The following steps describe the whole procedure to build and install CBICATk.

1. Dependencies

Before building the CBICA Toolkit (CBICATk), the following software libraries are required to be installed. Please note that to build in Windows, CMake needs to be used an appropriate compiler (Win32 or Win64 version of Visual Studio is recommended). The selected solution platform is needed to match with dependent libraries.

Package	Version	Description
Archiver		(7-zip for Windows, gzip for Linux)
C++ compiler		(MSVC/11.x, MSVC/12.x, GCC/4.8.1, GCC/4.9.2)
CMake	2.8.4 or higher	To compile and build CBICATk and its dependencies
ITK	4.7 or higher	Build VTK before proceeding to compile ITK. Instructions to compile ITK are given here. During CMake configuration, enable the Module_ITKVtkGlue flag
OpenCV	3.0 or higher	All machine learning algorithms. This generally comes pre-compiled; if not found for your system, steps similar to those done for VTK and ITK can be done.
Doxygen		[OPTIONAL] For documentation only

Ensure all dependencies are met before proceeding.

2. Build

Please follow commands below in a shell/terminal (e.g., Bash). They will configure and build CBICATk using GNU Make. The main CMake configuration file (CMakeLists.txt) is located in the root directory of the package.

2.1 Extract source files and create the build directory

tar xzf CBICATk-${version}-source.tar.gz
mkdir CBICATk-${version}-build
cd CBICATk-${version}-build

[Note: In Windows, an appropriate compression program (e.g., 7-zip) might be used to extract the files.]

2.2 Run CMake to configure the build tree

cmake ../CBICATk-${version}-source

Use the CMake variable CMAKE_INSTALL_PREFIX to specify the installation directory, as in:

cmake -DCMAKE_INSTALL_PREFIX=/opt/software/geodesic ../CBICATk-${version}-source

For Windows, open CMake-GUI and select CBICATk-${version}-source as the "source" directory and select CBICATk-${version}-build as the "build" directory. Click on "Configure" and select the appropriate C++ compiler. If there weren't any configuration errors, click "Generate".

CMake should be able to find the dependencies if they are specified in the $PATH variable in your environment. If you have custom installation directories, then ensure that they have been added to the $PATH variable or point the variable(s) ${Dependency}_DIR to the appropriate build paths where ${Dependency}Config.cmake is/are present (for example, in the case of ITK, point ITK_DIR to the directory where ITKConfig.cmake is present) - this should be either the build directory or the installation directory. If you are using a bash shell, it can be done using the following command:

cmake -DITKDIR=${path_to_custom_ITK_build_dir} -DOpenCV_DIR=${path_to_custom_OpenCV_build_dir} CBICATk-${version}-source

This step will generate platform-specific project files (for example, Make file for GCC and Visual Studio solution file for MSVC).

Some of the options that can be set are:

BUILD_DOCUMENTATION	Builds the documentation from scratch
BUILD_TESTING	Enables unit testing
CMAKE_INSTALL_PREFIX	Path where the project will be installed

2.3 Compile the project

make

For Windows, you should launch the generated solution file of Visual Studio (by default, only Release version of the code will be compiled - if this needs to be changed, it can be done so by editing the variable CMAKE_CONFIGURATION_TYPE during the CMake configuration step), and then build solution.

2.3 [OPTIONAL] Compile the documentation

To build the documentation from scratch, the BUILD_DOCUMENTATION option in the CMake configuration needs to be enabled.

make doc

For Windows, build the doc project in the loaded solution.

2.4 [OPTIONAL] Test

To perform tests, the BUILD_TESTING option in the CMake configuration needs to be enabled.

make test

For Windows, you should build the RUN_TESTS project.

In case of failing tests, re-run the tests, but this time by executing CTest directly with the '-V' option to enable verbose output and redirect the output to a text file, as in the example below (works for both Windows and Linux on the command line or shell):

ctest -V >& CBICATk-test.log

And send the file CBICATk-test.log as attachment of the issue report to softw.nosp@m.are@.nosp@m.cbica.nosp@m..upe.nosp@m.nn.ed.nosp@m.u.

2.4 [OPTIONAL] Install

make install

For Windows, you should build the INSTALL project.

Upon the success of the above compilation and build process, CBICATk is installed into the directory specified by the CMAKE_INSTALL_PREFIX, which was set during step 2.2 above.