Dear freesurfer experts,
I have tried the dev version of Segmentation of hippocampal subfields and nuclei of the amygdala for OSX el Capitan, downloaded today. I did get an error message similar to a previous error I found on this mailing list:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-November/054973....
I have pasted the hippocampal-subfields-T2.HippoAMYT1andT2.log below
Is this a matlab runtime problem?
Many thanks in advance Eva
-------------------------------------------- #@# Hippocampal Subfields processing (T1+T2) left Wed Jan 31 22:36:38 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: Invalid MEX-file '/tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64': dlopen(/tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64, 6): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv Referenced from: /tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64 (which was built for Mac OS X 10.11) Expected in: /usr/lib/libstdc++.6.dylib in /tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64
Error in kvlClear (line 11)
Error in segmentSubjectT1T2_autoEstimateAlveusML (line 135)
MATLAB:invalidMEXFile Darwin Evas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64
T2 hippocampal subfields exited with ERRORS at Wed Jan 31 22:36:49 CET 2018
We are looking into all this. We’ll have updates soon. 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 Eva Hilland evahilland@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 31 January 2018 at 22:26 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] segmentHA_T2.sh
Dear freesurfer experts,
I have tried the dev version of Segmentation of hippocampal subfields and nuclei of the amygdala for OSX el Capitan, downloaded today. I did get an error message similar to a previous error I found on this mailing list:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-November/054973....https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-November/054973.html
I have pasted the hippocampal-subfields-T2.HippoAMYT1andT2.log below
Is this a matlab runtime problem?
Many thanks in advance
Eva
-------------------------------------------- #@# Hippocampal Subfields processing (T1+T2) left Wed Jan 31 22:36:38 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: Invalid MEX-file '/tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64': dlopen(/tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64, 6): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv Referenced from: /tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64 (which was built for Mac OS X 10.11) Expected in: /usr/lib/libstdc++.6.dylib in /tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64
Error in kvlClear (line 11)
Error in segmentSubjectT1T2_autoEstimateAlveusML (line 135)
MATLAB:invalidMEXFile Darwin Evas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64
T2 hippocampal subfields exited with ERRORS at Wed Jan 31 22:36:49 CET 2018
Hi Eva, I believe this should be fixed in the most recent El Capitan dev version. Let me know if the issue persists.
best Andrew
On February 1, 2018 at 7:02:19 AM, Iglesias Gonzalez, Eugenio (e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk) wrote: We are looking into all this. We’ll have updates soon. 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 Eva Hilland evahilland@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 31 January 2018 at 22:26 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] segmentHA_T2.sh
Dear freesurfer experts,
I have tried the dev version of Segmentation of hippocampal subfields and nuclei of the amygdala for OSX el Capitan, downloaded today. I did get an error message similar to a previous error I found on this mailing list:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-November/054973....https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-November/054973.html
I have pasted the hippocampal-subfields-T2.HippoAMYT1andT2.log below
Is this a matlab runtime problem?
Many thanks in advance
Eva
-------------------------------------------- #@# Hippocampal Subfields processing (T1+T2) left Wed Jan 31 22:36:38 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: Invalid MEX-file '/tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64': dlopen(/tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64, 6): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv Referenced from: /tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64 (which was built for Mac OS X 10.11) Expected in: /usr/lib/libstdc++.6.dylib in /tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64
Error in kvlClear (line 11)
Error in segmentSubjectT1T2_autoEstimateAlveusML (line 135)
MATLAB:invalidMEXFile Darwin Evas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64
T2 hippocampal subfields exited with ERRORS at Wed Jan 31 22:36:49 CET 2018
freesurfer@nmr.mgh.harvard.edu
-
Eva Hilland -
Hoopes, Andrew -
Iglesias Gonzalez, Eugenio