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Hello Alex, I would try unseting LD_LIBRARY_PATH altogether or at least take the matlab paths out of it. My understanding is freesurfer commands don't need matlab paths in LD_LIBRARY_PATH to use matlab after you have setup the freesurfer environment (set FREESURFER_HOME, and source’d the freesurfer setup script). It looks like the matlab libraries in LD_LIBRARY_PATH are overriding other binaries trying to find the system libc with the symbols they need (and are instead finding the matlab copy of the system libraries). - R.
On May 27, 2020, at 23:22, Alexandru Hanganu <hanganu.alexandru@gmail.com> wrote: External Email - Use Caution Hello FreeSurfer Developers,I attemting to run brainstem/ hippocampus/ thalamus segmentation with FS 7.1 and there seems to be a problem with environment variables. Based on comments on other forums, I cannot install GlibC (if this is the case) since it's a cluster. Are there any methods that can be used to avoid this limitation?FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.0Platform: CentOS Linux 7 (Core)uname -a: Linux cedar5.cedar.computecanada.ca 3.10.0-1062.12.1.el7.x86_64 #1 SMP Tue Feb 4 23:02:59 UTC 2020 x86_64 GNU/Linuxerror:Setting up environment variables---grep: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time referenceLD_LIBRARY_PATH is .:/lib64:/home/user/freesurfer/MCRv84//runtime/glnxa64:/home/user/freesurfer/MCRv84//bin/glnxa64:/home/user/freesurfer/MCRv84//sys/os/glnxa64:/home/user/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/home/user/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/home/userfreesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/home/userfreesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/opt/software/slurm/libod: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time referencetr: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time referenceRegistering imageDump.mgz to mask from ASEGcp: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time referencegzip: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time referenceERROR: problem reading fnameSWITCH expression must be a scalar or string constant.Error in myMRIread>load_mgh (line 550)Error in myMRIread>myMRIread_aux (line 92)Error in myMRIread (line 63)Error in SegmentThalamicNuclei (line 278)MATLAB:badSwitchExpressionrm: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time reference255Best regards,Alex_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer