simnibs-analyze 0.0.1

Modular pipeline for brain stimulation modelling (tDCS/TMS) with SimNIBS

simnibs-analyze

Post-processing and analysis pipeline for SimNIBS e-field outputs. Built for non-invasive brain stimulation studies (TMS/tDCS).

What it does

Starting from SimNIBS outputs, the pipeline covers the full analysis workflow:

• Target definition — generate ROI masks in MNI and subject space from MNI coordinates or atlas parcels (sphere, atlas-based)
• E-field preparation — coregister, skull-strip, smooth, and mask NIfTI volumes; intra/extra-ROI decomposition
• E-field analysis — extract scalar features (mean, max, percentiles, focality ratio) per subject and condition
• Single-subject optimisation assessment — evaluate how well a given montage targets the intended ROI
• Simulation robustness — assess sensitivity of the e-field distribution to input variability
• Stimulation method comparison — contrast montages or stimulation parameters across conditions
• Group-level analysis — inter-subject summary statistics, condition comparisons, and effect-size reporting
• Visualisation — 2D slice overlays, 3D surface rendering, histograms, and group bar plots

Installation

# TODO: publication sur PyPI
pip install simnibs-pipeline

En attendant, cloner le dépôt et installer les dépendances manuellement :

git clone <repo>
cd simnibs-pipeline
pip install -e .

Documentation

Ressource	Description
Documentation API	Classes et fonctions (généré par pdoc)
Référence config.yaml	Toutes les clés du fichier de configuration
Structure des outputs	Fichiers générés dans simnibs_output/ et results_dir/