External Email - Use Caution
Hello Yujunjie, Bruce,
This file in the packages archive, ./netcdf_3_6_0_p1/putget.c, has an assertion at line 322 that looks like the failure. I don't know this code, but something is going wrong trying to fill the buffer, e.g., maybe it works for smaller images but not for larger images ? It could be that older version of freesurfer used a different version of netcdf. I've attached a screenshot of the code.
You could try setting all the soft limits for the shell to be unlimited, e.g., in bash,
$ ulimit -c unlimited
1013364183 November 5, 2018 at 21:22 via Postbox 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
External Email - Use Caution
Dear fsbuild, Thank you very much for your help, I will try to enter this line of statements and then run high-resolution data, but I did not find the putget.c file, is it under the installation of freesurfer file, or a system file.
yours yujunjie
------------------ 原始邮件 ------------------ 发件人: "fsbuild"fsbuild@contbay.com; 发送时间: 2018年11月6日(星期二) 中午11:50 收件人: "freesurfer"freesurfer@nmr.mgh.harvard.edu;
主题: Re: [Freesurfer]回复： Recon-all run error
External Email - Use Caution
Hello Yujunjie, Bruce,
This file in the packages archive, ./netcdf_3_6_0_p1/putget.c, has an assertion at line 322 that looks like the failure. I don't know this code, but something is going wrong trying to fill the buffer, e.g., maybe it works for smaller images but not for larger images ? It could be that older version of freesurfer used a different version of netcdf. I've attached a screenshot of the code.
You could try setting all the soft limits for the shell to be unlimited, e.g., in bash, $ ulimit -c unlimited
1013364183 November 5, 2018 at 21:22 via Postbox
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
freesurfer@nmr.mgh.harvard.edu
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1013364183 -
fsbuild