External Email - Use Caution Dear Bruce, I am sorry to let you wait so long, I have some troubles in transferring the data set, but it has been solved. Now I have sent the data set to ftp. I hope you can take the time to help us deal with the data set. We have already Running this data set for a long time but did not get results, the name of the data set is data_Yujunjie.zip,. The run command and the expert file are in the attachment.
Express your heartfelt thanks again?? 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 Instructions on how you can upload tarred and gzipped files here: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange 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 > > > > > _______________________________________________ > 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
expert.opts
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recon-all.txt
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