Configuring Inverse Runfiles

Sentinel's inverse solver reads its configuration from .dat text files that specify mesh files, material model, zone decomposition parameters, iteration structures, and regularization settings. This page documents the runfile format and key parameters.

Runfile Format

Inverse runfiles use alternating label lines and data lines. Each label line describes what the next data line contains; the parser reads them in strict sequence, skipping labels and extracting values from data lines.

Region Stack File:
0
Measured Displacement File:
1
60.0
../meshfiles/brain_mre.dsp

The parser (parse_inverse_runfile) handles two format versions:

Version	Origin	Detection
v7p3	Original NLI format	Default when v937 fields are absent
v937	Matches Fortran MRE-Zone v9.37	Detected via peek-ahead on additional fields

Both versions share the same core structure. The parser uses peek-ahead to detect whether v937-specific sections are present and reads them if found.

v937 Additions

Version v937 adds several fields after the core sections. For the MGH brain MRE dataset (and most single-frequency isotropic reconstructions), these have default or benign values:

Field	Purpose	Typical Value
Pressure BC File	Pressure boundary conditions for poroelastic models	0 (disabled)
Zone Displacement BC Option	How zone BCs are built: 1 = measured, 2 = calculated	1
Multi-Frequency Indicators	Per-property flag for multi-frequency alpha weighting	.false. for each property
Multi-Frequency Alpha	Frequency-dependent weighting exponents	1.0 (no effect)
Material Mesh Structures	Inline node/element files for material meshes	Not used when meshes are generated from resolutions
Global Forward Solve Indicator	Whether to run a global forward solve each iteration	.false.

Sentinel currently implements zonedispbcopt=1 (zone BCs from measured displacement) and globfwdind=false (no global forward solve), matching the standard MGH reconstruction workflow.

Key Parameters

Material Model

The mtrlmodel integer selects the constitutive model:

Value	Model	Properties
1	IsotropicIncompressible	${\mu }^{\ast }$, $\rho$
2	Orthotropic	$E_1^{\ast }$, $E_2^{\ast }$, $E_3^{\ast }$, $\rho$
3	IsotropicCompressible	${\mu }^{\ast }$, ${\kappa }^{\ast }$, $\rho$
5	TransverseIsotropicV1	${\mu }^{\ast }$, ${\mu }_s^{\ast }$, $E_t^{\ast }$, ${\kappa }^{\ast }$, $\rho$
6	TransverseIsotropicV2	${\mu }^{\ast }$, $\varphi$, $\zeta$, ${\kappa }^{\ast }$, $\rho$
7	GeneralizedAnisotropic	$E_1^{\ast }$, $E_2^{\ast }$, ${\mu }^{\ast }$, ${\kappa }^{\ast }$, $\rho$

Property Scalars

Each property has a real/imaginary scalar pair that converts normalized internal values (centered at 1.0) to physical units. For example, with isotropic incompressible brain MRE:

Property Scalars:
3300.0, -200.0, 1000.0, 0.0

This means property 1 (shear modulus) has s_re = 3300.0 Pa and s_im = -200.0 Pa, while property 2 (density) has s_re = 1000.0 kg/m^3 and s_im = 0.0. The physical value is value * scalar: a normalized value of 1.0 corresponds to 3300 Pa real shear modulus.

Material Mesh Resolutions

The inverse solver uses a dual-mesh architecture: displacement on hex27 elements and material properties on structured hex8 grids. The runfile specifies up to 3 material mesh resolution levels (coarse to fine):

Number of Material Property Mesh Resolutions:
3
Material Property Mesh Resolutions (dx, dy, dz in meters):
0.006, 0.006, 0.006
0.004, 0.004, 0.004
0.002, 0.002, 0.002

Each property maps to a resolution level via the meshind matrix.

Zone Sizes and Overlap

Zone decomposition parameters control how the domain is partitioned:

Zone Sizes (x, y, z half-extents in meters):
0.04, 0.04, 0.04
Zone Overlap Percentage (x, y, z):
0.50, 0.50, 0.50

An overlap of 0.50 means 50% of each zone edge overlaps with neighboring zones. Higher overlap improves smoothness at zone boundaries but increases computation.

Tolerances

Tolerance values are in PERCENT

The "Minimum Parameter Update Size" values in the runfile are specified in percent, not as fractions. The Fortran code divides by 100 after reading: minepsglob = minepsglob / 100.d0. Sentinel applies the same conversion.

Minimum Parameter Update Size [global, zone, line]:
0.1, 0.1, 0.01

This means:

• Global tolerance: 0.1% = 0.001 internal threshold

• Zone tolerance: 0.1% = 0.001 internal threshold

• Line search tolerance: 0.01% = 0.0001 internal threshold

The convergence check computes material_epsilon –- the maximum relative change in any reconstructed property between iterations. When epsilon < global_tol, the solver declares convergence.

Iteration Structures

Iteration structures define how the zone-level optimizer behaves at different stages of the reconstruction. The runfile specifies N structures with threshold limits that partition the global iteration range:

Number of Zone Iteration Structures:
2
Iteration Limits for Zone Iteration Structures:
10
Zone Iteration Structures [CG, GN, QN, LS]:
1, 0, 0, 1
2, 0, 0, 2

This defines two structures:

Structure	Global Iters	CG Iters	GN Iters	QN Iters	LS Iters
1	1–10	1	0	0	1
2	11–150	2	0	0	2

For the first 10 global iterations, each zone runs 1 CG iteration with 1 line search step. From iteration 11 onward, each zone runs 2 CG iterations with 2 line search steps. The optimizer is selected by the first nonzero count: QN > 0 selects L-BFGS, GN > 0 selects Gauss-Newton, otherwise CG is used.

See ZoneIterationStructure and run_inverse_solve! for implementation details.

Regularization Indicators

The regularization section begins with a 10-element boolean array that enables or disables each method:

Regularization Indicators [TV,SF,TK,MQ,JW,Con,CGr,VH,McG,SP]:
.false., .true., .false., .false., .false., .true., .true., .false., .true., .false.

Index	Abbreviation	Regularization	Type
1	TV	TotalVariationReg	Penalty
2	SF	SpatialFilterReg	Post-processing
3	TK	TikhonovReg	Penalty
4	MQ	MarquardtReg	Hessian modifier
5	JW	JoachimowiczReg	Hessian modifier
6	Con	ExteriorConstraintReg	Penalty
7	CGr	CG residual scaling	Weight schedule
8	VH	VanHoutenReg	Post-processing
9	McG	BoundsReg	Post-processing
10	SP	SoftPriorReg	Penalty

Each enabled regularization has its own parameter block following the indicators. These blocks specify which properties to treat, initial and final weights (for scheduled ramps), and method-specific parameters such as filter widths (SF), delta smoothing values (TV), or constraint bounds (Con).

Weight schedules interpolate linearly from initial to final values over the total iteration count, with an optional constant-weight delay period controlled by const_reg_iters. See WeightSchedule for details.