This code implements the AMICO framework in the Python language.
This is a work-in-progress project!
This version of AMICO is written in Python and it internally makes use of the DIPY library. Please install and configure them by following the guidelines on the corresponding websites.
- Download the python interfaces of the software and follow the instructions provided here to install it.
Depending on the forward-model employed, AMICO can 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.
This version of AMICO doesn not require the NODDI MATLAB toolbox to be present on your system; all the necessary MATLAB functions for generating the response functions of the NODDI model have in fact been ported to Python.
Open the system shell, go to the folder containing this file and run:
python setup.py installAMICO is now available in your Python interpreter and can be imported as usual:
import amico