External Email - Use Caution

Hello，Bruce I attached my subjects. Please help me. Thank you. Abby 2851A_T1_w4.nii https://drive.google.com/file/d/16rwuarmjHdyV3cImi_Gy0N71aqGytlzO/view?usp=drive_web

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 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

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 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
  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

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 fischl@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 <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
  >       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

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.wanniarachchi@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 https://drive.google.com/file/d/1ZUk9Ss3I8IcZYXUEW4e3bWa-txFUegh1/view?usp=drive_web

On Mon, Apr 22, 2019 at 10:38 PM Bruce Fischl fischl@nmr.mgh.harvard.edu 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 <

fischl@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 <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

...

  >       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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer