NiftySeg install

Revision as of 12:14, 18 June 2015 by Mmodat (Talk | contribs) (Build)

Jump to: navigation, search


The code can be easily build using cmake ( The latest version can be downloaded from

To download the latest version, please check out the code by copying the following line to the terminal:

git clone git:// niftyseg-git

A packaged stable release is also available at this website.

Linux & OSX


Assuming that the code source are in the source path folder, you will have to first create a new folder, i.e. build path (step 1) and then to change directory to move into that folder (step 2).

mkdir build_path

cd build_path

There you will need to call ccmake (step 3a) in order to fill in the build options. If you don’t want to specify options, we could just use cmake (step 3b) and the default build values will be used.

ccmake source_path

cmake source_path

The main option in the ccmake gui are defined bellow: > CMAKE BUILD INSTALL options are Release, RelWithDebInfo or Debug

> INSTALL_PRIORS Will install the population atlas for the segmentation pipeline

> INSTALL_PRIORS_DIRECTORY Directory where the population atlas is going to be installed

> INSTALL_NIFTYREG Will fetch and automatically configure and install the niftireg package.

Once all the flags are properly filled in, just press the ”c” to configure the Make- file and then the ”g” key to generate them.


In the prompt, you just have to make (step 4) first and then make install (step 5).


make install



The building process is the following:

  • Get the source
  • Create a new directory for the build: "niftyseg-build"
  • Launch CMake-Gui, set the source path to "niftyseg" and the build path to "niftyseg-build" then hit configure
    • Cmake will prompt you to select the generator, which means you'll need to select the Visual Studio version you have installed earlier
    • Make sure the Use OpenMP option is enabled.
    • Set the CMAKE_INSTALL_PREFIX to the folder where you want to install NiftySeg.
    • Note, that if you want to install NiftySeg under Program Files, you'll need to create the folder yourself and explicitly apply full write permissions.
  • Once the flags are set, hit configure and generate. This will generate the Visual Studio project files.


  • Go to "niftyseg-build", and launch NiftySeg.sln. This will start Visual Studio.
  • In Visual Studio select build type, for generic use select Release and build the project (hit F7).
  • Once the build finished Select and run the Install task (Right Click on Install > Project Only > Build only Install). This will install NiftySeg to the folder you selected earlier.
  • Probably you'll want to add the install folder to your system path.