Installation#

Make sure all of SDCflows’ 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, SDCflows can be installed using the habitual command

$ python -m pip install sdcflows

Check your installation with the following command line

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

External Dependencies#

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

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

  • FSL (version 5.0.9)

  • ANTs (version 2.2.0 - NeuroDocker build)

  • AFNI (version Debian-16.2.07)

  • FreeSurfer (version 6.0.1)