Hi Freesurfer Experts, I'm trying to run the new version 6.0 hippocampus/amygdala segmentation procedure (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields) on data from subjects with whom I have already completed recon-all. I have downloaded the newest development version (and license), as well as the required matlab runtime. However, I am getting the following error:
“LD_LIBRARY_PATH is .:freesurfer/MCRv80//runtime/glnxa64:freesurfer/MCRv80//bin/glnxa64:freesurfer/MCRv80//sys/os/glnxa64:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64/server:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64/client:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64: Registering imageDump.mgz to hippocampal mask from ASEG cp: cannot stat ‘freesurfer/average/HippoSF/atlas/AtlasDump.mgz’: No such file or directory Error using myMRIread (line 16) Error in myMRIread: temporary directory does not exist Error in segmentSubjectT1_autoEstimateAlveusML (line 134) Command exited with non-zero status 255 @#@FSTIME 2017:09:22:15:55:53 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 2.85 S 0.11 U 2.85 P 103% M 205292 F 1 R 22759 W 0 c 2477 w 641 I 0 O 63584 L 0.41 0.56 0.64 @#@FSLOADPOST 2017:09:22:15:55:56 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.41 0.56 0.64 All done! ” Have you ever seen this error before? If not, can you provide any suggestions for ways that I might troubleshoot it? I have attached the command I used and the error log if this is of help. Thanks very much for your time, Max -- Max Owens, M.S. Graduate Student in Psychology Clinical Neuroscience Lab University of Georgia
------------------------------ USER cns HOST nic PROCESSID 3392 PROCESSOR x86_64 OS Linux Linux nic 4.4.0-79-generic #100~14.04.1-Ubuntu SMP Fri May 19 18:36:51 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux ------------------------------ #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Fri Sep 22 15:55:49 EDT 2017 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:freesurfer/MCRv80//runtime/glnxa64:freesurfer/MCRv80//bin/glnxa64:freesurfer/MCRv80//sys/os/glnxa64:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64/server:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64/client:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64: Registering imageDump.mgz to hippocampal mask from ASEG cp: cannot stat ‘freesurfer/average/HippoSF/atlas/AtlasDump.mgz’: No such file or directory Error using myMRIread (line 16) Error in myMRIread: temporary directory does not exist Error in segmentSubjectT1_autoEstimateAlveusML (line 145) Command exited with non-zero status 255 @#@FSTIME 2017:09:22:15:55:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 3.68 S 0.19 U 2.99 P 86% M 203156 F 12 R 23139 W 0 c 3076 w 722 I 384 O 63584 L 0.36 0.55 0.63 @#@FSLOADPOST 2017:09:22:15:55:53 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.41 0.56 0.64 #-------------------------------------------- #@# Hippocampal Subfields processing (T1) right Fri Sep 22 15:55:53 EDT 2017 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:freesurfer/MCRv80//runtime/glnxa64:freesurfer/MCRv80//bin/glnxa64:freesurfer/MCRv80//sys/os/glnxa64:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64/server:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64/client:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64: Registering imageDump.mgz to hippocampal mask from ASEG cp: cannot stat ‘freesurfer/average/HippoSF/atlas/AtlasDump.mgz’: No such file or directory Error using myMRIread (line 16) Error in myMRIread: temporary directory does not exist Error in segmentSubjectT1_autoEstimateAlveusML (line 134) Command exited with non-zero status 255 @#@FSTIME 2017:09:22:15:55:53 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 2.85 S 0.11 U 2.85 P 103% M 205292 F 1 R 22759 W 0 c 2477 w 641 I 0 O 63584 L 0.41 0.56 0.64 @#@FSLOADPOST 2017:09:22:15:55:56 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.41 0.56 0.64
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