Slicer Extension: Advanced White Matter Analysis

This Slicer extension provides tools for advanced white matter analysis using diffusion MRI data. It includes three modules designed for FODF generation, tractography, and metric analysis of white matter fiber tracks.

Features

1. Generate FODF (First Module)
   Responsible for generating Fiber Orientation Distribution Functions (FODFs) from diffusion MRI data.

   Inputs:

   • White Mask: Binary mask for white matter regions.
   • Diffusion NIfTI: Diffusion-weighted image file.
   • BVALS: File containing b-values (.bvals).
   • BVECS: File containing b-vectors (.bvecs).

   

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2. Tractography (Second Module)
   Generates white matter fiber tracts using seeding masks and FODF data. Tracks can be visualized directly in 3D Slicer.

   Inputs:

   • Approximate Mask: Binary mask approximating regions of interest for tractography.
   • FODF: Fiber Orientation Distribution Function file generated from the first module.
   • Step Size: Step size for tractography.
   • Algorithm: Choice of tractography algorithm (deterministic or probabilistic).

   Outputs:

   • .trk file: Generated track file containing white matter fiber tracts.
   • .vtk file: Visualization-ready track file for rendering in Slicer.

   Key Features:

   • Automatically generates a seeding mask from the approximate mask.
   • Converts .trk files to .vtk for 3D visualization in Slicer.

   

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3. Metric Analysis (Third Module)
   Computes metrics between two .trk files to quantify overlap, overreach, and agreement.

   Metrics:

   • Dice Score: Measures spatial agreement between tracks.
   • Overreach Score: Quantifies tracks extending beyond the target area.
   • Overlap Score: Measures the shared region between two tractographies.

   

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Installation

1. Clone the repository or download the source code:

   git clone https://github.com/yourusername/white-matter-analysis-extension.git
   

2. Switch to extension-with-submodules branch and then Clone the scilpy library inside each module directory:

   cd MTP
   git clone https://github.com/scilus/scilpy.git FirstModule/scilpy
   git clone https://github.com/scilus/scilpy.git SecondModule/scilpy
   git clone https://github.com/scilus/scilpy.git ThirdModule/scilpy
   

The scilpy library provides essential tools for diffusion MRI processing and tractography.

3. Open 3D Slicer and navigate to the Extensions Manager.

4. Install the extension manually by adding the repository directory to Slicer's module paths:

   • Go to Edit > Application Settings > Modules > Additional Module Paths.
   • Add the path to the downloaded repository.

5. Restart Slicer to load the extension.