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:
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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:
> > 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