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Hi,
I have this error when I try to run segmentHA_T1.sh It seems that it sets up the wrong DYLD_LIBRARY_PATH, the one I have in my bash_profile is /Applications/MATLAB_R2016a.app/bin/maci64:/Applications/MATLAB_R2016a.app/sys/os/maci64:/Applications/MATLAB_R2016a.app/bin/maci64:/Applications/MATLAB_R2016a.app/sys/os/maci64:
[~/val...V/003_SAG_3D_IR] $ segmentHA_T1.sh sujeto_uno #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Tue Oct 30 12:04:16 CET 2018 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv84//runtime/maci64:/Applications/freesurfer/MCRv84//bin/maci64:/Applications/freesurfer/MCRv84//sys/os/maci64: dyld: Library not loaded: @loader_path/libmwmclmcrrt.8.0.dylib Referenced from: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML Reason: image not found /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 38: 7887 Abort trap: 6 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $args #--------------------------------------------
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It seems it could be a version conflict. Please try unsetting DYLD_LIBRARY_PATH. Cheers, /Eugenio
-- Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) Department of Medical Physics and Biomedical Engineering University College London http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Jaime Gomez borriquear@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 30 October 2018 at 11:10 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] segmentHA_T1 error DYLD_LIBRARY_PATH
External Email - Use Caution
Hi,
I have this error when I try to run segmentHA_T1.sh It seems that it sets up the wrong DYLD_LIBRARY_PATH, the one I have in my bash_profile is /Applications/MATLAB_R2016a.app/bin/maci64:/Applications/MATLAB_R2016a.app/sys/os/maci64:/Applications/MATLAB_R2016a.app/bin/maci64:/Applications/MATLAB_R2016a.app/sys/os/maci64:
[~/val...V/003_SAG_3D_IR] $ segmentHA_T1.sh sujeto_uno #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Tue Oct 30 12:04:16 CET 2018 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv84//runtime/maci64:/Applications/freesurfer/MCRv84//bin/maci64:/Applications/freesurfer/MCRv84//sys/os/maci64: dyld: Library not loaded: @loader_path/libmwmclmcrrt.8.0.dylib Referenced from: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML Reason: image not found /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 38: 7887 Abort trap: 6 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $args #-------------------------------------------- --
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Hi , segmentHA_T1.sh of the dev version produces very often segmentation violation errors. In the case I attach, it did the left hemisphere but when started the Hippocampal Subfields processing (T1) right it terminates with Segmentation Violation Error. The computer where I'm running the script is a 16GB ProductName: Mac OS X ProductVersion: 10.14.1 BuildVersion: 18B75
Thanks
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Without the full command line and error message it is hard to tell, but this may be an issue with the System Integrity Protection of Mac OS. Try turning it off and see whether that helps.
Tim
On December 13, 2018 at 10:05 AM Jaime Gomez borriquear@gmail.com wrote:
External Email - Use CautionHi , segmentHA_T1.sh of the dev version produces very often segmentation violation errors. In the case I attach, it did the left hemisphere but when started the Hippocampal Subfields processing (T1) right it terminates with Segmentation Violation Error. The computer where I'm running the script is a 16GB ProductName: Mac OS X ProductVersion: 10.14.1 BuildVersion: 18B75
Thanks _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
freesurfer@nmr.mgh.harvard.edu
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