Automated characterization of noise distributions in diffusion MRI data

The example and documentation

The latest version can be installed with

pip install autodmri

You can find a quick example and datasets over here and the full documentation at https://samuelstjean.github.io/autodmri/.

An example, super basic call to the script would be

autodmri_get_distribution dwi.nii.gz sigma.nii.gz N.nii.gz mask.nii.gz

Be sure to check the options by passing --help to the script.

The manuscript and references

You can read the journal version in Medical Image Analysis and the datasets are available here https://zenodo.org/record/2483105.

The conference version of the manuscript (as published in MICCAI 2018) is available here for free and from the publisher.

Here is a bibtex entry for the journal version

@article{St-jean2020_media,
author = {St-Jean, Samuel and {De Luca}, Alberto and Tax, Chantal M.W. and Viergever, Max A. and Leemans, Alexander},
doi = {10.1016/j.media.2020.101758},
eprint = {1906.12121},
issn = {13618415},
journal = {Medical Image Analysis},
month = {jun},
pages = {101758},
title = {{Automated characterization of noise distributions in diffusion MRI data}},
url = {https://linkinghub.elsevier.com/retrieve/pii/S1361841520301225},
year = {2020}
}

and for the conference manuscript in MICCAI

@InProceedings{St-jean2018_miccai,
author="St-Jean, Samuel
and De Luca, Alberto
and Viergever, Max A.
and Leemans, Alexander",
editor="Frangi, Alejandro F.
and Schnabel, Julia A.
and Davatzikos, Christos
and Alberola-L{\'o}pez, Carlos
and Fichtinger, Gabor",
title="Automatic, Fast and Robust Characterization of Noise Distributions for Diffusion MRI",
booktitle="Medical Image Computing and Computer Assisted Intervention -- MICCAI 2018",
year="2018",
publisher="Springer International Publishing",
address="Cham",
pages="304--312",
isbn="978-3-030-00928-1"
}

Referencing the code itself

The code is also autoarchived on zenodo for those wanting to refer to a specific version over here