csttool Documentation

Welcome to the csttool documentation!

csttool is a Python-based command-line tool for automated assessment of the corticospinal tract (CST) using diffusion-weighted MRI (DW-MRI) data.

Quick Start

# Install (recommended: conda)
git clone https://github.com/alemnalo/csttool.git
cd csttool
conda env create -f environment.yml
conda activate csttool
csttool fetch-data --accept-fsl-license

# Run complete pipeline
csttool run --dicom /path/to/dicom --out results --subject-id sub-01

See the Installation Guide for the pip path and Windows notes, or the Quick Start Guide for analysis examples.

Pipeline Overview

graph LR
    A[DICOM / NIfTI] --> B[Import]
    B --> C[Preprocess]
    C --> D[Track]
    D --> E[Extract]
    E --> F[Metrics / Reports]

csttool processes diffusion MRI data through six stages:

1. Check - Verify environment and dependencies
2. Import - Convert DICOM to NIfTI format
3. Preprocess - Denoise and skull strip
4. Track - Generate whole-brain tractogram
5. Extract - Isolate bilateral CST using anatomical ROIs
6. Metrics - Compute microstructural measures and generate reports

Documentation Structure

This documentation follows the Diátaxis framework.

Tutorials

COMING SOON

How-To Guides

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Reference

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Explanation

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License

csttool is released under the MIT License. See LICENSE for details.