Installation

Installation notes for Ubuntu 16.04 (September 2016)

1. MINC Toolkit V2

The first thing you'll need to install is the MINC Toolkit V2. For instructions see: https://bic-mni.github.io/

2. Coin3D

hg clone https://bitbucket.org/Coin3D/coin
cd coin/
hg update CMake
cd ../
mkdir coin-build
cd coin-build
cmake -DCMAKE_INSTALL_PREFIX=/path/to/where/you/want/to/install/brain-view-2/ -DCMAKE_BUILD_TYPE=Release ../coin
make
make install
cd ..

3. Qt4 (system packages)

The brain-view2 code is based on Qt4. You'll need the following packages:

apt-get install qt4-default libqt4-dev libqt4-dbg qt4-qmake libqt4-opengl-dev

4. Quarter

hg clone https://bitbucket.org/Coin3D/quarter
cd quarter

Note: Quarter wants to use Qt5 if it's installed, but I got a fair bit of errors when trying that. So, I turned it off as follows. Edit the CMakeLists.txt in the quarter directory. Replace these lines:

FIND_PACKAGE(Qt5 QUIET COMPONENTS UiTools OpenGL)
IF(Qt5_FOUND)
  SET(QT_LIBRARIES Qt5::UiTools Qt5::OpenGL)
ELSE(Qt5_FOUND)
  FIND_PACKAGE(Qt4 REQUIRED)
  INCLUDE(${QT_USE_FILE})
ENDIF(Qt5_FOUND)

with:

FIND_PACKAGE(Qt4 REQUIRED)
INCLUDE(${QT_USE_FILE})

You can now continue the installation process:

cd ..
mkdir quarter-build
cd quarter-build
export PATH=/path/to/install/all-minc-tools/bin:$PATH
export LD_LIBRARY_PATH=/path/to/install/all-minc-tools/lib
cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/path/to/where/you/want/to/install/brain-view-2/ ../quarter
make
make install
cd ..

5. Boost (system packages)

apt-get install libboost-all-dev libboost-chrono1.58-dev libboost-thread1.58-dev libboost-filesystem1.58-dev libboost-iostreams1.58-dev libboost-program-options1.58-dev libboost-regex1.58-dev libboost-signals1.58-dev libboost-system1.58-dev

6. pcre++ (system libraries)

apt-get install libpcre++-dev

7. bicInventor

git clone https://github.com/BIC-MNI/bicInventor.git
cd bicInventor/
./autogen.sh
./configure --prefix=/path/to/where/you/want/to/install/brain-view-2/ --with-build-path=/path/to/installed/minc-tools/ --with-minc2
make
make install
cd ..

8. brain-view2

git clone https://github.com/Mouse-Imaging-Centre/brain-view2.git
cd brain-view2/
qmake MINCDIR=/path/to/installed/minc-tools/ INVENTORDIR=/path/to/where/you/want/to/install/brain-view-2/ QUARTERDIR=/path/to/where/you/want/to/install/brain-view-2/ HDF5DIR=/path/to/installed/minc-tools/ brain-view2.pro
make
cp brain-view2 /path/to/where/you/want/to/install/brain-view-2/bin/
cd ..