Hello Aaron,
The build timestamp from the output below shows mri_convert is from 8/2014. When I look at the build timestamp on our stable 5.3 version of mri_convert I see it is from 5/2013. So the version that you listed is about 1 year newer than the 5.3 release I can see. It is possible that someone downloaded a daily/dev build of freesurfer at that time.
You might want to consider running the latest 6.0 release of Freesurfer (released in January 2017), which should be fine on CentOS 7. It can be downloaded from, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
I also suggest that you start out in a default/clean shell, set FREESURFER_HOME, and then source the setup script for linux, You can see the instructions on that same web page under “Setup and Configuration”. The setup steps should work for version 5 or 6.
- rob
On Jun 12, 2018, at 2:43 PM, Aaron Tanenbaum <aaron.b.tanenbaum@gmail.commailto:aaron.b.tanenbaum@gmail.com> wrote:
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I checked my system is not encrypted. I had someone else run the command on the same machine. It worked for them. So I changed my BASH environment to a default environment. I still get the same error.
I tried this again but with a different FreeSurfer 5.3. turns out the one I was using has been altered version of FreeSurfer. I do not know how it was altered. It worked. so it has to do with the altered FreeSurfer. I ran the command mri_convert -version on both FreeSurfer.
for the unaltered i get the out put mri_convert -version stable5 altered version i get mri_convert -version dev build (use --all-info flag for full version info)
with this output i type in mri_convert --all-info mri_convert ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/06/12-18:32:17-GMT BuildTimeStamp: Aug 22 2014 21:04:47 CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ User: tanenbauma Machine: rocky Platform: Linux PlatformVersion: 3.10.0-862.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Wondering is this version of mri_convert a developmental version? Also both version are the CentOS 6 build.
On Tue, Jun 12, 2018 at 1:01 PM Dicamillo, Robert <RDICAMILLO@mgh.harvard.edumailto:RDICAMILLO@mgh.harvard.edu> wrote: Hello Aaron,
You could check to see if the CentOS 7 system is using disk encryption, e.g., if the following command return 1, then it would mean encryption is in use (which can be an issue with FreeSurfer).
$ cat /proc/sys/crypto/fips_enabled
If it returns zero, it could be an issue with a system library like glibc on CentOS 7.5 (that does not happen on older versions of CentOS).
Either way, this is not your doing ;-)
On Jun 12, 2018, at 11:51 AM, Aaron Tanenbaum <aaron.b.tanenbaum@gmail.commailto:aaron.b.tanenbaum@gmail.com> wrote:
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I am currently running CentOS 7.5 and attempting to run FreeSurfer 5.3. When i get to the part where MRI_convert is creating the the orig001.mgz its gives me a segmentation fault. if i run this on a centos 6 system it works fine. below is the output of the program.
/data/gizmo/data1/freesurfer5.3/bin/mri_convert /data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm /data/anlab/Aaron/JoEtzl_testing/FreeSurfer/Test1/mri/orig/001.mgz $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm... crypt_gkey = (null) Segmentation fault (core dumped)
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