Python Environment

The TI-Toolbox operates within a containerized environment that includes SimNIBS. The simnibs_python interpreter is SimNIBS’s bundled Python environment that provides all libraries for TI-Toolbox operations. If you want to add a package for a new feature, follow the steps below.

Environment Management

Key Points

• Containerized Setup: The environment is defined in container/blueprint/Dockerfile.simnibs, which installs SimNIBS v4.6.0 and additional Python packages (meshio, nilearn, PyOpenGL-accelerate, trimesh, seaborn) required for TI-Toolbox functionality.

• Script executions: All python scripts should be executed using the simnibs_python script.py.

Import Patterns

As of v2.2.4, the tit.core sub-package has been dissolved. Modules that used to live under tit.core are now top-level within the tit package:

One-liner imports for common operations:

# Core (logging auto-initializes on import — no setup needed)
from tit import get_path_manager, paths, constants

# Simulation
from tit.sim import SimulationConfig, Montage, run_simulation, load_montages

# Optimization
from tit.opt import FlexConfig, run_flex_search
from tit.opt import ExConfig, run_ex_search

# Analysis
from tit.analyzer import Analyzer, run_group_analysis

# Statistics
from tit.stats import run_group_comparison, GroupComparisonConfig

# Preprocessing
from tit.pre import run_pipeline

All imports are eager — SimNIBS and nibabel are always available in the Docker environment.

JSON Config Modules

Each major module can be invoked as a subprocess accepting a JSON config file:

simnibs_python -m tit.sim        config.json
simnibs_python -m tit.analyzer   config.json
simnibs_python -m tit.opt.flex   config.json
simnibs_python -m tit.opt.ex     config.json
simnibs_python -m tit.stats      config.json
simnibs_python -m tit.pre        config.json

Config files are generated programmatically via tit.config_io.write_config_json(). See the Scripting page for details.