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
>       >       >
>       >       >_______________________________________________
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>       >
>       >
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