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YAML Configuration

YAML lets users change experiment settings without editing source code — manage parameters, share reproducible pipelines, and switch between presets instantly.

Why Configuration Matters

Reproducible research requires exact parameter recording. HINEC's YAML system lets you version-control experiment configurations, share pipelines, and switch between parameter presets without modifying any source code.

Available Presets

Preset	Algorithm	Integration	Step Size	Seeds	Speed
hinec_default.yml	HINEC	RK4	0.2	4	Medium
high_precision.yml	HINEC	RKF45	0.1	6	Slow
fast_exploration.yml	Standard	Euler	0.5	1	Fast
standard_fact.yml	Standard	Euler	0.5	5	Medium
irontract.yml	HINEC	RK4	0.2	4	Medium

Full Configuration Example

yaml|my_experiment.yml

1preprocessing:
2  run_denoising: true
3  denoise_method: 'dwidenoise'
4  run_motion_correction: true
5  run_eddy: true
6  improve_mask: true
7  atlas_type: 'jhu'
8 
9tractography:
10  algorithm: 'hinec'
11  integration_order: 4
12  interp_method: 'trilinear'
13  step_size: 0.2
14  seed_density: 4
15  termination_fa: 0.15
16  angle_thresh: 35
17  max_steps: 1000
18  min_length: 35
19  act_enabled: true
20 
21output:
22  tractography_dir: 'tractography_results'
23  include_timestamp: true

Preprocessing Parameters

Parameter	Type	Required	Default	Description
run_denoising	bool	No	true	Enable MP-PCA or Gaussian denoising
denoise_method	string	No	'dwidenoise'	'dwidenoise', 'susan', 'nlmeans', or 'gaussian'
run_motion_correction	bool	No	true	Enable rigid body motion correction
run_eddy	bool	No	true	Enable eddy current correction
improve_mask	bool	No	true	Apply mask refinement
atlas_type	string	No	'jhu'	'jhu', 'aal', or 'desikan'
t1_available	bool	No	false	T1 structural data is available
use_t1_registration	bool	No	false	Use T1 for enhanced registration

Tractography Parameters

Parameter	Type	Required	Default	Description
algorithm	string	No	'standard'	'standard' (FACT) or 'hinec' (high-order)
integration_order	int	No	1	1=Euler, 2=RK2, 4=RK4, 5=RKF45
step_size	float	No	0.2	0.1-0.2 (precise), 0.2-0.3 (balanced), 0.3-0.5 (fast)
seed_density	int	No	4	1-2 (fast), 4 (balanced), 6-8 (dense)
termination_fa	float	No	0.15	0.05 (long tracks), 0.15 (balanced), 0.20 (short/fast)
angle_thresh	float	No	35	30° (strict), 35-45° (balanced), 60° (permissive)
adaptive_step	bool	No	false	Enable adaptive step size (RKF45 only)
rkf_tolerance	float	No	0.01	Error tolerance in voxels (RKF45)

Common Patterns

Publication-Quality Results

yaml

tractography:
  integration_order: 5     # RKF45 adaptive
  adaptive_step: true
  rkf_tolerance: 0.005     # Tight tolerance
  step_size: 0.1           # Small initial step
  seed_density: 6          # Dense seeding
  termination_fa: 0.1      # Continue in low FA
  angle_thresh: 30         # Strict curvature

Expected runtime: 2-3x slower than default. Maximum accuracy with smooth tracks.

Fast Exploration

yaml

tractography:
  algorithm: 'standard'    # Simple FACT
  integration_order: 1     # Euler
  step_size: 0.5           # Large steps
  seed_density: 1          # Sparse seeding
  termination_fa: 0.2      # Quick termination

Use for rapid iteration during development or data exploration.

Tip

Create a custom config by copying a template: cp config/hinec_default.yml config/my_experiment.yml, then run with ./bin/run_hinec.sh data/mydata data.mat config/my_experiment.yml.

Visualization

Function Reference