This repository aims to share data from the article titled "Investigating microstructural changes between in vivo and perfused ex vivo marmoset brains using oscillating gradient and b-tensor encoded diffusion MRI at 9.4T" by Tales Santini, Alyson Shim, Jr-Jiun Liou, Naila Rahman, Gabriel Varela-Mattatall, Matthew D. Budde, Wataru Inoue, Stefan Everling, and Corey A. Baron, published at MRM journal in 2024.

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Here is the folder structure for this repository:

• 01-Diffusion_gradient_waveforms: OGSE and b-tensor encoding diffusion gradient waveforms used in the Monte Carlo simulations performed with the command datasynth from the Camino package (http://camino.cs.ucl.ac.uk/).
• 02-Geometry: Geometry files based on (Budde et al., PNAS 2010) used in the Monte Carlo simulations with the command datasynth from the Camino package (http://camino.cs.ucl.ac.uk/). In the file name, Rad is the radius of the geometry (in micrometers), Amp is the amplitude of beading, and Volfract is the intracellular volume fraction.
• 03-Simulation_results: Results of the fitting of the Monte Carlo simulation results to the OGSE- and b-tensor-encoding metrics using MatMRI (https://gitlab.com/cfmm/matlab/matmri).
• 04-Experimental_results: Experimental results of MRI data acquired from two marmosets: in vivo under anesthesia and perfused/fixed ex vivo tissue.
• Dockerfile: Recipe for the Camino environment installation, also available via docker pull tsantini/camino or at https://hub.docker.com/r/tsantini/camino.