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
>
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