HINEC: HIgh-order NEural Connectivity

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

Whole-brain tractogram of the ISMRM 2015 phantom — RK4 with a C² spline interpolant. Colour encodes direction: red left–right, green anterior–posterior, blue superior–inferior.

Pipeline

HINEC takes raw diffusion-weighted MRI (dMRI) and produces streamline tractography, in six stages:

1. Preprocessing — denoising, motion and eddy-current correction, brain extraction and registration, via FSL
2. Diffusion tensor estimation — SPD-constrained fitting
3. FA computation — fractional anisotropy maps
4. Parcellation — atlas-based brain region labelling
5. Tractography — FACT, interpolated high-order streamlines, or connection-form Method of Moving Frames
6. Visualization — 3D rendering and pre-cached slice viewing

Three trackers share one processed nim struct, selected by algorithm: in the config: standard (FACT, discrete voxel tensors), hinec (interpolated direction field, Euler/RK2/RK4/RKF45 integration, optional ACT) and mmf (moving frames driven by the connection 1-form). The direction source is dti (tensor principal eigenvector) or csd (FOD peaks), independently of the integrator.

Quick Start

Preprocess once, then iterate on tractography:

# Build the processed nim (preprocessing + DTI + FA + parcellation)
./bin/run_hinec.sh data/ismrm2015/ismrm2015 ismrm2015.mat config/ismrm2015.yml

# Track on the already-processed nim — one run directory per config
./bin/run_tractography.sh hinec_dti --score

# Sweep a parameter without writing a new config
./bin/run_tractography.sh hinec_dti --set integrator.step=0.05

Or from MATLAB:

config   = load_config_yaml('config/hinec_dti.yml');
run_info = create_run_directory('config/hinec_dti.yml');
main('data/ismrm2015/ismrm2015', 'ismrm2015.mat', config, run_info);
runTractography(fullfile(run_info.output_dir, 'ismrm2015.mat'), config, run_info);

Navigation

Section	Description
Getting Started	Prerequisites, installation and first run
Pipeline	End-to-end data flow and module overview
Tractography	Standard, high-order and MMF fibre tracking
Configuration	YAML parameter reference
Visualization	3D and distributed slice viewing
API Reference	Complete function reference
Math Foundations	Formulas and numerical methods
Solution Verification	Convergence under refinement, and the observed order
Team	Researchers and advisor