External Email - Use Caution
Dear Bruce,
Thank you very much for your reply, I will submit our data set as soon as
possible.
yours yujunjie
------------------ ???????? ------------------
??????: "Bruce Fischl"<fis...@nmr.mgh.harvard.edu>;
????????: 2018??11??18??(??????) ????11:15
??????: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>;
????: Re: [Freesurfer] ?????? ?????? Recon-all run error
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On Sun, 18 Nov
2018,
1013364183 wrote:
>
> External Email - Use Caution
>
> Dear Bruce,
> I am very sorry to bother you. We are currently experimenting with
> freesurfer, but I have
> encountered a lot of problems during the experiment. We have three
> resolutions of data, the skull of
> medium-resolution data can't be removed (neck can't be removed), and with
> high-resolution data, it
> will report memory transfer errors. You said before that we can submit data
> sets to you, how should
> we provide you with data sets?
>
> 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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