dMRI-Lab: advanced diffusion MRI with Matlab

PURPOSE This is a Work-In-Process toolbox designed for Matlab(R) and aimed at the computational analysis of diffusion MRI. It addresses basic concepts such as Diffusion Tensor Imaging (DTI), but also advanced topics like High Angular Resolution Diffusion Imaging (HARDI, including estimation and representation of Orientation Distribution Functions-ODF), multi-shell samplings, and computational diffusion MRI. We have tested the library for Matlab versions starting R2015b, but we advice using a more recent version. A working license for the Parallel Computing Toolbox is strongly recommended (but not necessary). GET STARTED

  1. Download the package and unzip to a local folder at will.
  2. From the Matlab command window, cd to the home folder, i. e. that containing the setup script "setup__DMRIMatlab_toolbox.m".
  3. Run the setup script as either:
    • >> setup__DMRIMatlab_toolbox('useparallel',true);
    • >> setup__DMRIMatlab_toolbox('useparallel',false); or simply: >> setup__DMRIMatlab_toolbox;

    for using/avoid using the Parallel Computing Toolbox. In case you don't have a working license for it, the script will not throw an error. This will setup your Matlab path for the present session (it won't make any permanent change).

  4. Open/run some of the demo files in the "examples" folder to get started.

LICENSING The package is by now distributed as an alpha version in obfuscated p-code for the purpose of peer reviewing. It will be released as open-source with a GPL-like license upon publication of the related scientific papers (see below). Until then, you are free to download, try, and use it "as-it-is". In case you use the package for your own research, we ask you to kindly cite it as: Antonio Tristán-Vega and Santiago Aja-Fernández "dMRI-Lab: advanced diffusion MRI with Matlab" [Online resource] http://www.lpi.tel.uva.es/node/848 April 2020. Universidad de Valladolid. Spain SEE ALSO You might be as well interested in other related software products developed at the LPI.

PUBLICATIONS Note this library is a compendium of many techniques delivered from the original research carried out at the LPI for more than a decade. As such, you will find implementations for the methods described in several papers listed in our publications site.

On DTI:

https://www.lpi.tel.uva.es/node/107

https://www.lpi.tel.uva.es/node/210

https://www.lpi.tel.uva.es/node/113

On dMRI denoising:

https://www.lpi.tel.uva.es/node/93

https://www.lpi.tel.uva.es/node/85

https://www.lpi.tel.uva.es/node/161

On HARDI imaging and ODF estimation:

https://www.lpi.tel.uva.es/node/80

https://www.lpi.tel.uva.es/node/103

https://www.lpi.tel.uva.es/node/89

On computational dMRI:

https://www.lpi.tel.uva.es/node/781

https://www.lpi.tel.uva.es/node/759

https://www.lpi.tel.uva.es/node/818

https://www.lpi.tel.uva.es/node/844

https://www.lpi.tel.uva.es/node/899

https://www.lpi.tel.uva.es/node/900

Additionally, you will find implementations for the methods described in this paper currently under review:

Antonio Tristán-Vega, Guillem París, Rodrigo de Luis García and Santiago Aja-Fernández. "Accurate free water estimation in the white matter from DTI-compatible acquisitions using spherical means" May 2021. Submitted to Magnetic Resonance in Medicine.