It works from the terminal windows. I start from within Matlab, to get FDR correction as Freeview do not have it. And I use an FDR correction that uses data from both hemisphere. I have managed to get it working under Ubuntu 14.04.3.
> On 15 Sep 2015, at 18:49, dgw <[email protected]> wrote: > > Starting Freeview from MATLAB is an odd thing to do. What happens if > you just start freeview normally? > > hth > D > > On Tue, Sep 15, 2015 at 12:21 PM, Knut Jørgen Bjuland > <[email protected]> wrote: >> When I load Freeview developmental version from Freesurver developmental >> version from Matlab 2015b. >> I used this command to load freeview. >> >> fdrthresh=sprintf('%s,%s',num2str(lowerfdr),num2str(upperfdr)); >> >> commandline=sprintf('freeview -f >> %s/%s/surf/%s.%s:annot=aparc.annot:annot_outline=1:overlay=%s:overlay_threshold=%s >> &',SUBJECTS_DIR,template,hemi,surface,overlayfile,fdrthresh); >> >> system(commandline) >> >> >> >> >> I get this error.dyld: lazy symbol binding failed: Symbol not found: >> ___emutls_get_address >> Referenced from: >> /Applications/freesurfer//Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib >> Expected in: /usr/lib/libSystem.B.dylib >> >> dyld: Symbol not found: ___emutls_get_address >> Referenced from: >> /Applications/freesurfer//Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib >> Expected in: /usr/lib/libSystem.B.dylib >> >> [0]PETSC ERROR: >> ------------------------------------------------------------------------ >> [0]PETSC ERROR: Caught signal number 5 TRAP >> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger >> [0]PETSC ERROR: or see >> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC >> ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to >> find memory corruption errors >> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and >> run >> [0]PETSC ERROR: to get more information on the crash. >> [0]PETSC ERROR: --------------------- Error Message >> ------------------------------------ >> [0]PETSC ERROR: Signal received! >> [0]PETSC ERROR: >> ------------------------------------------------------------------------ >> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 >> CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 >> [0]PETSC ERROR: See docs/changes/index.html for recent updates. >> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. >> [0]PETSC ERROR: See docs/index.html for manual pages. >> [0]PETSC ERROR: >> ------------------------------------------------------------------------ >> [0]PETSC ERROR: Unknown Name on a darwin12. named Knuts-MacBook-Pro.local by >> knutjorgenbjulan Tue Sep 15 18:16:13 2015 >> [0]PETSC ERROR: Libraries linked from >> /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt >> [0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012 >> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc >> --with-fc=0 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 >> --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 >> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >> [0]PETSC ERROR: >> ------------------------------------------------------------------------ >> [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown >> file >> [unset]: aborting job: >> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 >> [0]PETSC ERROR: >> ------------------------------------------------------------------------ >> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, >> probably memory access out of range >> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger >> [0]PETSC ERROR: or see >> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC >> ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to >> find memory corruption errors >> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and >> run >> [0]PETSC ERROR: to get more information on the crash. >> [0]PETSC ERROR: --------------------- Error Message >> ------------------------------------ >> [0]PETSC ERROR: Signal received! >> [0]PETSC ERROR: >> ------------------------------------------------------------------------ >> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 >> CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 >> [0]PETSC ERROR: See docs/changes/index.html for recent updates. >> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. >> [0]PETSC ERROR: See docs/index.html for manual pages. >> [0]PETSC ERROR: >> ------------------------------------------------------------------------ >> [0]PETSC ERROR: Unknown Name on a darwin12. named Knuts-MacBook-Pro.local by >> knutjorgenbjulan Tue Sep 15 18:16:13 2015 >> [0]PETSC ERROR: Libraries linked from >> /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt >> [0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012 >> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc >> --with-fc=0 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 >> --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 >> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >> [0]PETSC ERROR: >> ------------------------------------------------------------------------ >> [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown >> file >> [unset]: aborting job: >> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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