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fix link paths and active in clinical test navbar
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‎clinical/aortofemoral2.html‎

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<div class="navSubLink">
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<a href="coronary.html">Coronary Normal</a>
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</div>
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<div class="navSubLink active">
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<div class="navSubLink">
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<a href="aortofemoral1.html">Aortofemoral Normal - 1</a>
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</div>
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<div class="navSubLink">
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<div class="navSubLink active">
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<a href="aortofemoral2.html">Aortofemoral Normal - 2</a>
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</div>
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<div class="navSubLink">

‎clinical/coronary.html‎

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<details>
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<summary class="navTitle"><i class="iconInHeader fa-solid fa-stethoscope" style="padding-right: 15px"></i>Clinical Cases</summary>
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<div>
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<div class="navSubLink">
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<div class="navSubLink active">
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<a href="coronary.html">Coronary Normal</a>
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</div>
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<div class="navSubLink active">
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<div class="navSubLink">
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<a href="aortofemoral1.html">Aortofemoral Normal - 1</a>
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</div>
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<div class="navSubLink">

‎clinical/pulmonary.html‎

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<div class="navSubLink">
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<a href="coronary.html">Coronary Normal</a>
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</div>
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<div class="navSubLink active">
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<div class="navSubLink">
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<a href="aortofemoral1.html">Aortofemoral Normal - 1</a>
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</div>
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<div class="navSubLink">
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<a href="aortofemoral2.html">Aortofemoral Normal - 2</a>
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</div>
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<div class="navSubLink">
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<div class="navSubLink active">
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<a href="pulmonary.html">Healthy Pulmonary</a>
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</div>
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<div class="navSubLink">

‎documentation/python_interface/modules/function_arguments/readme.md‎

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</pre>
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<br>
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All API errors are handled using exceptions. See the <a href="#modules_error_handling"> Error Handling </a> section.
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All API errors are handled using exceptions. See the <a href="#error_handling"> Error Handling </a> section.

‎documentation/quickguide/gui/display/readme.md‎

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mouse button in a 2D view centers the crosshair on that point. Pressing the right mouse button and moving the mouse zooms
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in and out. Scrolling the mouse wheel changes the principal plane slice for which the mouse cursor is in.
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Changing the principal planes slice changes the values displayed in the <a href="#image_navigator"> Image Navigator </a>
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Changing the principal planes slice changes the values displayed in the <a href="#gui_image_navigator"> Image Navigator </a>
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and vice versa.
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The function of the mouse buttons depends on the window the mouse cursor is in.

‎documentation/quickguide/tutorial/create_paths/readme.md‎

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The following sections demonstrate how to create a path defining the main aorta and right iliac, and another for the left iliac.
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A detailed discussion about creating paths can be found in the SimVascular
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<a href="modeling.html#modelingPathPlanning.html">Modeling Guide / Path Planning</a> documentation.
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<a href="modeling.html#modelingPathPlanning">Modeling Guide / Path Planning</a> documentation.
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<h3 id="tutorial_create_paths_1"> Create an instance of a <i>Paths Tool</i> for the aorta/right iliac </h3>
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Create an instance of a <i>Paths Tool</i> named <b>aorta</b> used to define <i>Path</i> geometry for the main aorta
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end of the right iliac arteries. Path points are added interactively by positioning crosshairs in the three 2D
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views to select the approximate center of a vessel lumen.
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The crosshairs are moved using the left mouse button or the <a href="#image_navigator"><i>Image Navigator</i></a>.
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The crosshairs are moved using the left mouse button or the <a href="#gui_image_navigator"><i>Image Navigator</i></a>.
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<table class="table table-bordered" style="width:100%">
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<caption> Add <i>Path</i> points using the <b>aorta</b> <i>Paths Tool</i> </caption>

‎documentation/quickguide/tutorial/create_segmentations/readme.md‎

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The following sections demonstrate how to create segmentations using the <b>aorta</b> and <b>left-iliac</b> <i>Paths</i>.
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A detailed discussion about segmentation can be found in the SimVascular
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<a href="modeling.html#modelingSegmentation.html">Modeling Guide / Segmentation</a> documentation.
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<a href="modeling.html#modelingSegmentation">Modeling Guide / Segmentation</a> documentation.
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<h3 id="tutorial_create_segs_1"> Create an instance of a <i>Segmentations Tool</i> for the aorta/right iliac </h3>
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‎documentation/rom_simulation/0d-solver/refs/readme.md‎

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# References
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<a id="ref-1">
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Seo J, Fleeter C, Kahn A, Marsden A, Schiavazzi D. **Multi-fidelity estimators for coronary artery models under clinically-informed data uncertainty**. Int J Uncertain Quantif. 2020.
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</a>
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<p><a id="ref-1">
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Seo J, Fleeter C, Kahn A, Marsden A, Schiavazzi D. <strong>Multi-fidelity estimators for coronary artery models under clinically-informed data uncertainty</strong>. Int J Uncertain Quantif. 2020.
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</a></p>
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<a id="ref-2">
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K.E. Jansen, C.H. Whiting, G.M. Hulbert, **A generalized-$\alpha$ method for integrating the filtered Navier–Stokes equations with a stabilized finite element method**, Comp. Methods Appl. Mech. Engrg. 190 (1999) 305–319.
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</a>
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<p><a id="ref-2">
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K.E. Jansen, C.H. Whiting, G.M. Hulbert, <strong>A generalized-$\alpha$ method for integrating the filtered Navier–Stokes equations with a stabilized finite element method</strong>, Comp. Methods Appl. Mech. Engrg. 190 (1999) 305–319.
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</a></p>
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<a id="ref-3">
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Mehran Mirramezani and Shawn C. Shadden. **A distributed lumped parameter model of blood flow. Annals
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of Biomedical Engineering**, 2020.
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</a>
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<p><a id="ref-3">
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Mehran Mirramezani and Shawn C. Shadden. <strong>A distributed lumped parameter model of blood flow. Annals
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of Biomedical Engineering</strong>, 2020.
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</a></p>
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<a id="ref-4">
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H.J. Kim, I.E. Vignon-Clementel, J.S. Coogan, C.A. Figueroa, K.E. Jansen and C.A. Taylor, **Patient-specific modeling of blood flow and pressure in human coronary arteries**, Annals of Biomedical Engineering, 38(10):3195-3209, 2010.
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</a>
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<p><a id="ref-4">
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H.J. Kim, I.E. Vignon-Clementel, J.S. Coogan, C.A. Figueroa, K.E. Jansen and C.A. Taylor, <strong>Patient-specific modeling of blood flow and pressure in human coronary arteries</strong>, Annals of Biomedical Engineering, 38(10):3195-3209, 2010.
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</a></p>

‎documentation/rom_simulation/1d-solver/refs/readme.md‎

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# References
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<a id="ref-1">
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[1] T.J.R. Hughes and J. Lubliner, **On the One-Dimensional Theory of Blood Flow in the Larger Vessels** , Mathematical Biosciences , 18(1-2) (1973), 161-170.
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</a>
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<p><a id="ref-1">
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[1] T.J.R. Hughes and J. Lubliner, <strong>On the One-Dimensional Theory of Blood Flow in the Larger Vessels</strong>, Mathematical Biosciences , 18(1-2) (1973), 161-170.
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</a></p>
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<a id="ref-2">
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[2] T.J.R. Hughes, **A Study of the One-Dimensional Theory of Arterial Pulse Propagation**, 1974, U.C. Berkeley, Ph.D. Thesis. </a>
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<p><a id="ref-2">
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[2] T.J.R. Hughes, <strong>A Study of the One-Dimensional Theory of Arterial Pulse Propagation</strong>, 1974, U.C. Berkeley, Ph.D. Thesis. </a></p>
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<a id="ref-3">
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[3] M.S. Olufsen, **Structured Tree Outflow Condition for Blood Flow in Larger Systemic Arteries** , American Journal of Physiology , 276 (1999), H257-268.
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</a>
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<p><a id="ref-3">
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[3] M.S. Olufsen, <strong>Structured Tree Outflow Condition for Blood Flow in Larger Systemic Arteries</strong>, American Journal of Physiology , 276 (1999), H257-268.
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</a></p>
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<a id="ref-4">
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[4] J. Wan, B.N. Steele, S.A. Spicer, S. Strohband, G.R. Feijoo, T.J.R. Hughes and C.A. Taylor, **A One-Dimensional Finite Element Method for Simulation-Based Medical Planning for Cardiovascular Disease** , Computer Methods in Biomechanics and Biomedical Engineering , 5(3) (2002), 195-206.
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</a>
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<p><a id="ref-4">
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[4] J. Wan, B.N. Steele, S.A. Spicer, S. Strohband, G.R. Feijoo, T.J.R. Hughes and C.A. Taylor, <strong>A One-Dimensional Finite Element Method for Simulation-Based Medical Planning for Cardiovascular Disease</strong>, Computer Methods in Biomechanics and Biomedical Engineering , 5(3) (2002), 195-206.
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</a></p>
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<a id="ref-5">
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[5] D. Givoli and J.B. Keller, **A Finite Element Method for Large Domains** , Computer Methods in Applied Mechanics and Engineering , 76(1) (1989), 41-66.
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</a>
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<p><a id="ref-5">
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[5] D. Givoli and J.B. Keller, <strong>A Finite Element Method for Large Domains</strong>, Computer Methods in Applied Mechanics and Engineering , 76(1) (1989), 41-66.
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</a></p>
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[6] J.B. Keller and D. Givoli, **Exact Non-Reflecting Boundary-Conditions** , Journal of Computational Physics , 82(1) (1989), 172-192.
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</a>
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<p><a id="ref-6">
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[6] J.B. Keller and D. Givoli, <strong>Exact Non-Reflecting Boundary-Conditions</strong>, Journal of Computational Physics , 82(1) (1989), 172-192.
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</a></p>
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<a id="ref-7">
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[7] D. Givoli, **Numerical Methods for Problems in Infinite Domains**, 1992, Elsevier Science.
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</a>
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<p><a id="ref-7">
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[7] D. Givoli, <strong>Numerical Methods for Problems in Infinite Domains</strong>, 1992, Elsevier Science.
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</a></p>
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<a id="ref-8">
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[8] M. Grote and J. Keller, **Exact Nonreflecting Boundary Conditions for the Time Dependent Wave Equation** , SIAM Journal on Applied Mathematics , 55(2) (1995), 280-297.
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</a>
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<p><a id="ref-8">
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[8] M. Grote and J. Keller, <strong>Exact Nonreflecting Boundary Conditions for the Time Dependent Wave Equation</strong>, SIAM Journal on Applied Mathematics , 55(2) (1995), 280-297.
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</a></p>
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<a id="ref-9">
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[9] I. Patlashenko, D. Givoli and P. Barbone, **Time-Stepping Schemes for Systems of Volterra Integro-Differential Equations** , Computer Methods in Applied Mechanics and Engineering , 190 (2001), 5691-5718.
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</a>
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<p><a id="ref-9">
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[9] I. Patlashenko, D. Givoli and P. Barbone, <strong>Time-Stepping Schemes for Systems of Volterra Integro-Differential Equations</strong>, Computer Methods in Applied Mechanics and Engineering , 190 (2001), 5691-5718.
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</a></p>
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<a id="ref-10">
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[10] T.J.R. Hughes and M. Mallet, **A New Finite Element Formulation for Computational Fluid Dynamics: III. The Generalized Streamline Operator for Advective-Diffusive Systems** , Computer Methods in Applied Mechanics and Engineering , 58 (1986), 305-328.
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<p><a id="ref-10">
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[10] T.J.R. Hughes and M. Mallet, <strong>A New Finite Element Formulation for Computational Fluid Dynamics: III. The Generalized Streamline Operator for Advective-Diffusive Systems</strong>, Computer Methods in Applied Mechanics and Engineering , 58 (1986), 305-328.
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</a>
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<a id="ref-11">
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[11] T.J.R. Hughes, L.P. Franca and G.M. Hulbert, **A New Finite Element Formulation for Computational Fluid Dynamics: VIII. The Galerkin/Least-Squares Method for Advective-Diffusive Equations** , Computer Methods in Applied Mechanics and Engineering , 73(2) (1989), 173-189.
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</a>
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<p><a id="ref-11">
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[11] T.J.R. Hughes, L.P. Franca and G.M. Hulbert, <strong>A New Finite Element Formulation for Computational Fluid Dynamics: VIII. The Galerkin/Least-Squares Method for Advective-Diffusive Equations</strong>, Computer Methods in Applied Mechanics and Engineering , 73(2) (1989), 173-189.
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</a></p>
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<p><a id="ref-12">
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[12] N. Xiao, J. Alastruey, and C. Alberto Figueroa (2014), A systematic comparison between 1‐D and 3‐D hemodynamics in compliant arterial models. Int. J. Numer. Meth. Biomed. Engng., 30: 204-231.
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</a>
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</a></p>

‎documentation/rom_simulation/intro/readme.md‎

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The geometry of the one-dimensional networks used by the **sv1DSolver** is based on the centerlines computed from the surface
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of a 3D geometric model. The 3D geometric model is created from image data using the typical
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SimVascular <a href="modeling.html"> modeling workflow </a>.
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SimVascular <a href="modeling.html"> modeling workflow</a>.
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Centerlines represent a 1D characterization of blood vessel geometry. The centerlines are computed for a 3D surface using
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the <a href="http://www.vmtk.org/tutorials/Centerlines.html"> Vascular Modeling Toolkit </a>. The computation solves a wave propagation
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the <a href="http://www.vmtk.org/tutorials/Centerlines.html"> Vascular Modeling Toolkit</a>. The computation solves a wave propagation
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problem using a source point representing the start of the centerlines and target points representing the ends of the centerlines.
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The source and target points are selected from the model caps defined in the SimVascular **Modeling Tool**.
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