External Email - Use Caution 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 < rdicami...@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.tanenb...@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? > _______________________________________________ > 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 > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. >
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