neurofunctionx

Bottom layer of the neuro / DBS stack: reusable helper functions and portable DBS-simulation logic that the higher packages (neurodatax, neurobuildx, neuromodex, neuromodex_thal) build on. It has no BIDS, config or model dependencies of its own.

Layout

• core/ — BaseProcessor (shared logging / timing base class) and ImageSpace (the image-space enum).
• subject/ — SubjectDataBase, the abstract base for all subject-data containers (subject name, data dir, versioned files access).
• io/ — file, image and mesh I/O: data_helper, socket_helper, sitk/ (SimpleITK load/save and image transforms), vtk/ (mesh I/O, transforms, e-field-to-volume sampling).
• comsol/ — COMSOL coordinate/conductivity handling, electrode setup, trajectory desorientation.
• simulation/ — ElectrodeTrajectoryExtractor and extract_electrode_trajectories (electrode fitting on direct images), ConductivityMapper, and ComsolSimulationRunner (the portable Apptainer/MATLAB e-field run core). BIDS-facing orchestration such as ElectrodeHandler lives in neurodatax, not here.

Dependency position

neurofunctionx  ->  neurodatax  ->  { neurobuildx, neuromodex ->  neuromodex_thal }

Everything depends on neurofunctionx; neurofunctionx depends on nothing in the stack.