[MINC-users] installing brain-view2

[Jason Lerch]

Thanks Mishkin!

I recognize that we need to update the installation instructions - but in the meantime I've taken the liberty of adding your email in its entirety to the bottom of that wiki page. Please take a look and let me know in case you have any issues with that.

And one of these days, hopefully soon, we'll write more complete installation instructions.

Jason

On 2012-07-14, at 11:13 PM, Mishkin Derakhshan wrote:

> I had a hell of time installing brain-view2 so I documented my errors
> and solutions/hacks in case others come across the same problems
> (read: when I have to do this again I can look back at this post).
> 
> This was on a ubuntu 12.04 64 bit machine.
> 
> I followed the instruction here (thank you jason and sghanavati):
> https://wiki.phenogenomics.ca/display/MICePub/brain-view
> 
> Pre-requisites
> 1. MINC. I used the minc-toolkit binaries and only ran into one minor problem.
> opus[~]$ sudo apt-get install libc6 libstdc++6 imagemagick perl
> freeglut3 libgl1 libxcb1 libxdmcp6 libx11-6 libxext6 libxau6 libuuid1
> libjpeg62 libexpat1 libtiff4
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> Package libgl1 is a virtual package provided by:
>  libgl1-mesa-swx11 8.0.2-0ubuntu3.1
>  libgl1-mesa-glx 8.0.2-0ubuntu3.1
> You should explicitly select one to install.
> 
> E: Package 'libgl1' has no installation candidate
> 
> I chose libgl1-mesa-glx at random, and then everything else worked.
> 
> 2. Qt4: sudo apt-get install qt4-qmake libqt4-dev libqt4-core
> 3. Boost: sudo apt-get install libboost1.48
> 4.Coin:
> wget http://ftp.coin3d.org/coin/src/all/Coin-3.1.3.tar.gz
> tar xvzf Coin-3.1.3.tar.gz
> mkdir coin-build
> cd coin-build/
> ../Coin-3.1.3/configure
> make
> sudo make install
> 
> 5. Quarter:
> wget http://ftp.coin3d.org/coin/src/all/Quarter-1.0.0.tar.gz
> tar xvzf Quarter-1.0.0.tar.gz
> mkdir quarter-build
> cd quarter-build/
> ../Quarter-1.0.0/configure
> make
> 
> ERROR:../../../Quarter-1.0.0/src/Quarter/Quarter.cpp:148:13: error:
> 'stderr' was not declared in this scope
> SOLUTION:Added
> #include "stdio.h"
> to this file: ../Quarter-1.0.0/src/Quarter/Quarter.cpp
> 
> make
> sudo make install
> 
> 6. HDF5 1.8.9:
> Downloaded a build of HDF5 1.8.9:
> http://www.hdfgroup.org/HDF5/release/obtain5.html
> tar xvzf hdf5-1.8.9-linux-x86_64-static.tar.gz
> 
> 7. BicInventor:
> wget http://packages.bic.mni.mcgill.ca/tgz/bicInventor-0.3.1.tar.gz
> cd bicInventor-0.3.1
> ./configure --prefix=/opt/minc --with-build-path=/opt/minc
> --includedir=/opt/minc/include --libdir=/opt/minc/lib --with-minc2
> ERROR: (lots of erros when I tried to configure)
> SOLUTION: sudo apt-get install build-essential realpath zlib1g-dev
> bison flex libx11-dev libxmu-dev byacc libsoqt4-dev automake libtool
> libdbi- perl libblas-dev liblapack-dev libblitz0-dev libreadline-dev
> bzr bzrtools octave3.2 imagemagick
> 
> ./configure --prefix=/opt/minc --with-build-path=/opt/minc
> --includedir=/opt/minc/include --libdir=/opt/minc/lib --with-minc2
> make
> sudo make install
> 
> ACTUALLY INSTALLING BRAIN-VIEW2
> mkdir bv2
> cd bv2
> git init
> git remote add origin git at github.com:sghanavati/brain-view2.git
> git pull -u origin master
> 
> qmake-qt4 MINCDIR=/opt/minc/
> HDF5DIR=/home/mishkin/hdf5-1.8.9-linux-x86_64-static/ brain-view2.pro
> make
> ERROR: GeometryNode.h:25:30: fatal error: H5Cpp.h: No such file or directory
> SOLUTION: sudo apt-get install libhdf5-serial-dev (probably a bad hack
> because it installed 1.8.4 but it worked)
> 
> ERROR: H5AtomType.cpp:(.text+0x257): undefined reference to `H5Tget_pad'
> SOLUTION: put -lhdf5_cpp before -lhdf5 in the g++ command
> g++ -m64 -o brain-view2 MainWindow.o BrainQuarter.o TreeItem.o
> TreeModel.o ResourceForm.o GeometryScene.o GeometryNode.o main.o
> textureColumn.o textureFileItem.o tagFileItem.o tagPointItem.o
> moc_MainWindow.o moc_BrainQuarter.o moc_TreeItem.o moc_TreeModel.o
> moc_ResourceForm.o moc_GeometryNode.o moc_textureColumn.o
> qrc_colourbars.o    -L/usr/lib/x86_64-linux-gnu -L/usr/X11R6/lib64
> -L/usr/local/lib -lCoin -L/lib/ -lQuarter -L/opt/minc//lib -loobicpl
> -lpcre++ -lbicpl -lvolume_io2 -lminc2 -L/lib -lbicInventor
> -L/home/mishkin/hdf5-1.8.9-linux-x86_64-static//lib/ -lhdf5_cpp -lhdf5
> -lQtOpenGL -lQtGui -lQtCore -lGL -lpthread
> 
> And that gave me the brain-view2 binary which i copied into /opt/minc/bin.
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users