Default tissue parameters

src/Models_Functions/adiabatic_inv/pulseDefaultParams/AI_defaultTissueParams.m

@@ -0,0 +1,129 @@
+%% Sort based on field strength and tissue type
+function Params = AI_defaultTissueParams(Params)
+% currently only 3T and 7T are supported fields;
+% currently only 'GM' and 'WM' are the supported tissue types.
+
+% 3T parameters taken from:
+% Sled, J.G., Pike, B.G., 2001. Quantitative imaging of magnetization transfer exchange and relaxation properties in vivo using MRI. Magn. Reson. Med. 46, 923–931. https://doi.org/10.1002/mrm.1278
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
+%%%%%%%%%%%%%  3T %%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
+if Params.B0 == 3
+
+    if strcmp(Params.TissueType, 'GM')
+        Params.M0a = 1;
+        Params.Raobs = 1/1.4; 
+        Params.R = 50; % 
+        Params.T2a = 50e-3; % Sled and Pike 2001
+        Params.T1D = 7.5e-4; % Varma 2017 was 6ms
+        Params.lineshape = 'SuperLorentzian'; % or 'SuperLorentzian';
+        Params.R1b = 0.25;
+        Params.T2b = 11.5e-6; 
+        Params.Ra = [];
+        Params.M0b =  0.071;
+        Params.D = 0.8e-3/1e6; % diffusion coefficient-> convert from mm^2/s to m^2/s
+
+    elseif strcmp(Params.TissueType, 'WM')
+        Params.M0a = 1;
+        Params.Raobs = 1/0.85; 
+        Params.R = 35;
+        Params.T2a = 35e-3; % Sled and Pike 2001
+        Params.T1D = 1.25e-3; % Varma 2017 was 6ms
+        Params.lineshape = 'SuperLorentzian'; % or 'SuperLorentzian';
+        Params.R1b = 0.25;
+        Params.T2b = 11.1e-6;
+        Params.Ra = [];
+        Params.M0b =  0.155;
+        Params.D = 1e-3/1e6; % diffusion coefficient-> convert from mm^2/s to m^2/s
+
+    else
+        error('Please set Params.TissueType to either GM or WM, or build an additional field')
+    end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
+%%%%%%%%%%%%  7T %%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
+elseif Params.B0 == 7
+
+    if strcmp(Params.TissueType, 'GM')
+        Params.M0a = 1;
+        Params.Raobs = 1/2; 
+        Params.R = 33; % 
+        Params.T2a = 45e-3; 
+        Params.T1D = 5.25e-4; % Varma 2017 was 6ms
+        Params.lineshape = 'SuperLorentzian'; % or 'SuperLorentzian';
+        Params.R1b = 0.25;
+        Params.T2b = 11e-6; 
+        Params.Ra = [];
+        Params.M0b =  0.075;
+        Params.D = 0.8e-3/1e6; % diffusion coefficient-> convert from mm^2/s to m^2/s
+
+    elseif strcmp(Params.TissueType, 'WM')
+        Params.M0a = 1;
+        Params.Raobs = 1/1.4; 
+        Params.R = 27;
+        Params.T2a = 45e-3; 
+        Params.T1D = 5.25e-4; % Varma 2017 was 6ms
+        Params.lineshape = 'SuperLorentzian'; % or 'SuperLorentzian';
+        Params.R1b = 0.25;
+        Params.T2b = 11.1e-6;
+        Params.Ra = [];
+        Params.M0b =  0.155;
+        Params.D = 1e-3/1e6; % diffusion coefficient-> convert from mm^2/s to m^2/s
+
+    else
+        error('Please set Params.TissueType to either GM or WM, or build an additional field')
+    end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
+%%%%%%%%%%%% 1.5T %%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
+% Use the optimizations from: Levesque, I.R., Sled, J.G., Pike, G.B., 2011. 
+% Iterative optimization method for design of quantitative magnetization transfer 
+% imaging experiments. Magn. Reson. Med. 66, 635–643. https://doi.org/10.1002/mrm.23071
+elseif Params.B0 == 1.5
+
+    if strcmp(Params.TissueType, 'GM')
+        Params.M0a = 1;
+        Params.Raobs = 1/2; 
+        Params.R = 25.7; % 
+        Params.T2a = 51e-3; 
+        Params.T1D = 5.25e-4; % Varma 2017 was 6ms
+        Params.lineshape = 'SuperLorentzian'; % or 'SuperLorentzian';
+        Params.R1b = 0.25;
+        Params.T2b = 11e-6; 
+        Params.Ra = 1;
+        Params.M0b =  0.07;
+        Params.D = 0.8e-3/1e6; % diffusion coefficient-> convert from mm^2/s to m^2/s
+
+    elseif strcmp(Params.TissueType, 'WM')
+        Params.M0a = 1;
+        Params.Raobs = 1/0.55; 
+        Params.R = 25;
+        Params.T2a = 35e-3; 
+        Params.T1D = 5.25e-4; % Varma 2017 was 6ms
+        Params.lineshape = 'SuperLorentzian'; % or 'SuperLorentzian';
+        Params.R1b = 0.25;
+        Params.T2b = 12e-6;
+        Params.Ra = 1.8;
+        Params.M0b =  0.16;
+        Params.D = 1e-3/1e6; % diffusion coefficient-> convert from mm^2/s to m^2/s
+
+    else
+        error('Please set Params.TissueType to either GM or WM, or build an additional field')
+    end
+
+else
+    error('Please set Params.B0 to either 3,7, or build an additional field')
+end
+
+
+if isempty(Params.Ra) % allow you to specify either Ra or Raobs
+    Params.Ra = Params.Raobs - ((Params.R * Params.M0b * (Params.R1b - Params.Raobs)) / (Params.R1b - Params.Raobs + Params.R));
+    if isnan(Params.Ra)
+        Params.Ra = 1;
+    end
+end
+