Installation

COMMIT is written in Python and requires Python 3; version 2 is no longer supported. Also, COMMIT internally makes use of several libraries, e.g.:

• AMICO for the generation/rotation of the response functions;
• DIPY to handle the diffusion data;
• NiBabel to read/write neuroimaging file formats;
• Cython to compile parts of the code.

The following installation procedures will install all these required libraries. In case of problems with a package, please refer to the corresponding website or write to us for assistance.

Install from PYPI

Open the system shell and run:

pip install dmri-commit

This will download and install COMMIT from the Python Package Index.

Import from sources

To be sure of having the latest updates, download the source code from this repository, open the system shell and go to the folder where you downloaded this repository, and run:

pip install . -U

Import COMMIT and configure it

COMMIT is now installed and can be imported in your Python interpreter as usual. The first time you use it, please run the following to configure it:

import commit
commit.setup()

Uninstall COMMIT

Open the system shell and run:

pip uninstall dmri-commit

Notes

1. In order to use COMMIT, it is only necessary to install the Python code; no additional modules (e.g. SPAMS and NODDI) are required.

2. Depending on the forward-model employed, COMMIT may require the Camino toolkit to generate the response functions, e.g., in case of the Cylinder-Zeppelin-Ball model. Please follow the corresponding documentation to install Camino and make sure to include the folder containing the script datasynth in your system path.