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.wanniarach...@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 <fis...@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 < >> 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 >> > > >> 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 > >
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