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
> >
> >
> >
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