BrainVISA on Mac OS X 10.11.1 (El Capitan)

Questions about BrainVisa usage and installation

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f4bry
Posts: 29
Joined: Wed Mar 25, 2009 1:46 pm

BrainVISA on Mac OS X 10.11.1 (El Capitan)

Post by f4bry »

Hi,

I am trying to run BrainVISA 4.4.0 on a Mac OS X 10.11.1 (El Capitan) pc.
When the BV GUI is opened the following errors are reported.

Can you help me to fix this?

Thank you!
Fab

Code: Select all



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/lib/python2.6/site-packages/scipy/sparse/linalg/isolve/_iterative.so, 2): Library not loaded: /usr/local/gfortran/lib/libgfortran.3.dylib Referenced from: /Applications/brainvisa/lib/python2.6/site-packages/scipy/sparse/linalg/isolve/_iterative.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



this constructor takes no arguments 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 



dlopen(/Applications/brainvisa/python/soma/aims/aimssip.so, 2): Library not loaded: libcartobase.4.4.0.dylib Referenced from: /Applications/brainvisa/python/soma/aims/aimssip.so Reason: image not found 
User avatar
riviere
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Posts: 1361
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Location: CEA NeuroSpin, Saint Aubin, France
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Re: BrainVISA on Mac OS X 10.11.1 (El Capitan)

Post by riviere »

Hi,
The problem is that we don't have a recent MacOS system to test. This looks like if recent systems do not follow the same methods as they used to to find libraries. The file libcartobase.4.4.0.dylib is actually here in lib/, we set this path in the DYLD_LIBRARY_PATH environment variable in the launching script, so I don't know what"s wrong or if there is another way of setting libraries paths on Mac...
Denis
f4bry
Posts: 29
Joined: Wed Mar 25, 2009 1:46 pm

Re: BrainVISA on Mac OS X 10.11.1 (El Capitan)

Post by f4bry »

Hi,

Ok, I can not find a solution, I will use a linux-virtual machine.

Thank you!
Fab
User avatar
riviere
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Posts: 1361
Joined: Tue Jan 06, 2004 12:21 pm
Location: CEA NeuroSpin, Saint Aubin, France
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Re: BrainVISA on Mac OS X 10.11.1 (El Capitan)

Post by riviere »

Hi,

This problem with MacOS 10.11 seems to be the same as this one:
https://forums.developer.apple.com/thread/9233

I's specific to MacOS 10.11 apparently and linked to a new system feature: "system integrity protection" which limits things in process execution.
I don't really know if it's a bug (as they say they have filed a bug report) or a "feature" which is quite annoying. The only solution I have seen is to disable this system integrity protection:
http://macbookcity.fr/astuces/1414/desa ... el-capitan

To date I don't find another workaround which would not require to change administration setup on the host Mac side. If someone finds anything, please tell us...

Denis
f4bry
Posts: 29
Joined: Wed Mar 25, 2009 1:46 pm

Re: BrainVISA on Mac OS X 10.11.1 (El Capitan)

Post by f4bry »

Hi Denis,

Great! Disabling the system integrity protection, as described in the link you have posted, allows to use BrainVISA on the OS X 10.11.1
Thank you very much!

However, I got the following error when I try to take a snapshot with 'Multi Subject Sulci Snapshot Board' function (same error with SnapBase tool):

Code: Select all

ImportError: No module named site 


in Multi Subject Sulci Snapshot Board 4 System command exited with non null value : 1 


RuntimeError
processes.py (2554) in _processExecution: 
result = process.execution( self )
multiSubjectSulciSnapshotBoard.py (194) in execution: 
context.system( *cmd )
neuroProcessesGUI.py (2741) in system: 
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
processes.py (2678) in system: 
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )
Have you already encountered this problem? Or do you think it is related to El Capitan?

Thank you!
Fab
User avatar
riviere
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Posts: 1361
Joined: Tue Jan 06, 2004 12:21 pm
Location: CEA NeuroSpin, Saint Aubin, France
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Re: BrainVISA on Mac OS X 10.11.1 (El Capitan)

Post by riviere »

Hi,
For Multi Subject Sulci Snapshot Board, this process makes use of ImageMagick's "convert" tool, which has to be installed externally. I don't know if this is the only problem, and I agree that the error message is not explicit enough.
For snapbase, I have made a few fixes on it yesterday (not specific to Mac), and I will make sure that it is working on Mac for the next release 4.5 (still coming soon...)
Denis
f4bry
Posts: 29
Joined: Wed Mar 25, 2009 1:46 pm

Re: BrainVISA on Mac OS X 10.11.1 (El Capitan)

Post by f4bry »

Hi Denis,

The Multi Subject Sulci Snapshot Board creates a script 'bv_num.py' where several parameters are defined, like:

Code: Select all

 import anaSulciSnapshot
res = anaSulciSnapshot.main( [ ......
] )
Running this script with the python included in brainvisa, like

Code: Select all

/brainvisa/bin/python bv_num.py
I can obtain the snapshots without errors.

Thank you very much for your help Denis!
Fab
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