Installation

Make sure all of NIWorkflows’ External Dependencies are installed. These tools must be installed and their binaries available in the system’s $PATH. A relatively interpretable description of how your environment can be set-up is found in the Dockerfile. As an additional installation setting, FreeSurfer requires a license file ..

On a functional Python 3.5 (or above) environment with pip installed, NIWorkflows can be installed using the habitual command

$ python -m pip install niworkflows

Check your installation with the following command line

$ python -c "from niworkflows import __version__; print(__version__)"

External Dependencies

The NIWorkflows are written using Python 3.5 (or above), and is based on nipype.

NIWorkflows require some other neuroimaging software tools that are not handled by the Python’s packaging system (Pypi) used to deploy the niworkflows package:

  • FSL (version 5.0.9)

  • ANTs (version 2.2.0 - NeuroDocker build)

  • AFNI (version Debian-16.2.07)

  • C3D (version 1.0.0)

  • FreeSurfer (version 6.0.1)