BrainShapeToolKit

Overview

BrainShapeToolKit is a Python toolkit for brain shape analysis from MRI data. It provides tools for surface extraction, mesh processing, and quantitative shape feature computation.

Repositoryhttps://github.com/SSTDV-Project/BrainShapeToolKit
LicenseMIT

Installation

pip install brainshapetoolkit

Quick Start

import brainshapetoolkit as bst
processor = bst.MeshProcessor()
mesh = processor.load('brain_mesh.gii')
mesh_smooth = processor.smooth(mesh, iterations=10)
features = bst.ShapeFeatures().compute(mesh_smooth)
print(f"Surface area: {features['surface_area']}")

Core Modules

  • MeshProcessor — Load, preprocess, and smooth brain surface meshes from MRI or GIFTI files.
  • ShapeFeatures — Compute quantitative shape descriptors including area, volume, thickness, and curvature.
  • SurfaceStatistics — Run group-level statistical analyses on shape feature distributions.

Features

FeatureDescriptionUnits
surface_areaTotal surface areamm²
volumeEnclosed volumemm³
thicknessCortical thicknessmm
curvatureMean curvature1/mm

Dependencies

  • numpy>=1.21
  • scipy>=1.7
  • nibabel>=3.2
  • numba>=0.55

Citation

@software{brainshapetoolkit,
  title   = {BrainShapeToolKit},
  author  = {SSTDV Project},
  year    = {2024},
  url     = {https://github.com/SSTDV-Project/BrainShapeToolKit}
}

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