI did't get your reply message  yet. I have send the subject
> file to you. Could you give me
> > your advises?
> > Thank you for your help.
> > Abby
> >
> > Abby tang  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  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
> >   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
> >   this error.
> >   >
> >   > CORRECTING DEFECT 0 (vertices=67, convex hull=73, v0=950)
> >   > After retessellation of defect 0 (v0=950), euler #=20
> (87340,255044,167724) :
> >   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
> >   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
> >   >
> >   > 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
> >   >
> >   >___
> >   Freesurfer mailing list
> >   Freesurfer@nmr.mgh.harvard.edu
> >   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] CORRECTING DEFECT 1 problem

[Bruce Fischl]

Hi Ruwan

have you looked at the data? Can you tell us what the acquisition 
parameters are or send us a 3-plane image of the norm.mgz with the 
lh.orig.nofix and rh.orig.nofix surfaces? The big defects are usually a 
symptom of something else


cheers
Bruce
On Mon, 22 Apr 2019, Pradeepa 
Ruwan 
wrote:




External Email - Use Caution

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

  >
  > External Email - Use Caution
  >
  > Hi BruceI did't get your reply message  yet. I have send the subject 
file to you.
  Could you give me
  > your advises?
  > Thank you for your help.
  > Abby
  >
  > Abby tang  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  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
  >       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
  >       this error.
  >       >
  >       > CORRECTING DEFECT 0 (vertices=67, convex hull=73, v0=950)
  >       > After retessellation of defect 0 (v0=950), euler #=20 
(87340,255044,167724) :
  >       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
  >       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
  >       >
  >       > 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
  >       >
  >       >___
  >       Freesurfer mailing list
  >       Freesurfer@nmr.mgh.harvard.edu
  >       https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  >
  >
  >___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] CORRECTING DEFECT 1 problem

[Pradeepa Ruwan]

External Email - Use Caution

Dear Prof.Bruce,

I am sending my raw data and the images that you requested to send.
I have two datasets that I got trouble with.
I appreciate if you can take a look at this data.
Thank you very much in advance.

Best regards,
Ruwan
 Freesurfer-ruwan.zip





On Mon, Apr 22, 2019 at 10:38 PM Bruce Fischl 
wrote:

> Hi Ruwan
>
> have you looked at the data? Can you tell us what the acquisition
> parameters are or send us a 3-plane image of the norm.mgz with the
> lh.orig.nofix and rh.orig.nofix surfaces? The big defects are usually a
> symptom of something else
>
> cheers
> Bruce
> On Mon, 22 Apr 2019, Pradeepa
> Ruwan
> wrote:
>
> >
> > External Email - Use Caution
> >
> > 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 <
> fis...@nmr.mgh.harvard.edu> wrote:
> >   sorry, I've been traveling
> >   On Mon, 22 Apr 2019, Abby tang wrote:
> >
> >   >
> >   > External Email - Use Caution
> >   >
> >   > Hi BruceI did't get your reply message  yet. I have send the
> subject file to you.
> >   Could you give me
> >   > your advises?
> >   > Thank you for your help.
> >   > Abby
> >   >
> >   > Abby tang  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  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
> >   >   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
> >   >   this error.
> >   >   >
> >   >   > CORRECTING DEFECT 0 (vertices=67, convex hull=73, v0=950)
> >   >   > After retessellation of defect 0 (v0=950), euler #=20
> (87340,255044,167724) :
> >   >   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
> >   >   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
> >   >   >
> >   >   > 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
> >   >   >
> >   >   >___
> >   >   Freesurfer mailing list
> >   >   Freesurfer@nmr.mgh.harvard.edu
> >   >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >   >
> >   >
> >   >___
> >   Freesurfer mailing list
> >   Freesurfer@nmr.mgh.harvard.edu
> >   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >___
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Re: [Freesurfer] CORRECTING DEFECT 1 problem

[Pradeepa Ruwan]

External Email - Use Caution

Hello,
Have you got some time to check my data?
I appreciate if you can give me some advices.
Thank you very much.

Ruwan

On Tue, Apr 23, 2019 at 7:41 PM Pradeepa Ruwan <
pradee.wanniarach...@gmail.com> wrote:

> Dear Prof.Bruce,
>
> I am sending my raw data and the images that you requested to send.
> I have two datasets that I got trouble with.
> I appreciate if you can take a look at this data.
> Thank you very much in advance.
>
> Best regards,
> Ruwan
>  Freesurfer-ruwan.zip
> 
>
>
>
>
> On Mon, Apr 22, 2019 at 10:38 PM Bruce Fischl 
> wrote:
>
>> Hi Ruwan
>>
>> have you looked at the data? Can you tell us what the acquisition
>> parameters are or send us a 3-plane image of the norm.mgz with the
>> lh.orig.nofix and rh.orig.nofix surfaces? The big defects are usually a
>> symptom of something else
>>
>> cheers
>> Bruce
>> On Mon, 22 Apr 2019, Pradeepa
>> Ruwan
>> wrote:
>>
>> >
>> > External Email - Use Caution
>> >
>> > 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 <
>> fis...@nmr.mgh.harvard.edu> wrote:
>> >   sorry, I've been traveling
>> >   On Mon, 22 Apr 2019, Abby tang wrote:
>> >
>> >   >
>> >   > External Email - Use Caution
>> >   >
>> >   > Hi BruceI did't get your reply message  yet. I have send the
>> subject file to you.
>> >   Could you give me
>> >   > your advises?
>> >   > Thank you for your help.
>> >   > Abby
>> >   >
>> >   > Abby tang  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  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
>> >   >   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
>> >   >   this error.
>> >   >   >
>> >   >   > CORRECTING DEFECT 0 (vertices=67, convex hull=73,
>> v0=950)
>> >   >   > After retessellation of defect 0 (v0=950), euler #=20
>> (87340,255044,167724) :
>> >   >   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
>> >   >   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
>> >   >   >
>> >   >   > 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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>> >   >
>> >   >
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>>