Radiology, Radiation Oncology & Computer-Assisted Surgery Reference

ModelScript provides first-class polyglot compilation, static safety verification (M9101–M9910), numerical simulation, and cross-domain projections for Radiology, Radiation Oncology, Biomechanics, and Computer-Assisted Surgery (CAS). All nine clinical engineering packages lower directly into the linear-memory DAEBuilder arena and interoperate with Modelica 3.x, SysML v2, OpenSCAD, ISO 10303-21 STEP, CalculiX/Abaqus, SBML, and ROS/Gazebo URDF.

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1. Domain Package Matrix

Package	Clinical Domain	File Extensions	Diagnostic Range	Primary Projections
@modelscript/opensim	Musculoskeletal Biomechanics & Surgical Rehabilitation	.osim	M9101–M9110	Modelica 3.x (.mo), ROS/Gazebo URDF (.urdf), DAE Arena
@modelscript/dicom-rt	Clinical Radiotherapy (RTSTRUCT, RTPLAN, RTDOSE)	.rtplan, .rtstruct, .rtdose, .dicom-rt	M9201–M9210	OpenSCAD 3D CSG (.scad), SysML v2 (.sysml), DAE Arena
@modelscript/cellml	Physiological & Electrophysiology Modeling (CellML 1.0/1.1/2.0)	.cellml	M9301–M9310	Modelica 3.x (.mo), SBML Level 3 (.sbml), DAE Arena
@modelscript/febio	Soft-Tissue Hyperelastic/Biphasic FEA & SOFA Surgical Scenes	.feb, .scn	M9401–M9410	CalculiX/Abaqus (.inp), Modelica 3.x (.mo), DAE Arena
@modelscript/nifti	Volumetric Medical Imaging & Segmentation (NIfTI-1/2 & NRRD)	.nii, .nrrd, .nhdr	M9501–M9510	OpenSCAD (.scad), ISO 10303-21 STEP (.stp), DAE Arena
@modelscript/topas	Monte Carlo Proton/Hadrontherapy & Radiotherapy Physics	.topas, .mac	M9601–M9610	OpenSCAD (.scad), Modelica 3.x (.mo), DAE Arena
@modelscript/three-mf	Patient-Specific Surgical Guides & 3D-Printed Implants (ISO/ASTM 52915)	.3mf	M9701–M9710	ISO 10303-21 STEP (.stp), OpenSCAD (.scad), DAE Arena
@modelscript/igtl	OpenIGTLink & PLUS Toolkit Surgical Navigation & Tracking	.igtl, .plus.xml	M9801–M9810	ROS URDF (.urdf), Modelica 3.x (.mo), DAE Arena
@modelscript/owl2 (ontospm)	OntoSPM / LapOntoSPM Surgical Process & Safety Ontology	.ofn, .owl, .ontospm	M9901–M9910	SysML v2 (.sysml), OWL 2 Functional Syntax (.ofn)

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2. @modelscript/opensim — Musculoskeletal Biomechanics (.osim)

Parses OpenSim 3.x and 4.x XML (<OpenSimDocument>, <Model>, <BodySet>, <JointSet>, <ForceSet>, <MarkerSet>, <WrapObjectSet>, <ConstraintSet>), simulates Hill-type muscle-tendon equilibrium and multibody joint dynamics, and projects to Modelica 3.x and URDF.

Mathematical Foundations

1. Neural Excitation-Contraction Activation Dynamics (Thelen 2003 / Millard 2012):

   $$\frac{da}{dt}=\frac{u-a}{\tau (a,u)},\tau (a,u)=\{\begin{array}{ll}{\tau }_{\text{act}}(0.5+1.5a)& u>a\\ {\displaystyle \frac{{\tau }_{\text{deact}}}{0.5+1.5a}}& u\le a\end{array}$$

2. Active & Passive Force-Length and Force-Velocity Equilibrium:

   $$f_L({\tilde{l}}^M)=\exp (-\frac{({\tilde{l}}^M-1{)}^2}{\gamma }),f_{PE}({\tilde{l}}^M)=\frac{\exp (k_{PE}({\tilde{l}}^M-1)/{ϵ}_0^M)-1}{\exp (k_{PE})-1}$$$$F^T=F_0^M(a{f}_L({\tilde{l}}^M)f_V({\tilde{v}}^M)+f_{PE}({\tilde{l}}^M))\cos \alpha$$

Diagnostic Rules (M9101–M9110)

Code	Rule ID	Severity	Description
M9101	opensim-unresolved-body-frame	error	Joint, marker, wrap object, or muscle path point references an undefined body frame.
M9102	opensim-non-positive-body-mass	error	Body specifies $\text{mass}\le 0$ or non-positive principal moments of inertia ($I_{xx},I_{yy},I_{zz}\le 0$).
M9103	opensim-kinematic-tree-cycle	error	Kinematic joint graph contains a directed cycle or multiple parent joints without a <ConstraintSet> loop constraint.
M9104	opensim-invalid-coordinate-range	error	Coordinate rangeMin >= rangeMax or defaultValue lies outside [rangeMin, rangeMax].
M9105	opensim-invalid-muscle-parameters	error	Muscle maxIsometricForce <= 0, optimalFiberLength <= 0, or tendonSlackLength <= 0.
M9106	opensim-excessive-pennation-angle	error	Muscle pennationAngleAtOptimal is outside $[0,\pi /2)$ radians.
M9107	opensim-insufficient-muscle-path-points	error	Muscle has fewer than 2 path points or all path points attach to the exact same body frame.
M9108	opensim-unresolved-wrap-object	error	Muscle <PathWrap> references an undefined <WrapObject> identifier.
M9109	opensim-invalid-time-constants	warning	Muscle ${\tau }_{\text{act}}\le 0$, ${\tau }_{\text{deact}}\le 0$, or ${\tau }_{\text{act}}>{\tau }_{\text{deact}}$.
M9110	opensim-duplicate-component-name	error	Duplicate body, joint, coordinate, or muscle name declared in the model.

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3. @modelscript/dicom-rt — Clinical Radiotherapy (.rtplan, .rtstruct, .rtdose)

Models DICOM-RT treatment plans, anatomical ROI contour stacks, linac Multi-Leaf Collimator (MLC) control points, and cumulative Dose-Volume Histograms (DVHs).

Mathematical Foundations

1. Linear-Quadratic (LQ) Biologically Effective Dose (BED) & EQD2:

   $$\text{BED}=nd(1+\frac{d}{\alpha /\beta }),\text{EQD2}=\frac{\text{BED}}{1+{\displaystyle \frac{2}{\alpha /\beta }}}$$

   where $n$ is the number of fractions, $d=D/n$ is the dose per fraction in Gy, and $\alpha /\beta$ is the tissue fractionation sensitivity ($\alpha /\beta =10\text{ Gy}$ for tumors, $\alpha /\beta =3\text{ Gy}$ for late-responding normal tissues).

2. ICRU Report 83 Homogeneity Index (HI) & Paddick Conformity Index (CI):

   $$\text{HI}=\frac{D_{2\mathrm{\%}}-D_{98\mathrm{\%}}}{D_{50\mathrm{\%}}},{\text{CI}}_{\text{RTOG}}=\frac{V_{\text{PIV}}}{V_{\text{PTV}}},{\text{CI}}_{\text{Paddick}}=\frac{(V_{\text{PTV}}\cap V_{\text{PIV}}{)}^2}{V_{\text{PTV}}\cdot V_{\text{PIV}}}$$

Diagnostic Rules (M9201–M9210)

| Code | Rule ID | Severity | Description | | :------ | :--------------------------------------- | :-------- | :--------------------------------------------------------------------------------------------------------- | ---------------------- | ------------------------------------------------------------------------------------------- | | M9201 | dicom-rt-missing-target-volume | error | Plan contains no clinical target volume ROI (PTV, CTV, or GTV). | | M9202 | dicom-rt-mlc-leaf-overlap | error | Opposite MLC leaf pair violates minimum physical gap ($\text{bankB}-\text{bankA}<0.5\text{ mm}$). | | M9203 | dicom-rt-mlc-speed-exceeded | error | MLC leaf speed between consecutive control points exceeds physical motor limit ($25.0\text{ mm/s}$). | | M9204 | dicom-rt-gantry-couch-collision | error | Non-coplanar couch angle ($ | \theta_{\text{couch}} | > 15^\circ$) combined with lateral/posterior gantry angle enters the collision hazard zone. | | M9205 | dicom-rt-oar-dose-constraint-violated | error | Organ-at-Risk (ORGAN) DVH exceeds clinical QUANTEC maxDoseLimitGy or meanDoseLimitGy. | | M9206 | dicom-rt-non-monotonic-cum-meterset | error | Control point cumulativeMetersetWeight sequence is not monotonically non-decreasing from 0.0 to 1.0. | | M9207 | dicom-rt-unclosed-roi-contour | error | CLOSED_PLANAR contour slice contains fewer than 3 vertices. | | M9208 | dicom-rt-unresolved-frame-of-reference | error | RTSTRUCT or RTDOSE FrameOfReferenceUID does not match the RTPLAN FrameOfReferenceUID. | | M9209 | dicom-rt-invalid-beam-meterset | error | TREATMENT beam specifies metersetMu <= 0 or energyMeV <= 0. | | M9210 | dicom-rt-ptv-underdosage | warning | Target PTV $D_{95\mathrm{\%}}$ is less than $95\mathrm{\%}$ of prescribedDoseGy. |

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4. @modelscript/cellml — Cellular Electrophysiology & Systems Physiology (.cellml)

Supports CellML 1.0, 1.1, and 2.0 component networks, 7-dimensional SI unit verification, Content MathML 2.0 ODEs (Hodgkin-Huxley, Noble, Ten Tusscher cardiac electrophysiology, microvascular hemodynamics), and projections to Modelica 3.x and SBML Level 3.

Mathematical Foundations

$$\mathbf{d}(u)={\left[\begin{array}{ccccccc}{d}_{\text{A}}& d_{\text{K}}& d_{\text{kg}}& d_{\text{m}}& d_{\text{mol}}& d_{\text{s}}& d_{\text{cd}}\end{array}\right]}^T\in {\mathbb{R}}^7,C_m\frac{d{V}_m}{dt}=-\sum _k{g}_k{m}_k^{p_k}{h}_k^{q_k}(V_m-E_k)+I_{\text{stim}}(t)$$

Diagnostic Rules (M9301–M9310)

Code	Rule ID	Severity	Description
M9301	cellml-missing-model-name	error	<model> element is missing a non-empty name attribute.
M9302	cellml-unresolved-units	error	Variable or <unit> references an undeclared or non-standard CellML unit name.
M9303	cellml-interface-direction-conflict	error	<map_variables> connects variables with incompatible interface directions (e.g. both in or none).
M9304	cellml-unit-dimensional-mismatch	warning	Mapped variables in <map_variables> have incompatible 7-element SI base unit dimension vectors.
M9305	cellml-uninitialized-state-variable	warning	Differential state variable ($\text{ODE}$) lacks an initial_value attribute.
M9306	cellml-encapsulation-hierarchy-cycle	error	Circular component reference detected in <encapsulation> hierarchy.
M9307	cellml-unresolved-connection-member	error	<connection> references an undeclared component or variable name.
M9308	cellml-overconstrained-variable	error	Variable with an in interface or prior assignment is assigned by an equation or ODE.
M9309	cellml-undefined-math-ci	error	Content MathML <ci> references an identifier not declared in the enclosing <component>.
M9310	cellml-duplicate-variable-or-component	error	Duplicate <component> or <variable> name declared within the same scope.

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5. @modelscript/febio — Soft-Tissue Biomechanics & SOFA Surgical Simulation (.feb, .scn)

Parses FEBio 2.5–4.0 (.feb) continuum biomechanics models and SOFA Framework (.scn) real-time surgical simulation scene graphs. Evaluates Neo-Hookean, Mooney-Rivlin, Ogden, and Holzapfel-Gasser-Ogden (HGO) anisotropic arterial wall strain energy functions, plus biphasic poroelasticity.

Mathematical Foundations

$${\mathrm{\Psi }}_{\text{MR}}({\overline{I}}_1,{\overline{I}}_2,J)=c_1({\overline{I}}_1-3)+c_2({\overline{I}}_2-3)+\frac{K}{2}(\ln J{)}^2,\mathbf{q}=-\mathbf{k}\mathrm{\nabla }p$$

Diagnostic Rules (M9401–M9410)

Code	Rule ID	Severity	Description
M9401	febio-invalid-material-constant	error	Non-physical material constant ($E\le 0$, $\nu \notin (-1,0.5)$, $\rho \le 0$, or $c_1+c_2\le 0$).
M9402	febio-inverted-element-jacobian	error	Tetrahedral (tet4) or hexahedral (hex8) element has non-positive Jacobian determinant ($det(\mathbf{J})\le 0$).
M9403	febio-unresolved-node-or-set	error	Element connectivity, boundary condition, or load references an undefined node ID, <NodeSet>, or <Surface>.
M9404	febio-unconstrained-rigid-body	warning	Model defines no fixed or prescribed displacement boundary conditions to constrain rigid-body motion.
M9405	febio-invalid-biphasic-permeability	error	Biphasic/poroelastic tissue material specifies permeability $k\le 0$ or solid volume fraction ${\varphi }^s\notin (0,1)$.
M9406	febio-invalid-time-stepper	error	<Control> specifies time_steps <= 0 or step_size <= 0.
M9407	febio-unresolved-material-id	error	<SolidDomain> or element block references an undeclared material ID.
M9408	febio-contact-penalty-invalid	error	Contact interface specifies a non-positive penalty factor or empty primary/secondary surface.
M9409	febio-sofa-missing-mechanical-object	error	SOFA <Node> contains a force field without a <MechanicalObject> state container.
M9410	febio-duplicate-entity-id	error	Duplicate node, element, or material identifier.

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6. @modelscript/nifti — Volumetric Medical Imaging (.nii, .nrrd, .nhdr)

Parses NIfTI-1/NIfTI-2 headers and NRRD volumetric descriptors, validates qform quaternion and sform $4\times 4$ RAS affine transformations, extracts segmented anatomical iso-surfaces, and projects to OpenSCAD and ISO 10303-21 STEP.

Mathematical Foundations

$$\left[\begin{array}{c}{x}_{\text{RAS}}\\ y_{\text{RAS}}\\ z_{\text{RAS}}\\ 1\end{array}\right]=\left[\begin{array}{cc}\mathbf{R}(\mathbf{q})\text{diag}(\mathrm{\Delta }x,\mathrm{\Delta }y,q_{\text{fac}}\mathrm{\Delta }z)& {\mathbf{q}}_{\text{offset}}\\ {\mathbf{0}}^T& 1\end{array}\right]\left[\begin{array}{c}i\\ j\\ k\\ 1\end{array}\right],a=\sqrt{max(0,1-(b^2+c^2+d^2))}$$

Diagnostic Rules (M9501–M9510)

| Code | Rule ID | Severity | Description | | :------ | :-------------------------------------- | :-------- | :---------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------- | ------------ | | M9501 | nifti-invalid-dimensions | error | Volume dimension dim[0] is outside [1, 7] or spatial dimensions $n_x,n_y,n_z\le 0$. | | M9502 | nifti-non-positive-voxel-spacing | error | Voxel spacing pixdim[1..3] or NRRD space directions norm is $\le 0\text{ mm}$. | | M9503 | nifti-singular-affine-transform | error | $4\times 4$ sform affine transformation matrix is singular ($ | \det(\mathbf{A}) | < 10^{-9}$). | | M9504 | nifti-invalid-quaternion-norm | error | Quaternion parameters satisfy $b^2+c^2+d^2>1.0$. | | M9505 | nifti-qform-sform-handedness-mismatch | error | Active qform and sform transforms have opposite coordinate handedness ($\text{sign}(q_{\text{fac}})\ne \text{sign}(det({\mathbf{A}}_{\text{sform}}))$). | | M9506 | nifti-zero-intensity-scale-slope | error | scl_slope is explicitly 0 while intensity scaling is active. | | M9507 | nifti-unsupported-datatype | error | Unrecognized or unsupported NIfTI/NRRD voxel datatype code. | | M9508 | nifti-voxel-data-size-mismatch | error | Voxel payload count does not match $n_x\times n_y\times n_z\times n_t$. | | M9509 | nifti-empty-segmentation-mask | warning | Segmentation labelmap contains zero foreground voxels across all anatomical labels. | | M9510 | nifti-anisotropic-slice-gap-warning | warning | Slice thickness $\mathrm{\Delta }z$ exceeds in-plane resolution $min(\mathrm{\Delta }x,\mathrm{\Delta }y)$ by more than $5\times$. |

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7. @modelscript/topas — Monte Carlo Proton & Hadrontherapy (.topas, .mac)

Parses TOPAS (Ge/, So/, Sc/, Ph/, Ma/, Tf/) parameter files and GATE (.mac) macros, verifies hierarchical CSG beamline geometry containment, and computes analytical Bortfeld (1997) proton/carbon-ion Bragg peak depth-dose profiles.

Mathematical Foundations

$$R_0=\alpha E_0^p(\alpha \approx 0.0022\text{ cm}\cdot {\text{MeV}}^{-p},p\approx 1.77),-\frac{dE}{dz}\propto \frac{z^2}{{\beta }^2}[\ln \left(\frac{2m_e{c}^2{\beta }^2}{I(1-{\beta }^2)}\right)-{\beta }^2]$$

Diagnostic Rules (M9601–M9610)

Code	Rule ID	Severity	Description
M9601	topas-type-prefix-mismatch	error	Parameter value does not match its declared TOPAS type prefix (d:, i:, b:, s:, dv:, iv:, sv:).
M9602	topas-unresolved-parent-component	error	Geometry component Parent references an undeclared parent volume.
M9603	topas-non-positive-geometry-dimension	error	Box/Cylinder/Sphere dimension (HLX, HLY, HLZ, RMax, HL) is $\le 0$, or RMin >= RMax.
M9604	topas-child-exceeds-parent-bounds	error	Child geometry translation plus half-lengths protrude outside the parent volume bounding box.
M9605	topas-undefined-material	error	Component Material references an unknown material not in Geant4/NIST or custom Ma/<Name> definitions.
M9606	topas-invalid-beam-energy	error	Particle source BeamEnergy <= 0 MeV or negative energy spread.
M9607	topas-circular-include-file	error	Circular or self-referential includeFile chain detected.
M9608	topas-scorer-missing-component	error	Scorer Sc/<Name>/Component or Quantity is missing or references an undeclared geometry volume.
M9609	topas-vector-length-mismatch	error	Vector parameter (dv:, iv:, sv:) element count does not match its declared length token.
M9610	topas-duplicate-parameter-assignment	warning	Identical parameter path is assigned multiple times in the same file without an override qualifier.

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8. @modelscript/three-mf — Patient-Specific 3D-Printed Surgical Guides & Implants (.3mf)

Parses ISO/ASTM 52915 3MF models (<model>, <resources>, <mesh>, <vertices>, <triangles>, <build>, and <surgical_guide> osteotomy/drill sleeve annotations), verifies 2-manifold watertightness and signed volume, and projects to ISO 10303-21 STEP and OpenSCAD.

Mathematical Foundations

$$\chi =V-E+F=2-2g,V_{\text{signed}}=\frac{1}{6}\sum _{k=1}^F{\mathbf{v}}_{k,1}\cdot ({\mathbf{v}}_{k,2}\times {\mathbf{v}}_{k,3})>0$$

Diagnostic Rules (M9701–M9710)

Code	Rule ID	Severity	Description
M9701	three-mf-non-manifold-edge	error	Mesh is not a closed 2-manifold (contains open boundary edges or edges shared by $\ne 2$ triangles).
M9702	three-mf-degenerate-triangle	error	Triangle has duplicate vertex indices or zero surface area ($|{\mathbf{e}}_1\times {\mathbf{e}}_2|<{10}^{-12}$).
M9703	three-mf-negative-mesh-volume	error	Mesh has inverted outward face normals resulting in non-positive signed volume ($V\le 0$).
M9704	three-mf-unresolved-build-object	error	<build><item objectid="..."/> references an undefined <object> ID.
M9705	three-mf-wall-thickness-violation	error	Surgical guide or cannula wall thickness is below the $0.8\text{ mm}$ additive manufacturing safety threshold.
M9706	three-mf-invalid-osteotomy-guide-axis	error	Osteotomy cutting plane normal or drill sleeve axis vector has zero length.
M9707	three-mf-missing-biocompatible-material	error	Medical implant or surgical guide lacks an approved ISO 10993 / USP Class VI biocompatible material (Ti-6Al-4V, PEEK, BioMed Amber, etc.).
M9708	three-mf-singular-item-transform	error	<item transform="..."/> $4\times 3$ affine transformation matrix has $det(\mathbf{M})\le 0$.
M9709	three-mf-out-of-bounds-vertex-index	error	Triangle vertex index $v_i<0$ or $v_i\ge N_{\text{vertices}}$.
M9710	three-mf-duplicate-object-id	error	Duplicate <object id="..."/> declared in <resources>.

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9. @modelscript/igtl — OpenIGTLink & PLUS Surgical Navigation (.igtl, .plus.xml)

Parses PLUS Toolkit (<PlusConfiguration>, <DeviceSet>, <CoordinateDefinitions>, <PlusOpenIGTLinkServer>, <PivotCalibration>, <FiducialRegistration>) and OpenIGTLink transform streams. Solves $SE(3)$ coordinate frame chains, least-squares stylus pivot calibration, and Fitzpatrick (1998) Target Registration Error ($\text{TRE}$).

Mathematical Foundations

1. Least-Squares Stylus Pivot Calibration:

   $$\left[\begin{array}{cc}{\mathbf{R}}_1& -{\mathbf{I}}_3\\ ⋮& ⋮\\ {\mathbf{R}}_M& -{\mathbf{I}}_3\end{array}\right]\left[\begin{array}{c}{\mathbf{p}}_{\text{tip}}\\ {\mathbf{p}}_{\text{pivot}}\end{array}\right]=\left[\begin{array}{c}-{\mathbf{t}}_1\\ ⋮\\ -{\mathbf{t}}_M\end{array}\right]$$

2. Fitzpatrick (1998) Target Registration Error (TRE):

   $$⟨{\text{TRE}}^2(\mathbf{r})⟩=\frac{⟨{\text{FLE}}^2⟩}{N}(1+\frac{1}{3}\sum _{k=1}^3\frac{d_k^2}{f_k^2}),⟨{\text{FRE}}^2⟩=(1-\frac{2}{N})⟨{\text{FLE}}^2⟩$$

Diagnostic Rules (M9801–M9810)

Code	Rule ID	Severity	Description
M9801	igtl-non-orthogonal-rotation	error	Upper-left $3\times 3$ rotation block $\mathbf{R}$ violates $|{\mathbf{R}}^T\mathbf{R}-{\mathbf{I}}_3{|}_F>{10}^{-3}$ or $det(\mathbf{R})\le 0$.
M9802	igtl-invalid-homogeneous-bottom-row	error	Bottom row of $4\times 4$ homogeneous matrix is not [0, 0, 0, 1].
M9803	igtl-disconnected-coordinate-frame	error	Coordinate frame graph is disconnected or lacks a path for a requested <Transform Name="...To..."/>.
M9804	igtl-cyclic-transform-chain	error	<CoordinateDefinitions> contains a directed cycle in frame definitions.
M9805	igtl-excessive-registration-error	warning	Calibration or fiducial registration RMS error ($\text{FRE}$ / $\text{TRE}$) exceeds $2.0\text{ mm}$.
M9806	igtl-invalid-acquisition-rate	error	Tracker or ultrasound device AcquisitionRate <= 0 Hz.
M9807	igtl-unresolved-device-or-channel	error	<Device> or <PlusOpenIGTLinkServer> references an undeclared device or channel ID.
M9808	igtl-self-transform-identity-mismatch	error	Transform with From == To is not the $4\times 4$ identity matrix.
M9809	igtl-invalid-server-port	error	OpenIGTLink server ListeningPort is outside the valid TCP range [1024, 65535].
M9810	igtl-duplicate-transform-edge	error	Duplicate <Transform> declared for the same (From, To) coordinate frame pair.

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10. @modelscript/owl2 (ontospm) — OntoSPM Surgical Process Ontology

Models surgical workflows (Procedure $\to$ Phase $\to$ Step $\to$ Action + Instrument + AnatomicalStructure), enforces Critical View of Safety (CVS) verification before irreversible tissue division, and detects monopolar thermal spread hazards near critical neurovascular structures.

Diagnostic Rules (M9901–M9910)

Code	Rule ID	Severity	Description
M9901	ontospm-missing-critical-safety-view	error	Irreversible action (Clipping, Cutting, Transection, Resection) on a critical neurovascular or biliary structure executes without a verified SafetyCheckpoint (Critical View of Safety).
M9902	ontospm-instrument-action-incompatibility	error	Surgical step pairs an instrument category with an incompatible surgical action verb (e.g. ClipApplier performing Suturing).
M9903	ontospm-phase-transition-cycle	error	Surgical phase transition graph contains a directed cycle.
M9904	ontospm-unresolved-anatomical-target	error	Surgical step references an undeclared anatomical structure ID.
M9905	ontospm-unresolved-instrument-reference	error	Surgical step references an undeclared surgical instrument ID.
M9906	ontospm-missing-hemostasis-or-closure	warning	Invasive surgical procedure lacks a terminal Hemostasis or Closure phase.
M9907	ontospm-bipolar-monopolar-energized-near-nerve	error	Monopolar electrosurgical instrument is energized within $5.0\text{ mm}$ of a critical nerve or artery.
M9908	ontospm-non-positive-step-duration	error	Surgical step specifies an expected duration $\le 0\text{ s}$.
M9909	ontospm-unreachable-surgical-phase	warning	Surgical phase is unreachable from the initial preparation/exposure phase.
M9910	ontospm-duplicate-entity-iri	error	Duplicate OntoSPM entity identifier declared in the surgical procedure.

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11. Command-Line Interface (msx) Usage

# 1. OpenSim Musculoskeletal Biomechanics
npx msx opensim validate Arm26.osim
npx msx opensim simulate Arm26.osim
npx msx opensim to-modelica Arm26.osim > Arm26.mo
npx msx opensim to-urdf Arm26.osim > Arm26.urdf

# 2. DICOM-RT Radiation Oncology & Dosimetry
npx msx dicom-rt validate ProstateVMAT.rtplan
npx msx dicom-rt dosimetry ProstateVMAT.rtplan
npx msx dicom-rt to-scad ProstateVMAT.rtplan > ProstateVMAT.scad
npx msx dicom-rt to-sysml ProstateVMAT.rtplan > ProstateVMAT.sysml

# 3. CellML Electrophysiology & Microvascular Perfusion
npx msx cellml validate HodgkinHuxley.cellml
npx msx cellml simulate HodgkinHuxley.cellml
npx msx cellml to-modelica HodgkinHuxley.cellml > HodgkinHuxley.mo
npx msx cellml to-sbml HodgkinHuxley.cellml > HodgkinHuxley.sbml

# 4. FEBio & SOFA Soft-Tissue Biomechanics
npx msx febio validate LiverHyperelastic.feb
npx msx febio solve LiverHyperelastic.feb
npx msx febio to-inp LiverHyperelastic.feb > LiverHyperelastic.inp

# 5. NIfTI & NRRD Volumetric Medical Imaging
npx msx nifti validate BrainAtlas.nii
npx msx nifti mesh BrainAtlas.nii
npx msx nifti to-step BrainAtlas.nii > BrainAtlas.stp

# 6. TOPAS & GATE Hadrontherapy Monte Carlo
npx msx topas validate ProtonNozzle.topas
npx msx topas bragg-peak ProtonNozzle.topas
npx msx topas to-scad ProtonNozzle.topas > ProtonNozzle.scad

# 7. 3MF Medical Surgical Guides & Implants
npx msx three-mf validate MandibleOsteotomyGuide.3mf
npx msx three-mf topology MandibleOsteotomyGuide.3mf
npx msx three-mf to-step MandibleOsteotomyGuide.3mf > MandibleOsteotomyGuide.stp

# 8. OpenIGTLink & PLUS Surgical Navigation
npx msx igtl validate LaparoscopicTracker.plus.xml
npx msx igtl calibrate LaparoscopicTracker.plus.xml
npx msx igtl to-urdf LaparoscopicTracker.plus.xml > SurgicalTracker.urdf

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12. IDE Custom Editors & MCP Agent Tools

Visual Custom Editor Providers (@modelscript/ide-client)

• OpenSimEditorProvider (modelscript.opensimEditor): Interactive musculoskeletal kinematic chain diagram, Hill-type muscle force-length/force-velocity curves, RK4 tendon force trajectories, and one-click export to Modelica 3.x (.mo) and ROS URDF (.urdf).
• DicomRtEditorProvider (modelscript.dicomRtEditor): Cumulative Dose-Volume Histogram (DVH) plotter, ICRU 83 HI / Paddick CI / LQ BED / EQD2 dashboard, Beam's Eye View (BEV) Multi-Leaf Collimator (MLC) aperture SVG, and one-click export to OpenSCAD (.scad) and SysML v2 (.sysml).
• IgtlEditorProvider (modelscript.igtlEditor): $SE(3)$ coordinate frame chain topology viewer, rotation matrix orthogonality auditor, least-squares stylus pivot calibration & Fitzpatrick $\text{TRE}$ panel, and one-click export to ROS URDF (.urdf) and Modelica 3.x (.mo).

Model Context Protocol (@modelscript/mcp) Tools

MCP Tool Name	Input Schema	Capabilities
opensim_analyze	{ opensimContent, duration?, dt? }	Parses .osim models, runs M9101–M9110 lints, lowers to DAEBuilder, and integrates Hill-type muscle & coordinate trajectories.
dicom_rt_verify_dvh	{ dicomRtContent }	Evaluates RTPLAN/RTSTRUCT/RTDOSE documents, checks M9201–M9210 QUANTEC & MLC safety rules, and computes DVH, BED, EQD2, HI, and CI.
cellml_simulate	{ cellmlContent, duration?, dt? }	Verifies 7-dimensional SI unit consistency (M9301–M9310), lowers to DAEBuilder, and integrates cellular electrophysiology ODEs.
igtl_verify_calibration	{ igtlContent }	Audits $SE(3)$ transforms (M9801–M9810), solves shortest transform chains, stylus pivot calibration RMS error, and Fitzpatrick $\text{TRE}$.
three_mf_verify_guide	{ threeMfContent }	Verifies 3MF surgical guides & implants (M9701–M9710) for 2-manifold watertightness, Euler characteristic $\chi$, wall thickness, and osteotomy axes.