[DOCS] - Write a user-guide on the pipeline

[jerdra]

Should write up some documentation on how to run and configure the pipeline to get things up and running. The following documentation is required for the main pipeline:

1. nextflow configuration file paths (container locations etc... for singularity)
2. required singularity containers (mri2mesh, rtms_bayesian, connectome workbench)
3. input data specification (BIDS)
4. output specification - where to find outputs, what does each output mean
5. how to work with outputs (gmsh simulation and mesh files, surfaces)
6. how to make custom weight functions on the surface (parcellation-based/FC-based/etc)

In addition documentation is needed for:

1. tetrahedral projection (tetrapro) - the methods used
2. geometry library (geolib) - description of each function and implementation
3. surface patch extraction - how a sampling surface is defined
4. objective function (FieldFunc) - reference documentation of methods and use