I suspect the issue with the neurodebian version is due to matlab adding things to LD_LIBRARY_PATH. Try doing "system('env');" in matlab and see what LD_ variables show up. You may be able to get it to work by using "env -u LD_LIBRARY_PATH wb_command" instead of just "wb_command" as the argument in ciftiopen and friends. Really, matlab needs to undo its library path mess before issuing the system command. You could also simplify that with a generic wrapper script, call it something like "unmatlab_wrapper", put it in some bin folder in your PATH, and have it contain:
#!/bin/bash unset LD_LIBRARY_PATH "$@" Then any time you use system in matlab, put 'unmatlab_wrapper ' (or whatever you named it) on the front of the command, like "system('unmatlab_wrapper wb_command');". Tim On Wed, Oct 24, 2018 at 2:30 PM, Angstadt, Mike <mangs...@med.umich.edu> wrote: > Yep, using the version in bin_linux64 from the zip fixes things. > > > > Thanks > > > > -Mike > > > > *From:* hcp-users-boun...@humanconnectome.org <hcp-users-bounces@ > humanconnectome.org> *On Behalf Of *Angstadt, Mike > *Sent:* Wednesday, October 24, 2018 3:07 PM > *To:* 'Timothy Coalson' <tsc...@mst.edu> > > *Cc:* HCP Users <HCP-Users@humanconnectome.org> > *Subject:* Re: [HCP-Users] ciftiopen problems > > > > Running the neurodebian version on Ubuntu 16.04. I’ll take a look at the > zipped distribution to see if that fixes things. > > > > -Mike > > > > > > *From:* Timothy Coalson <tsc...@mst.edu> > *Sent:* Wednesday, October 24, 2018 2:53 PM > *To:* Angstadt, Mike <mangs...@med.umich.edu> > *Cc:* HCP Users <HCP-Users@humanconnectome.org> > *Subject:* Re: [HCP-Users] ciftiopen problems > > > > *CAUTION:* This email originated outside the University of Michigan > > DO NOT click links or open attachments if the sender is unknown to you. > > That implies that when launched by matlab, it is either not finding QT > libraries at all, or finding a version it doesn't work with. > > > > Are you using linux? Are you using a zip distribution downloaded from the > website (as opposed to neurodebian or the older default version the > distribution may have)? If it is a zip distribution, are you telling > matlab to call the version in bin_linux64 or similar, rather than the one > in exe_linux64? The ones in bin_linux64 are scripts that specifically look > at LD_LIBRARY_PATH, clear it if it sees any matlab stuff, and add the > libraries we ship in the zip distributions. > > > > Tim > > > > > > On Wed, Oct 24, 2018 at 1:38 PM, Angstadt, Mike <mangs...@med.umich.edu> > wrote: > > Hey HCP experts, > > This might be a long shot as I expect there’s something weird going on on > our system, but I'm no longer able to use ciftiopen in matlab to read in > cifti images. This used to work just fine, and to my knowledge neither > connectome workbench or the ciftiopen script or the gifti toolbox has > changed on our system. However, now I'm getting the following error when > trying to load a cifti image: > /usr/bin/wb_command: symbol lookup error: /usr/bin/wb_command: undefined > symbol: _ZNK19QAbstractTableModel7siblingEiiRK11QModelIndex > > Obviously this is fairly easily narrowed down to the matlab system call in > ciftiopen that calls out to wb_command to conver the image to gifti. The > problem is that issuing the exact same wb_command directly in a bash > terminal works fine, but it always fails with the above error when trying > to issue it through a system call from matlab. > > I'm just hoping someone might have some ideas for resolving this, even > though it doesn't seem directly releated to workbench or the ciftiopen > script. > > -- > Mike Angstadt > Research Area Specialist Lead / PANLab Lab Manager > Department of Psychiatry / University of Michigan > (734) 936-8229 > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not > be used for urgent or sensitive issues > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not > be used for urgent or sensitive issues > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not > be used for urgent or sensitive issues > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users