The Diffusion-Simulated Connectivity Dataset
Description
The Diffusion-Simulated Connectivity Dataset was generated from three numerical phantoms and Monte-Carlo simulation of the diffusion-weighted MRI signal [Rafael-Patino et al., Frontiers in Neuroinformatics, 2020]. The dataset was created to evaluate diffusion-weighted MRI methods, such as voxel-wise fiber orientation estimation, tractography, and structural connectome estimation. Each phantom was constructed from synthetic tubular fibers (strands) ranging in diameter from 1.4μm to 4.2μm. Phantoms geometry was obtained using the optimization procedure included in the Numerical Fiber Generator [Close et al., NeuroImage, 2009]. For each phantom, sixteen regions of interest (ROIs) located on the surface of a sphere are connected through a variable number of strands. The strands form complex white matter configurations that include kissing, branching, and crossing at different angles. The weights of the three 16x16 ground truth connectivity matrices are defined by the total cross-sectional area of the strands forming the connections. The three phantoms have a volume of 1 cubic millimeter, divided into a 40x40x40 voxel image matrix. After the Monte-Carlo simulation of the diffusion-weighted MRI signals, the image header is set to a voxel size of 1.0 mm isotropic, creating a final image size of 4x4x4 cm³, compatible with conventional diffusion-weighted MRI methods. Additionally, the dataset contains images of 2.0 mm isotropic resolution, resulting in an image matrix of 20x20x20 voxels. The diffusion-weighted MRI simulation protocol includes 360 diffusion-weighted images and 4 non-diffusion-weighted images (b=0 s/mm²). The diffusion-weighted MRI signals are distributed on 4 b-shells (b=1000, 1925, 3094, 13191 s/mm²). The dataset includes the signal generated with the Monte Carlo simulation and the same signal corrupted with various levels of Rician noise. Additionally, the dataset contains the relevant phantom's ground-truth information, including: i) voxel maps indicating the number of strands, the volume fraction occupied by the strands, and their corresponding average diameter, ii) label maps of the location of the 16 ROIs, iii) strands' centerline trajectories, as well as their diameter and ending ROIs, iv) strand voxel-wise orientation distribution functions (ODF) images, and v) three-dimensional substrate meshes used for the Monte Carlo simulation.