HINEC: HIgh-order NEural Connectivity

Human brain white matter tractography pipeline with YAML-based parameter configuration.

What is HINEC?

HINEC processes raw diffusion-weighted MRI (dMRI) data through a complete pipeline:

1. Preprocessing — motion/eddy correction via FSL
2. Diffusion tensor estimation — SPD-constrained fitting
3. FA computation — fractional anisotropy maps
4. Parcellation — atlas-based brain region segmentation
5. Tractography — high-order fiber tracking (FACT, RK4, RKF45)
6. Visualization — 3D and fast slice-based viewing

Quick Start

# Default run — auto-creates organized run directory
./bin/run_hinec.sh data/parcellation_sample/sample sample.mat

# High precision (publication quality)
./bin/run_hinec.sh data/parcellation_sample/sample sample.mat config/high_precision.yml

# Fast exploration
./bin/run_hinec.sh data/parcellation_sample/sample sample.mat config/fast_exploration.yml

Or from MATLAB:

main('path/to/data', 'output.mat')
runhinec

Navigation

Section	Description
Pipeline	End-to-end data flow and module overview
Tractography	Standard and high-order fiber tracking
Configuration	YAML parameter system
Visualization	3D and distributed slice viewing
API Reference	Complete function reference
Math Foundations	Formulas and numerical methods