Difference between revisions of "Matlab based temperature solver"

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=== Citation ===
 
=== Citation ===
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Guérin B, Gebhardt M, Cauley S, Adalsteinsson E, Wald LL (2014). "[http://onlinelibrary.wiley.com/doi/10.1002/mrm.24800/pdf Local specific absorption rate (SAR), global SAR, transmitter power, and excitation accuracy trade‐offs in low flip‐angle parallel transmit pulse design.]" Magnetic Resonance in Medicine 71(4): 1446-1457.
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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 ===
 
=== What this code does ===
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This Matlab code (no MEX, no GPU code) computes least-squares and magnitude least-squares pTx spoke pulses. The MLS problem can be solved using the phase adoption approach of Setsompop et al. or a full optimization strategy (see the file spokes_3/run_spokes.m and options therein). Spokes can be optimized for several frequencies (spatio-spectral design) in order to build in robustness to off-resonance effects.
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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 ===
 
=== Download files ===
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The code can be downloaded [https://ptx.martinos.org/images/f/f2/SpokesMinExcErrLocGlobSARPuPow_fmincon_v12.zip here]. A test dataset can be downloaded [https://ptx.martinos.org/images/e/e2/Spokes_3.zip here]. If you wonder how I obtained the field maps, ROI and SODA (=slice information) files, download [https://ptx.martinos.org/images/c/c0/Prescan_data.zip this file].
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The code can be downloaded [https://ptx.martinos.org/index.php/File:PennesBioHeatSolver_LITE.zip here].
  
 
=== Instructions ===
 
=== Instructions ===
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==== Pre-scan data format ====
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==== Transient simulations ====
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The format of the pre-scan data (e.g., B0 map, B1+ maps, slice information in the SODA file) matches the Siemens pTx "Step 2" data format. To take a closer look at this, download the prescan_data.zip file,  
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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:
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* An ROI file in NIFTI format.
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*T0:        The initial temperature map (can be non-uniform) in K
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* A B0 map in NIFTI format.
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*DUR:        The total duration of the simulation in s
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* An FLD file containing the B1+ maps for the slice considered as obtained by pushing "save dataset" in the B1 mapping tab of the Siemens pTx "Step 2" interface.
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*[dx dy dz]: A 1x3 Matlab vector with the x, y and z spatial resolutions in m
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To get the ROI and B0 maps, I use the Siemens product gre_fieldmapping sequence (make sure to chose "save magnitude/phase" in order to get both the B0 and ROI maps in the same scan). The B0, B1 and ROI datasets must have the same number of pixels and same dimensions.
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*RHO:        The density map (can be non-uniform) in kg/m^3
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==== Spokes optimization ====
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*C:          The heat capacity map (can be non-uniform) in J/kg/K
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Unzip the code folder and add it to your path. Unzip the data folder and run the script run_spokes.m. There are several options in it that are straightforward to understand (e.g., LS/MLS, spatio-spectral design). The frequencies of the spatio-spectral design are expressed in Hz and are offset with respect to the Larmor frequency (i..e, +50 means Larmor frequency+50 Hz). Most of the spoke options (such as slice-thickness, slice-selection gradient, time-bandwidth product etc...) are specified in the text file spokes_def.txt and can be changed there.
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*K:          The thermal conductivity map (can be non-uniform) in W/m/K
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*Wb:        The blood perfusion map (can be non-uniform) in kg/s/m^3
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*Cb:        The blood heat capacity in J/kg/K
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*Tb:        The blood temperature in K
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*Q:          The heat rate generation map (i.e., SAR*RHO which can be non-uniform) in W/m^3
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==== Steady state simulations ====
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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.

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.

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