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 <abbytang0...@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 <fis...@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
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>
>
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