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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 > > [email protected] > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > >_______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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