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)
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NODDI MATLAB toolbox. Download the software and follow the instructions provided here to install it.
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CAMINO toolkit. Download the software and follow the instructions provided here to install it.
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SPArse Modeling Software (SPAMS). Download the software and follow the instructions provided here to install it.
Add the folder containing the source code of AMICO to your MATLAB PATH
.
Copy the file AMICO_Setup.txt
and rename it to AMICO_Setup.m
. Modify its content to set the paths to your specific needs, as follows:
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AMICO_code_path
: path to the folder containing the source code of AMICO (this repository). E.g./home/user/AMICO/code
. -
NODDI_path
: path to the folder containing the source code of the NODDI toolbox (in case you want to use NODDI, not needed for ActiveAx). E.g./home/user/NODDI_toolbox_v0.9
. -
CAMINO_path
: path to thebin
folder containing the executables of the Camino toolkit (in case you want to use ActiveAx, not needed for NODDI). E.g./home/user/camino/bin
. -
SPAMS_path
: path to the folder containing the source code of the SPAMS Library. E.g./home/user/spams
. -
AMICO_data_path
: path to the folder where you store all your datasets. E.g./home/user/AMICO/data
. Then, the software assumes the folder structure is the following:├── data ├── Study_01 --> all subjects acquired with protocol "Study_01" ├── Subject_01 ├── Subject_02 ├── ... ├── Study_02 --> all subjects acquired with protocol "Study_02" ├── Subject_01 ├── Subject_02 ├── ... ├── ...
This way, the kernels need to be computed only once per each study, i.e. same protocol (number of shells, b-values etc), and subsequently adapted to each subject (specific gradient directions) very efficiently.
Tutorials/demos are provided in the folder doc/demos
to help you get started with the AMICO framework.