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Dear there,
I tried to process “Segmentation of thalamic nuclei” using source the FreeSurfer development version(freesurfer-linux-centos6_x86_64-dev.tar.gz).
The OS of my notebook CentOS (6.10).
MATLAB --> /usr/local/MATLAB/R2017b
MRCv84 --> /usr/local/freesurfer/MCRv84
I filled out “segmentThalamicNuclei.sh bert [SUBJECTS_DIR].
In my notebook, there were the messages below.
Best,
Gwang-Won Kim
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[GW@gwkim 002_T1T2_Hippo]$ segmentThalamicNuclei.sh /002_T1T2_HippoSetting ITK threads to 1
#--------------------------------------------
#@# Thalamic Nuclei processing 2019. 06. 23. (일) 23:30:47 KST
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is .:/usr/lib64:/usr/local/freesurfer/MCRv84//runtime/glnxa64:/usr/local/freesurfer/MCRv84//bin/glnxa64:/usr/local/freesurfer/MCRv84//sys/os/glnxa64:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /usr/local/freesurfer/MCRv84//bin/glnxa64/libmwi18n.so)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /usr/local/freesurfer/MCRv84//bin/glnxa64/libmwservices.so)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /usr/local/freesurfer/MCRv84//bin/glnxa64/libmwctfpackage.so)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /usr/local/freesurfer/MCRv84//bin/glnxa64/libboost_date_time.so.1.49.0)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /usr/local/freesurfer/MCRv84//bin/glnxa64/libboost_thread.so.1.49.0)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /usr/local/freesurfer/MCRv84//bin/glnxa64/libut.so)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /usr/local/freesurfer/MCRv84//bin/glnxa64/libmwfl.so)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /usr/local/freesurfer/MCRv84//bin/glnxa64/libmwmlutil.so)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /usr/local/freesurfer/MCRv84//bin/glnxa64/libmwsettingscore.so)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /usr/local/freesurfer/MCRv84//bin/glnxa64/libmwms.so)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /usr/local/freesurfer/MCRv84//bin/glnxa64/libmwopccore.so)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /usr/local/freesurfer/MCRv84//bin/glnxa64/libmwopcmodel.so)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /usr/local/freesurfer/MCRv84//bin/glnxa64/libmwopczippackage.so)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /usr/local/freesurfer/MCRv84//bin/glnxa64/libmwopcmwservices.so)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /usr/local/freesurfer/MCRv84//bin/glnxa64/libboost_serialization.so.1.49.0)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /usr/local/freesurfer/MCRv84//bin/glnxa64/libboost_log.so.1.49.0)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /usr/local/freesurfer/MCRv84//bin/glnxa64/libboost_log_setup.so.1.49.0)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /usr/local/freesurfer/MCRv84//bin/glnxa64/libPocoFoundation.so.21)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /usr/local/freesurfer/MCRv84//bin/glnxa64/libboost_regex.so.1.49.0)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /usr/local/freesurfer/MCRv84//bin/glnxa64/libboost_signals.so.1.49.0)
/usr/local/freesurfer/bin/SegmentThalamicNuclei: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /usr/local/freesurfer/MCRv84//bin/glnxa64/libmwflnetwork.so)
@#@FSTIME 2019:06:23:23:30:47 run_SegmentThalamicNuclei.sh N 13 e 1.20 S 0.05 U 0.01 P 5% M 1452 F 102 R 4039 W 0 c 45 w 234 I 21648 O 0 L 0.01 0.02 0.00
@#@FSLOADPOST 2019:06:23:23:30:48 run_SegmentThalamicNuclei.sh N 13 0.01 0.02 0.00
1
Linux gwkim 2.6.32-754.14.2.el6.x86_64 #1 SMP Tue May 14 19:35:42 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
Thalamic nuclei exited with ERRORS at 2019. 06. 23. (일) 23:30:48 KST
For more details, see the log file /home/GW/test//002_T1T2_Hippo/scripts/thalamic-nuclei-mainFreeSurferT1.log
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