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: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Max Owens owensmax03@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, 22 September 2017 at 22:21 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu 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