Dear Max, It seems that a basic call to mri_robust_register is failing. Can you please try running this command, to make sure that there isn’t a problem with the license? Cheers, /Eugenio
-- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <[email protected]> on behalf of Max Owens <[email protected]> Reply-To: Freesurfer support list <[email protected]> Date: Friday, 22 September 2017 at 22:21 To: "[email protected]" <[email protected]> Subject: [Freesurfer] Problem with New Hippocampus/Amygdala Segmentation 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
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