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)
This is the current implementation of the AMICO framework and it is written in python.
This version of AMICO is written in Python and, internally, it makes use of the DIPY library.
SPAMS is on test.pypi.org and can be installed with:
pip install --index-url https://test.pypi.org/simple/ spams
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 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.
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 amicoOpen the system shell and run:
pip uninstall amico