AMICO

Implementation of the linear framework for Accelerated Microstructure Imaging via Convex Optimization (AMICO) described here:

Accelerated Microstructure Imaging via Convex Optimization (AMICO) from diffusion MRI data
Alessandro Daducci, Erick Canales-Rodriguez, Hui Zhang, Tim Dyrby, Daniel Alexander, Jean-Philippe Thiran
NeuroImage 105, pp. 32-44 (2015)

Code implementation

This is the current implementation of the AMICO framework and it is written in python.

Installation

Install dependencies

Python and DIPY

This version of AMICO is written in Python and, internally, it makes use of the DIPY library.
Please install and configure both Python and DIPY by following the guidelines on the corresponding websites.

SPArse Modeling Software (SPAMS)

• Download the python interfaces of the software and follow the instructions provided here to install it.

Camino toolkit

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.

NODDI toolbox

This implementation in AMICO does 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.

Install AMICO

Open the system shell, go to the folder containing this file and run:

pip install .

AMICO is now available in your Python interpreter and can be imported as usual:

import amico

Uninstall AMICO

Open the system shell and run:

pip uninstall amico