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
------------------ 原始邮件 ------------------ 发件人: "Bruce Fischl"fischl@nmr.mgh.harvard.edu; 发送时间: 2018年11月18日(星期天) 晚上11:15 收件人: "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu;
主题: 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 CautionDear 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"fischl@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 CautionDear 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"fischl@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 CautionDear 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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