[MINC-users] brain-view 0.8 on Ubuntu precise ...

[Mishkin Derakhshan]

Hi,
After much pain I finally did hack something together on a 64-bit
ubuntu precise (12.04) machine.
See this thread:
http://www.bic.mni.mcgill.ca/pipermail/minc-users/2012-July/003452.html

Also, below is the follow up email that I never did send out to the
list regarding the final, really ugly hacks to get things working.

Hope that at least gives you a place to start...and doesn't send you
down the wrong path.
mishkin


Hi,
I forgot to send a follow up email but it turns out I still have some
problems with brain-view2.
When I was compiling/testing brain-view2 I had done it remotely, using
ssh -X into my work computer. All seemed to work fine.
Then when i came into work and ran it locally i got this error:
opus[~]$ /opt/minc/bin/brain-view2
(brain-view2:5510): GLib-CRITICAL **: PCRE library is compiled without
UTF8 support

And it just hangs. I tried compiling pcre with utf support and linking
against that but i still got the same error. Could be that i didn't
link things properly, but I found a work around by looking at the
environment variables when I use ssh -X. Turns out I can set
DBUS_SESSION_BUS_ADDRESS and it will "work".

opus[~]$ DBUS_SESSION_BUS_ADDRESS=unix: /opt/minc/bin/brain-view2

I can load an object file, and I can load an object file with a
texture map (thickness.txt), but when I try to load a vertstats file
(output from mni.write.vertex.stats in R) I get a core dump:

DBUS_SESSION_BUS_ADDRESS=unix: /opt/minc/bin/brain-view2
../../../../fsaverage/surf/lh.mid.obj
lh.thickness.mid.asc.fwhm10.fsaverage.GROUP.vertstats

(process:5549): GConf-WARNING **: Client failed to connect to the D-BUS daemon:
Server address of type unix was missing argument path or abstract

(process:5549): GConf-WARNING **: Client failed to connect to the D-BUS daemon:
Server address of type unix was missing argument path or abstract

(process:5549): GConf-WARNING **: Client failed to connect to the D-BUS daemon:
Server address of type unix was missing argument path or abstract
QGtkStyle was unable to detect the current GTK+ theme.
Debug. [ MainWindow() ] Settings path 1:
"/home/mishkin/.config/MINC/brain-view.conf"
Debug. [ MainWindow() ] Settings path 2:
"/home/mishkin/.config/MINC/brain-view.ini"
Debug. [ MainWindow() ] Application Pid:  5549
Debug. [ initColourbars() ] TextureDir:  "/home/mishkin/.config/MINC/textures/"
Debug. [ initColourbars() ] Texture file full path:
":/resources/colourbars/sunrise.png"
Debug. [ initColourbars() ] Texture file basename:  "sunrise"
Debug. [ initColourbars() ] Texture file full path:
":/resources/colourbars/hotblue.png"
Debug. [ initColourbars() ] Texture file basename:  "hotblue"
Debug. [ initColourbars() ] Texture file full path:
":/resources/colourbars/spectral.png"
Debug. [ initColourbars() ] Texture file basename:  "spectral"
Debug. [ initColourbars() ] Texture file full path:
":/resources/colourbars/hotred.png"
Debug. [ initColourbars() ] Texture file basename:  "hotred"
Debug. [ initColourbars() ] Texture file full path:
":/resources/colourbars/full_saturation.png"
Debug. [ initColourbars() ] Texture file basename:  "full_saturation"

Debug. [ main ] Loading ...  ../../../../fsaverage/surf/lh.mid.obj
Loading Polygon object number: 0
Debug: << geometry->loadObj # 0  status =  true
Debug. [ somethingChanged() ]  GRUNKLE

Debug. [ main ] Loading ...
lh.thickness.mid.asc.fwhm10.fsaverage.GROUP.vertstats
Debug. [ fillTextureVector() ] Using texture directory:
"/home/mishkin/.config/MINC/textures/"
Debug. [ fillTextureVector() ] Texture full filename:
"/home/mishkin/.config/MINC/textures//full_saturation.png"
Debug. [ fillTextureVector() ] Texture full filename:
"/home/mishkin/.config/MINC/textures//hotblue.png"
Debug. [ fillTextureVector() ] Texture full filename:
"/home/mishkin/.config/MINC/textures//hotred.png"
Debug. [ fillTextureVector() ] Texture full filename:
"/home/mishkin/.config/MINC/textures//spectral.png"
Debug. [ fillTextureVector() ] Texture full filename:
"/home/mishkin/.config/MINC/textures//sunrise.png"
terminate called after throwing an instance of
'mniVertstatsFile::InvalidColumnError'
Aborted (core dumped)

I tried looking into the error a bit, and i think it is from oobicpl
but I'm not sure, and I had to abandon the project; Louis didn't like
me working on something other than my thesis, and despite the ugliness
of the hacks, i can visualize what i need to.

All that to say that this minc-users email might come in handy for
someone else who might get the same errors, but it certainly isn't a
foolproof recipe to get brain-view2 working.


On Tue, Apr 16, 2013 at 6:49 PM, Sylvain Milot
<sylvain at bic.mni.mcgill.ca> wrote:
>
> Hello Minc-users,
>
> has anyone successfuly compiled brain-view (version 0.8) on Ubuntu precise ?
>
> I get some undefined references at load time, here's the top of
> the list:
>
> g++  -DQT3_SUPPORT  -lQt3Support
> -L/data/software/BIC/Build/Minc-2/Ubuntu-12.04/install//usr/local/bic/lib
> -L/usr/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -L/usr/share/qt4/lib  -o
> brain-view  brain-view.o callbacks.o pointInfoWindow.o pointPicker.o
> brainApp.o brainWidget.o vertStatsFileDialog.o brainEnvironment.o
> vertstatsForm.o vertexInfo.o screenCaptureForm.o screenCapture.o
> optionsForm.o options.o rplotformbase.o anatconForm.o anatcon.o RPlot.o
> extselection.o Rinterface.o pointInfoWindow.moc.o pointPicker.moc.o
> brainApp.moc.o brainWidget.moc.o vertstatsForm.moc.o vertexInfo.moc.o
> screenCaptureForm.moc.o screenCapture.moc.o optionsForm.moc.o options.moc.o
> rplotformbase.moc.o RPlot.moc.o Rinterface.moc.o anatconForm.moc.o
> anatcon.moc.o  -lbicInventor -lCoin -lGL  -lSM -lICE -lXmu -lXext -lSM -lICE
> -lXi -lX11  -loobicpl -lpcre++ -lpcre -lbicpl -lvolume_io2 -lminc2 -lhdf5
> -lz -lnetcdf -lm -lSoQt4 -lQtOpenGL -lQtGui -lQtCore -lXmu -lXi -lCoin -lGL
> -lXext -lSM -lICE -lX11 -ldl -lpthread -lCoin -lGL -lXext -lSM -lICE -lX11
> -ldl -lpthread brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x18):
> undefined reference to `Q3GList::clear()'
> brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x20): undefined
> reference to `Q3GList::~Q3GList()'
> brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x28): undefined
> reference to `Q3GList::~Q3GList()'
> brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x30): undefined
> reference to `Q3PtrCollection::newItem(void*)'
> brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x40): undefined
> reference to `Q3GList::compareItems(void*, void*)'
> brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x48): undefined
> reference to `Q3GList::read(QDataStream&, void*&)'
> brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x50): undefined
> reference to `Q3GList::write(QDataStream&, void*) const'
> brain-view.o:(.rodata._ZTI7Q3GList[typeinfo for Q3GList]+0x10): undefined
> reference to `typeinfo for Q3PtrCollection'
> pointInfoWindow.o: In function
> `coordinateInfoSet::coordinateInfoSet(QWidget*, char const*)':
> pointInfoWindow.cc:(.text+0x53): undefined reference to
> `Q3HBox::Q3HBox(QWidget*, char const*, QFlags<Qt::WindowType>)'
> pointInfoWindow.o: In function `textureInfoSet::textureInfoSet(QWidget*,
> char const*)':
> pointInfoWindow.cc:(.text+0x7ff): undefined reference to
> `Q3HBox::Q3HBox(QWidget*, char const*, QFlags<Qt::WindowType>)'
> pointInfoWindow.o: In function `pointInfoWindow::pointInfoWindow(QWidget*,
> char const*)':
> pointInfoWindow.cc:(.text+0xbb4): undefined reference to
> `Q3VBox::Q3VBox(QWidget*, char const*, QFlags<Qt::WindowType>)'
> pointInfoWindow.o: In function `Q3HBox::~Q3HBox()':
> pointInfoWindow.cc:(.text._ZN6Q3HBoxD2Ev[_ZN6Q3HBoxD5Ev]+0x13): undefined
> reference to `vtable for Q3HBox'
> pointInfoWindow.cc:(.text._ZN6Q3HBoxD2Ev[_ZN6Q3HBoxD5Ev]+0x1f): undefined
> reference to `vtable for Q3HBox'
> pointInfoWindow.cc:(.text._ZN6Q3HBoxD2Ev[_ZN6Q3HBoxD5Ev]+0x2b): undefined
> reference to `Q3Frame::~Q3Frame()'
> pointInfoWindow.o: In function `Q3VBox::~Q3VBox()':
> pointInfoWindow.cc:(.text._ZN6Q3VBoxD2Ev[_ZN6Q3VBoxD5Ev]+0x13): undefined
> reference to `vtable for Q3VBox'
> pointInfoWindow.cc:(.text._ZN6Q3VBoxD2Ev[_ZN6Q3VBoxD5Ev]+0x1f): undefined
> reference to `vtable for Q3VBox'
> ...
>
> ideas anyone ?
>
> Sylvain
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>