This MATLAB toolbox contains all necessary functions for parameter estimation of the Standard Model (SM) of diffusion in white matter1. Check our paper for details on this implementation and on the Standard Model in general. Below we provide instructions on how to run the PIPE toolbox. See the 'PIPE_SM_estimation_human_data.m' script that performs the parameter estimation in an example dataset.
Do not hesitate to reach out to Santiago.Coelho@nyulangone.org (or @santicoelho in X/Twitter) for feedback, suggestions, questions, or comments1.
A US and PCT patent application contains some of the related developments.
% Authors: Santiago Coelho (santiago.coelho@nyulangone.org), Els Fieremans, Dmitry Novikov
% Copyright (c) 2025 New York University
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% REFERENCES:
% - Coelho, S., ..., 2025. ArXiv
% - Coelho, S., Baete, S., Lemberskiy, G., Ades-Aron, B., Barrol, G., Veraart, J., Novikov, D.S., Fieremans, E., 2022. Reproducibility of the Standard Model of diffusion in white matter on clinical MRI systems. Neuroimage. doi: 10.1016/j.neuroimage.2022.119290. Epub 2022 May 8. PMID: 35545197; PMCID: PMC9248353.