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: > > ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External 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 > ------------------?0?2?????????0?2------------------ > *??????:*?0?2"Bruce Fischl"<fis...@nmr.mgh.harvard.edu>; > *????????:*?0?22018??11??7??(??????) ????2:42 > *??????:*?0?2"Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>; > *????:*?0?2Re: [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: > > > > > ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution > > > > Dear?0?2Bruce, > > ?0?2 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.. > > ?0?2 ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % > 4 == 0' failed.'' > > ?0?2 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 > > > > ------------------?0?2?????????0?2------------------ > > ??????:?0?2"Bruce Fischl"<fis...@nmr.mgh.harvard.edu>; > > ????????:?0?22018??11??6??(??????) ????9:40 > > ??????:?0?2"Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>; > > ????:?0?2Re: [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: > > > > > > > > ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External 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 > > > > > _______________________________________________ > 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
