MRI Loop Coil Tutorial: Use the virtual family body model instead of a phantom
Signed-off-by: Thorsten Liebig <Thorsten.Liebig@gmx.de>
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Thorsten Liebig
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@ -6,6 +6,7 @@
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%
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% Tested with
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% - openEMS v0.0.31
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% - Matlab 7.12.0 (R2011a)
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%
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% (C) 2013 Thorsten Liebig <thorsten.liebig@uni-due.de>
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@ -23,49 +24,50 @@ loop.width = 60; % width of the loop (in y-direction)
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loop.strip_width = 5; % metal strip width
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loop.strip_N_cells = 3; % number of cells over the strip length
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loop.air_gap = loop.strip_width/3; % air gap width for lumped capacitors
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loop.pos_x = 110; % position of loop
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loop.C_gap = 5e-12; % lumped cap value
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loop.pos_x = -130; % position of loop
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loop.C_gap = 5.4e-12; % lumped cap value
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loop.port_R = 10; % feeding port resistance
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%% define the phantom material stackup material
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materials.name{1}='skin';
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materials.rad(1)=100;
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materials.eps_r(1)=49.8;
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materials.kappa(1)=0.64;
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materials.density(1)=1100;
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materials.prio(1)=10;
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%% define the human body model (virtual family)
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% set file name for human body model to create with "Convert_VF_DiscMaterial"
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% the file name should contain a full path
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body_model_file = [pwd '/Ella_centered_298MHz.h5'];
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materials.name{2}='headbone';
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materials.rad(2)=95;
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materials.eps_r(2)=13.4;
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materials.kappa(2)=0.08;
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materials.density(2)=1990;
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materials.prio(2)=11;
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% convert only part of the model (head/shoulder section)
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body_model_range = {[],[],[-0.85 -0.4]};
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materials.name{3}='CSF';
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materials.rad(3)=90;
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materials.eps_r(3)=72.734;
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materials.kappa(3)=2.2245;
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materials.density(3)=1007;
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materials.prio(3)=12;
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VF_raw_filesuffix = '/home/thorsten/Simulation/Virtual Family Voxel Models V1.0/Ella_26y_V2_1mm/Ella_26y_V2_1mm';
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VF_mat_db_file = '/home/thorsten/Simulation/Virtual Family Voxel Models V1.0/DB_h5_20120711_SEMCADv14.8.h5';
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materials.name{4}='brain'; % average of white/grey matter
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materials.rad(4)=86;
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materials.eps_r(4)=60;
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materials.kappa(4)=0.69;
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materials.density(4)=1039;
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materials.prio(4)=13;
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% delete(body_model_file); % uncomment to delete old model if something changed
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% convert model (if it does not exist)
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Convert_VF_DiscMaterial(VF_raw_filesuffix, VF_mat_db_file, body_model_file, ...
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'Frequency', 298e6, 'Center', 1, ...
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'Range', body_model_range);
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% rotate model to face the nose in x-dir, and translate
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body_model_transform = {'Rotate_X',pi,'Rotate_Z',pi/2, ...
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'Translate',[0,5,-720]};
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% the head should + part of shoulder should fit this box
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body_box.start = [-120 -150 -200];
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body_box.stop = [+100 +150 +130];
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% box with high res mesh
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mesh_box.start = [-120 -80 -120];
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mesh_box.stop = [+100 +80 +120];
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mesh_box.resolution = 2;
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%% some mesh parameter
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mat_mesh = 2; % mesh inside the phantom (2mm)
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Air_Box = 150; % size of the surrounding air box (150mm)
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%% setup FDTD parameter & excitation function
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% init FDTD structure
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FDTD = InitFDTD( 'EndCriteria', 1e-4 );
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FDTD = InitFDTD( 'EndCriteria', 1e-4, 'CellConstantMaterial', 0);
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% define gaussian pulse excitation signal
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f0 = 300e6; % center frequency
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f0 = 298e6; % center frequency
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fc = 300e6; % 20 dB corner frequency
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FDTD = SetGaussExcite( FDTD, f0, fc );
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@ -134,24 +136,24 @@ start = [loop.pos_x -loop.air_gap/2 -loop.length/2+loop.strip_width/2-loop.air_g
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stop = [loop.pos_x +loop.air_gap/2 -loop.length/2+loop.strip_width/2+loop.air_gap/2];
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[CSX port] = AddLumpedPort(CSX, 100, 1, loop.port_R, start, stop, [0 1 0], true);
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%% define materials in a loop
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for n=1:numel(materials.name)
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CSX = AddMaterial( CSX, materials.name{n} );
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CSX = SetMaterialProperty( CSX, materials.name{n}, 'Epsilon', materials.eps_r(n), 'Kappa', materials.kappa(n), 'Density', materials.density(n));
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CSX = AddSphere( CSX, materials.name{n}, materials.prio(n), [0 0 0], materials.rad(n),'Transform',{'Scale',[1 0.8 1] } );
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end
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%% define human body model
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CSX = AddDiscMaterial(CSX, 'body_model', 'File', body_model_file, 'Scale', 1/unit, 'Transform', body_model_transform);
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CSX = AddBox(CSX, 'body_model', 0, body_box.start, body_box.stop);
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%% finalize mesh
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% create loop mesh (detect only metal and the lumped elements)
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mesh = DetectEdges(CSX, [], 'SetPropertyType', {'Metal','LumpedElement'});
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% create loop mesh
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mesh = DetectEdges(CSX);
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% add a dense homegeneous mesh inside the phantom
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mesh.x = [mesh.x -materials.rad -mat_mesh/2 mat_mesh/2 materials.rad];
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mesh.y = [mesh.y -materials.rad*0.8 materials.rad*0.8];
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mesh.z = [mesh.z -materials.rad materials.rad];
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% add a dense homegeneous mesh inside the human body model
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mesh.x = [mesh.x mesh_box.start(1) mesh_box.stop(1)];
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mesh.y = [mesh.y mesh_box.start(2) mesh_box.stop(2)];
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mesh.z = [mesh.z mesh_box.start(3) mesh_box.stop(3)];
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% smooth the mesh for the loop & phantom
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mesh = SmoothMesh(mesh, mat_mesh);
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% add lines in x-dir for the loop and a cell centered around 0
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mesh.x = [mesh.x loop.pos_x -mesh_box.resolution/2 mesh_box.resolution/2];
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% smooth the mesh for the loop & body
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mesh = SmoothMesh(mesh, mesh_box.resolution);
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% add air spacer
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mesh.x = [-Air_Box+mesh.x(1) mesh.x mesh.x(end)+Air_Box];
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@ -160,18 +162,16 @@ mesh.z = [-Air_Box+mesh.z(1) mesh.z mesh.z(end)+Air_Box];
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mesh = SmoothMesh(mesh, c0 / (f0+fc) / unit / 10, 1.5, 'algorithm', 1);
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%% Add Dump boxes (3D box) for E,J and SAR
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CSX = AddDump(CSX,'Hf','DumpType',11,'FileType',1,'Frequency',f0);
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CSX = AddDump(CSX,'SAR','DumpType',20,'DumpMode',2,'FileType',1,'Frequency',f0);
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start = [-120 -120 -120];
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stop = [+120 +120 +120];
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CSX = AddBox(CSX,'Hf',0,start,stop);
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CSX = AddBox(CSX,'SAR',0,start,stop);
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%% Add Dump boxes (2D boxes) for H and SAR on xy- and xz-plane
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CSX = AddDump(CSX,'Hf_xy','DumpType',11,'FileType',1,'Frequency',f0);
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CSX = AddBox(CSX,'Hf_xy',0, body_box.start.*[1 1 0], body_box.stop.*[1 1 0]);
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CSX = AddDump(CSX,'SAR_xy','DumpType',20,'DumpMode',2,'FileType',1,'Frequency',f0);
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CSX = AddBox(CSX,'SAR_xy',0, body_box.start.*[1 1 0], body_box.stop.*[1 1 0]);
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%% add a nf2ff calc box; size is 3 cells away from MUR boundary condition
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start = [mesh.x(1) mesh.y(1) mesh.z(1)];
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stop = [mesh.x(end) mesh.y(end) mesh.z(end)];
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[CSX nf2ff] = CreateNF2FFBox(CSX, 'nf2ff', start, stop,'Frequency',f0,'OptResolution',c0/f0/unit/20);
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CSX = AddDump(CSX,'Hf_xz','DumpType',11,'FileType',1,'Frequency',f0);
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CSX = AddBox(CSX,'Hf_xz',0, body_box.start.*[1 0 1], body_box.stop.*[1 0 1]);
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CSX = AddDump(CSX,'SAR_xz','DumpType',20,'DumpMode',2,'FileType',1,'Frequency',f0);
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CSX = AddBox(CSX,'SAR_xz',0, body_box.start.*[1 0 1], body_box.stop.*[1 0 1]);
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%% add 10 lines in all direction to make space for PML or MUR absorbing
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%% boundary conditions
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@ -182,8 +182,8 @@ disp(['number of cells: ' num2str(1e-6*numel(mesh.x)*numel(mesh.y)*numel(mesh.z)
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CSX = DefineRectGrid( CSX, unit, mesh );
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%% prepare simulation folder
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Sim_Path = mfilename;
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Sim_CSX = [Sim_Path '.xml'];
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Sim_Path = ['tmp_' mfilename];
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Sim_CSX = [mfilename '.xml'];
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[status, message, messageid] = rmdir( Sim_Path, 's' ); % clear previous directory
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[status, message, messageid] = mkdir( Sim_Path ); % create empty simulation folder
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@ -192,7 +192,7 @@ Sim_CSX = [Sim_Path '.xml'];
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WriteOpenEMS( [Sim_Path '/' Sim_CSX], FDTD, CSX );
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%% show the structure and export as vtk data automatically
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CSXGeomPlot( [Sim_Path '/' Sim_CSX] , ['--export-polydata-vtk=' Sim_Path]);
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CSXGeomPlot( [Sim_Path '/' Sim_CSX] , ['--export-polydata-vtk=' Sim_Path ' --RenderDiscMaterial -v']);
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%% run openEMS
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RunOpenEMS( Sim_Path, Sim_CSX);
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@ -205,6 +205,7 @@ Zin = port.uf.tot ./ port.if.tot;
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s11 = port.uf.ref ./ port.uf.inc;
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P_in = real(0.5 * port.uf.tot .* conj(port.if.tot)); % antenna feed power
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% get the feeding power for frequency f0
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P0_in = interp1(freq, P_in, f0);
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@ -229,12 +230,12 @@ ylabel( 'admittance Y_{in} (S)' );
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legend( 'real', 'imag' );
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%% read SAR values on a xy-plane (range)
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[SAR SAR_mesh] = ReadHDF5Dump([Sim_Path '/SAR.h5'], 'Range', {[],[],0});
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SAR = SAR.FD.values{1};
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[SAR SAR_mesh] = ReadHDF5Dump([Sim_Path '/SAR_xy.h5']);
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SAR = SAR.FD.values{1}/P0_in;
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%%
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% SAR plot
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figure()
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subplot(1,2,1);
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[X Y] = ndgrid(SAR_mesh.lines{1},SAR_mesh.lines{2});
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colormap('hot');
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h = pcolor(X,Y,(squeeze(SAR)));
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@ -245,22 +246,38 @@ ylabel('y -->');
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title('local SAR');
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axis equal tight
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%%
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[H_field H_mesh] = ReadHDF5Dump([Sim_Path '/Hf.h5'], 'Range',{[],[],0});
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%% read SAR values on a xz-plane (range)
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[SAR SAR_mesh] = ReadHDF5Dump([Sim_Path '/SAR_xz.h5']);
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SAR = SAR.FD.values{1}/P0_in;
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% SAR plot
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subplot(1,2,2);
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[X Z] = ndgrid(SAR_mesh.lines{1},SAR_mesh.lines{3});
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colormap('hot');
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h = pcolor(X,Z,(squeeze(SAR)));
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% h = pcolor(X,Y,log10(squeeze(SAR)));
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set(h,'EdgeColor','none');
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xlabel('x -->');
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ylabel('z -->');
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title('local SAR');
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axis equal tight
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%% plot B1+/- on an xy-plane
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[H_field H_mesh] = ReadHDF5Dump([Sim_Path '/Hf_xy.h5']);
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% calc Bx,By, B1p, B1m normalize to the input-power
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Bx = MUE0*H_field.FD.values{1}(:,:,1,1)/sqrt(P0_in);
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By = MUE0*H_field.FD.values{1}(:,:,1,2)/sqrt(P0_in);
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Bx = MUE0*H_field.FD.values{1}(:,:,:,1)/sqrt(P0_in);
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By = MUE0*H_field.FD.values{1}(:,:,:,2)/sqrt(P0_in);
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B1p = 0.5*(Bx+1j*By);
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B1m = 0.5*(Bx-1j*By);
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% create a 2D grid to plot on
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[X Y] = ndgrid(H_mesh.lines{1},H_mesh.lines{2});
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filter = sqrt(X.^2+Y.^2)<0.1;
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Dump2VTK([Sim_Path '/B1p_xy.vtk'], abs(B1p).*filter, H_mesh, 'B-Field');
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Dump2VTK([Sim_Path '/B1m_xy.vtk'], abs(B1m).*filter, H_mesh, 'B-Field');
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Dump2VTK([Sim_Path '/B1p_xy.vtk'], abs(B1p), H_mesh, 'B-Field');
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Dump2VTK([Sim_Path '/B1m_xy.vtk'], abs(B1m), H_mesh, 'B-Field');
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% B1+ plot
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figure()
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subplot(1,2,1);
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h = pcolor(X,Y,log10(abs(B1p)));
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set(h,'EdgeColor','none');
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xlabel('x -->');
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@ -269,7 +286,7 @@ title('B_1^+ field (dB)');
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axis equal tight
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% B1- plot
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figure()
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subplot(1,2,2);
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h = pcolor(X,Y,log10(abs(B1m)));
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set(h,'EdgeColor','none');
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xlabel('x -->');
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@ -277,20 +294,42 @@ ylabel('y -->');
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title('B_1^- field (dB)');
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axis equal tight
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%% plot B1+/- on an xz-plane
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[H_field H_mesh] = ReadHDF5Dump([Sim_Path '/Hf_xz.h5']);
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% calc Bx,By, B1p, B1m normalize to the input-power
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Bx = MUE0*H_field.FD.values{1}(:,:,:,1)/sqrt(P0_in);
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By = MUE0*H_field.FD.values{1}(:,:,:,2)/sqrt(P0_in);
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B1p = 0.5*(Bx+1j*By);
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B1m = 0.5*(Bx-1j*By);
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% create a 2D grid to plot on
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[X Z] = ndgrid(H_mesh.lines{1},H_mesh.lines{3});
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Dump2VTK([Sim_Path '/B1p_xz.vtk'], abs(B1p), H_mesh, 'B-Field');
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Dump2VTK([Sim_Path '/B1m_xz.vtk'], abs(B1m), H_mesh, 'B-Field');
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% B1+ plot
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figure()
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subplot(1,2,1);
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h = pcolor(X,Z,log10(squeeze(abs(B1p))));
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set(h,'EdgeColor','none');
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xlabel('x -->');
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ylabel('z -->');
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title('B_1^+ field (dB)');
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axis equal tight
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% B1- plot
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subplot(1,2,2);
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h = pcolor(X,Z,log10(squeeze(abs(B1m))));
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set(h,'EdgeColor','none');
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xlabel('x -->');
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ylabel('z -->');
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title('B_1^- field (dB)');
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axis equal tight
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%% dump to vtk to view in Paraview
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Dump2VTK([Sim_Path '/SAR_xy.vtk'], SAR, SAR_mesh, 'SAR');
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ConvertHDF5_VTK([Sim_Path '/SAR_xy.h5'],[Sim_Path '/SAR_xy'], 'weight', 1/P0_in, 'FieldName', 'SAR');
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ConvertHDF5_VTK([Sim_Path '/SAR_xz.h5'],[Sim_Path '/SAR_xz'], 'weight', 1/P0_in, 'FieldName', 'SAR');
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%%
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ConvertHDF5_VTK([Sim_Path '/Hf.h5'],[Sim_Path '/B1_xy'], 'Range',{[],[],0}, 'weight', MUE0/sqrt(P0_in), 'FieldName', 'B1-field');
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%% validation by calculating the power budget
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% calculate the radiated power
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nf2ff = CalcNF2FF(nf2ff, Sim_Path, f0, 0, 0);
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p_rad = nf2ff.Prad;
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% read dissipated power in the phantom
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p_loss = ReadHDF5Attribute([Sim_Path '/SAR.h5'],'/FieldData/FD/f0','power');
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% display results, should add up to 100% (+/- 5% error margin)
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disp([' power loss in phantom: ' num2str(p_loss) ' W (' num2str(p_loss/P0_in*100) '%)']);
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disp([' power radiated: ' num2str(p_rad) ' W (' num2str(p_rad/P0_in*100) '%)']);
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ConvertHDF5_VTK([Sim_Path '/Hf_xy.h5'],[Sim_Path '/B1_xy'], 'weight', MUE0/sqrt(P0_in), 'FieldName', 'B1-field');
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ConvertHDF5_VTK([Sim_Path '/Hf_xz.h5'],[Sim_Path '/B1_xz'], 'weight', MUE0/sqrt(P0_in), 'FieldName', 'B1-field');
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