Difference between revisions of "Matlab based temperature solver"

Latest revision as of 14:15, 15 April 2016

Citation

Bastien Guérin, Jorge F. Villena, Athanasios G. Polimeridis, Elfar Adalsteinsson, Luca Daniel, Jacob K. White, Bruce R. Rosen and Lawrence L. Wald (2016). "Ultimate hyperthermia: Computation of the best achievable radio-frequency hyperthermia treatments in non-uniform body models". Annual meeting of the International Society for Magnetic Resonance in Medicine. Singapore.

What this code does

This is a Crank-Nicholson Matlab-based temperature solver with heat generation (=SAR) and tissue perfusion. The code mixed spatial and temporal finite differences using the Crank-Nicholson scheme. Non-homogeneous tissues properties (including tissue perfusion, thermal conductivity and heat capacity) are supported. The code is fully validated by comparison with the SEMCAD temperature solver. Two solve options are available: Transient and steady-state calculations.

Download files

The code can be downloaded here.

Instructions

Transient simulations

To run a simple example, go to the sub-folder SEMCAD_validation/Simu_1_Results and run the script "semcad_vs_pbhs.m". This runs a comparison of the transient solver with SEMCAD. This script should make it clear how the code is run. The input to the code are, in this order:

T0: The initial temperature map (can be non-uniform) in K
DUR: The total duration of the simulation in s
[dx dy dz]: A 1x3 Matlab vector with the x, y and z spatial resolutions in m
RHO: The density map (can be non-uniform) in kg/m^3
C: The heat capacity map (can be non-uniform) in J/kg/K
K: The thermal conductivity map (can be non-uniform) in W/m/K
Wb: The blood perfusion map (can be non-uniform) in kg/s/m^3
Cb: The blood heat capacity in J/kg/K
Tb: The blood temperature in K
Q: The heat rate generation map (i.e., SAR*RHO which can be non-uniform) in W/m^3

Steady state simulations

To run a simple example of the steady-state simulation, go to the TEST_SteadyState/ folder and run "TEST_SS.m". Again, the way to run the code should be straightforward. The input to the steady-state function are similar to the input to the transient solve function, except obviously the duration is not needed.

@@ Line 1: / Line 1: @@
-[[File:giorgio_phant.jpg|200px|thumb|right|]]
 === Citation ===
-Nadine N. Graedel, Jonathan R. Polimeni, Bastien Guerin, Borjan Gagoski and Lawrence L. Wald (2015). "An anatomically realistic temperature phantom for radiofrequency heating measurements". Magnetic Resonance in Medicine 73(1):442–450
+Bastien Guérin, Jorge F. Villena, Athanasios G. Polimeridis, Elfar Adalsteinsson, Luca Daniel, Jacob K. White, Bruce R. Rosen and Lawrence L. Wald (2016). "Ultimate hyperthermia: Computation of the best achievable radio-frequency hyperthermia treatments in non-uniform body models". Annual meeting of the International Society for Magnetic Resonance in Medicine. Singapore.
+=== What this code does ===
+This is a Crank-Nicholson Matlab-based temperature solver with heat generation (=SAR) and tissue perfusion. The code mixed spatial and temporal finite differences using the Crank-Nicholson scheme. Non-homogeneous tissues properties (including tissue perfusion, thermal conductivity and heat capacity) are supported. The code is fully validated by comparison with the SEMCAD temperature solver. Two solve options are available: Transient and steady-state calculations.
 === Download files ===
-Click [https://phantoms.martinos.org/images/3/36/MGH_head_1.zip here] to download the CAD model.
+The code can be downloaded [https://ptx.martinos.org/index.php/File:PennesBioHeatSolver_LITE.zip here].
-=== Phantom description ===
+=== Instructions ===
-This phantom is based on a 1mm isotropic segmented head model which was labeled as described in [http://www.ncbi.nlm.nih.gov/pubmed/18985401 Makris et al].
+==== Transient simulations ====
+To run a simple example, go to the sub-folder SEMCAD_validation/Simu_1_Results and run the script "semcad_vs_pbhs.m". This runs a comparison of the transient solver with SEMCAD. This script should make it clear how the code is run. The input to the code are, in this order:
+*T0:         The initial temperature map (can be non-uniform) in K
+*DUR:        The total duration of the simulation in s
+*[dx dy dz]: A 1x3 Matlab vector with the x, y and z spatial resolutions in m
+*RHO:        The density map (can be non-uniform) in kg/m^3
+*C:          The heat capacity map (can be non-uniform) in J/kg/K
+*K:          The thermal conductivity map (can be non-uniform) in W/m/K
+*Wb:         The blood perfusion map (can be non-uniform) in kg/s/m^3
+*Cb:         The blood heat capacity in J/kg/K
+*Tb:         The blood temperature in K
+*Q:          The heat rate generation map (i.e., SAR*RHO which can be non-uniform) in W/m^3
-The segmented head data was converted into a simplified surface model with two compartments: Brain and other soft tissues. Bone and air (both low epsilon, low conductivity) are printed together out of plastic material with similar electrical properties.
+==== Steady state simulations ====
+To run a simple example of the steady-state simulation, go to the TEST_SteadyState/ folder and run "TEST_SS.m". Again, the way to run the code should be straightforward. The input to the steady-state function are similar to the input to the transient solve function, except obviously the duration is not needed.
-=== Special considerations ===
-The sealing flange uses an o-ring.
-[[File:Phantom_figure_CT_MR.png|400px|thumb|right|]]