Unimportant or irrelevant Simulation Generator parameters are defined as constants and thus have no value in being parameterized for this application. Also, Simulation Generator offers a lot of flexibility with a multitude of parameters, many of which are interconnected. In order to reduce the noise and focus on more abstract concepts, some of Simulation Generator's general parameters are defined as conventions (constants).
Name in code : DIMENSIONALITY
Supporting both the 2D and 3D would significantly increase the complexity of the parameterization.
The goal of the project is to generate specific white matter bundles, perhaps a few of them together, in order to test new algorithms related to a novel microscope and prospects for usability with future microscopes. Thus, there is no need to generate multiple white matter clusters which themselves are comprised of multiple bundles, as the quantity of produced data would simply be excessive for the goal.
Name in code : MRI_RESOLUTION
Given that computing the MRI voxels (NRRD File Format specification, NifTI-2 Data Format specification) require hardware resources (CPU time, RAM, ...) and that this voXSim feature cannot be switched off due to fact that it is programmed into the voXSim singularity, the voxel resolution is set to the minimum acceptable value. voXSim singularity is a private modification of Fiberfox.
Name in code : MRI_VOXEL_SPACING
(2, 2, 2) is the absolute minimum voxel spacing, as a value below that induces the generation of erroneous fiber data.
See Drew, Z., Bell, D. Voxel size. Reference article, Radiopaedia.org. (accessed on 23 Jul 2022) .