Installation and dependencies

Caveats

Lyman is distributed with some hope that it might be useful but no promise of support or stability. The platform supports a specific approach to analyzing data and may not work for every study. The code is documented, but not every aspect of how the tools should be used will be obvious. Finally, the code is likely to change between releases without backwards compatibility.

Installing

Stable versions can be installed from PyPI:

pip install lyman

It is also possible to install development code from Github:

pip install git+https://github.com/mwaskom/lyman.git

Dependencies

Neuroimaging packages

Lyman’s preprocessing workflows take advantage of image registration algorithms from established neuroimaging analysis libraries, so these packages must be installed to run the lyman workflows.

• Freesurfer 6+

• FSL 5.0.9+

Python libraries

Lyman also depends on a number of packages from the scientific Python ecosystem. They will be installed automatically if they are not present when you install lyman.

• numpy

• scipy

• pandas

• matplotlib

• nipype

• nibabel

• traits

• pyyaml