Installing lyman

To install lyman, you can run

pip install lyman

This will install the stable version. To get the development version, you should run

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

However, there are a number of dependencies that should be installed first.

Dependencies

As a high-level package, lyman depends on a relatively large amount of external software. Getting set up to run an initial analysis can thus be somewhat of a hassle, which I apologize for. Below, I attempt to list the required packages and versions that are known to work with lyman. This isn’t updated that often, so later versions of these libraries will probably work. Older ones might too. It’s a hard problem.

Depending on what you are trying to do, it may not be necessary to install all of these packages. In the event that you don’t want to exhaust this list, the unit tests and the -dontrun switch for the command line interfaces can be useful for finding missing dependencies.

Lyman requires Python 2.7 or 3.6, although support for the latter is relatively new and may be incomplete. We strongly recommend using the Anaconda distribution, which ships with the majority of the Python packages needed to run lyman. The rest can be easily installed with conda, or failing that, pip.

Non-Python Software

• Freesurfer 5.3

• FSL 5.0.7+

Note

Due to changes in FSL, the lyman 0.0.7 and earlier only compatibile with FSL 5.0.6 and earlier, and lyman 0.0.8 and later are only compatibile with FSL 5.0.7 and later.

• ANTs 1.9

Note

Lyman is not compatible with later versions of ANTs.

Python Packages

• numpy

• scipy

• matplotlib

• seaborn

• nipype

• nibabel

• pandas

• scikit-learn

• scikit-image

• moss

• pysurfer