Dear Freesurfer Developers, For my research I'm trying to run the hippocampal subfield segmentation analysis however, I keep running into the following error. I tried to solve it by myself however I had no luck ( I tried by removing the exec flag from the files ).
I'm using the following sofftware Freesurfer : freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1 Ubuntu: 14.04.5 LTS WIndows 10 michel@-:~$ recon-all -s bob -hippocampal-subfields-T1 Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1 Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 michel 1590 1249629 Jan 24 13:40 /usr/local/freesurfer/subjects/bob/scripts/recon-all.log Linux - 3.4.0+ #1 PREEMPT Thu Aug 1 17:06:05 CST 2013 x86_64 x86_64 x86_64 GNU/Linux '/usr/local/freesurfer/bin/recon-all' -> '/usr/local/freesurfer/subjects/bob/scripts/recon-all.local-copy' #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Tue Jan 24 13:43:46 STD 2017 /usr/local/freesurfer/bin/segmentSF_T1.sh /usr/local/freesurfer/MCRv80 /usr/local/freesurfer bob /usr/local/freesurfer/subjects left See log file: /usr/local/freesurfer/subjects/bob/scripts/hippocampal-subfields-T1.log ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/MCRv80/runtime/glnxa64:/usr/local/freesurfer/MCRv80/bin/glnxa64:/usr/local/freesurfer/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64: /usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML: error while loading shared libraries: libut.so: cannot enable executable stack as shared object requires: Invalid argument #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Tue Jan 24 13:43:46 STD 2017 /usr/local/freesurfer/bin/segmentSF_T1.sh /usr/local/freesurfer/MCRv80 /usr/local/freesurfer bob /usr/local/freesurfer/subjects right See log file: /usr/local/freesurfer/subjects/bob/scripts/hippocampal-subfields-T1.log ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/MCRv80/runtime/glnxa64:/usr/local/freesurfer/MCRv80/bin/glnxa64:/usr/local/freesurfer/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64: /usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML: error while loading shared libraries: libut.so: cannot enable executable stack as shared object requires: Invalid argument Started at Tue Jan 24 13:43:45 STD 2017 Ended at Tue Jan 24 13:43:47 STD 2017 #@#%# recon-all-run-time-hours 0.001 recon-all -s bob finished without error at Tue Jan 24 13:43:47 STD 2017 done Sincerely, Michel
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