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.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.com> wrote:

External Email - Use Caution

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)

Did I do anything wrong?

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