External Email - Use Caution
Dear Greve,
Thank you very much for your reply.Where is the tutorial for checking for and
fixing defects? Is it the link below?
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFixV6.0
yours yujunjie
------------------ ???????? ------------------
??????: "Greve, Douglas N.,Ph.D."<dgr...@mgh.harvard.edu>;
????????: 2018??11??15??(??????) ????5:12
??????: "freesurfer@nmr.mgh.harvard.edu"<freesurfer@nmr.mgh.harvard.edu>;
????: Re: [Freesurfer]?????? ?????? Recon-all run error
It looks like you might have a very big defect. Probably there is a bit
of skull or cerebellum still attached. Follow the tutorial for checking
for and fixing defects.
On 11/14/2018 02:59 AM, 1013364183 wrote:
>
> External Email - Use Caution
>
> Dear Bruce Fischl,
> I am very sorry that I have not reply to you last week.
> Our data has been running for a few weeks, but the computer did not
> react. There is a log file in the attachment. We want to ask that
> could you help us run the data? We will send you a set of data
> firstly(We still have two sets of data). If you can help us run our
> high resolution data, we will be very grateful. And can we write your
> name in the acknowledgments section? Our tutor is now at Boston
> Children's Hospital (BCH). If possible, she would like to consult you
> in person.
> The download link is:
> https://drive.google.com/file/d/1_5tYKHipNOTFe96p4BOMc1kbNPK1O93W/view?usp=drive_web
> https://drive.google.com/file/d/12TZ0_J_njiZju9PDyvwxnHIiDe8D5SOA/view?usp=drive_web
>
> Looking forward to your reply.
> Thanks in advance
>
> yours yujunjie
> ------------------ ???????? ------------------
> *??????:* "Bruce Fischl"<fis...@nmr.mgh.harvard.edu>;
> *????????:* 2018??11??7??(??????) ????2:42
> *??????:* "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>;
> *????:* Re: [Freesurfer] ?????? Recon-all run error
>
> does it occur if you run it outside of recon-all? Do you have enough free
> ram? If so, you can filedrop us the dataset and we can try to
> replicate and
> fit ix.
>
> On Tue, 6 Nov 2018, 1013364183 wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear Bruce,
> > I found the error location in the recon-all.log folder. Here is
> the place where it went wrong??I
> > don't think it's the reason for insufficient memory..
> > ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz %
> 4 == 0' failed.''
> > This data is ok when we run with versions prior to freesurfer 6.0.
> But after we run the 6.0
> > version and set the expert file, this error will occur.Do I need to
> step through the instructions to
> > see the problem? How should this error be solved?
> >
> > Thanks in advance
> >
> > yours yujunjie
> >
> > ------------------ ???????? ------------------
> > ??????: "Bruce Fischl"<fis...@nmr.mgh.harvard.edu>;
> > ????????: 2018??11??6??(??????) ????9:40
> > ??????: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>;
> > ????: Re: [Freesurfer] Recon-all run error
> >
> > that certainly looks like something is running out of ram. Can you run
> > the command that failed directly on the command line and see if it
> works?
> > Was anything else running on the machine at the time? We do report total
> > and free memory at the start of the recon in the recon-all.log file
> >
> > cheers
> > Bruce
> > On Tue,
> > 6 Nov 2018, 1013364183 wrote:
> >
> > >
> > > External Email - Use Caution
> > >
> > > Dear FS,
> > > When we run ??recon-all?? with a 5GB high-resolution image, core
> dumped appears when the
> > mri_convert
> > > command is executed. The specific errors are as follows:
> > > /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3:
> 29235 Aborted (core dumped)
> > > mri_convert.bin "$@"
> > > ERROR: converting to minc
> > > We want to know if our high resolution image is too large for
> freesurfer to handle, or our
> > computer
> > > memory (64GB running memory) is limited.
> > >
> > > Thanks a lot in advance!
> > > yours sincerely,
> > > yu junjie
> > >
> > >
> > >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
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