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show_fit.m
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show_fit.m
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function [offsets, Mxy, Mxy_sim, p] = show_fit(study, fits, data, cache, lineshape, index, offsets_, sim_flag, eps)
%
% [offsets, Mxy] = show_fit(study, fits, data, cache, lineshape, index, [offsets, sim_flag, eps])
%
if(nargin < 9 | isempty(eps))
eps = 0.0005; % accuracy for simulations
end
if(~isfield(study, 'b0_shift'))
study.b0_shift = zeros(1,length(study.nominal_offsets));;
end
% scale b1
if(~isfield(study, 'b1_scale'))
study.b1_scale = ones(1,length(study.nominal_offsets));
end
l = length(fits.model);
dual_flag = strcmp(fits.model((l-4):l), '_dual');
if(dual_flag == 0)
p = create_try(fits, study, index);
else
p = create_try_dual(fits, study, index);
end
for i = 1:length(cache)
if(isa(cache{i},'char'))
cache{i} = sf_cache(cache{i});
end
end
if(nargin < 8)
sim_flag = 0;
end
Mxy_sim = [];
% create pulses
if(~isempty(data))
p.mt_angles = study.nominal_angles*data.b1(index)*study.b1_scale(1); % degrees
else
p.mt_angles = study.nominal_angles; % degrees
end
for j = 1:length(p.mt_angles)
if(strcmp(study.pulse_type,'gaussian_hann'))
p.pulses{j} = gaussian_hann(p.mt_angles(j), ...
p.mt_duration(j), 0, p.TR(j), p.mt_bw(j));
elseif(strcmp(study.pulse_type,'gaussian'))
p.pulses{j} = gaussian(p.mt_angles(j), ...
p.mt_duration(j), 0, p.TR(j));
elseif(strcmp(study.pulse_type,'fermi'))
p.pulses{j} = fermi(p.mt_angles(j), ...
p.mt_duration(j), 0, p.TR(j), '', p.s(j));
else
error('Unknown pulse type.');
end
end
p.tau = p.mt_duration*0.235;
if(dual_flag == 0)
p = set_T1(p, p.T1(1), 1);
else
p = set_T1(p, [], 1, 1);
end
if(~isempty(data))
N = length(data.measurements);
voxel_data = struct('samples', {cell(N,1)});
for j = 1:N
% P = size(data.measurements{j},2);
% norm = mean(data.measurements{j}(index,((P-1):P)));
voxel_data.samples{j,1} = [study.nominal_offsets{j} + data.b0(index,min(size(data.b0,2),j)) + study.b0_shift(j); ...
data.measurements{j}(index,:)];
end
end
if(nargin < 7 | isempty(offsets_))
if(~isempty(data))
offsets = p.offsets{1} + data.b0(index,min(size(data.b0,2),j)) + study.b0_shift(1);
else
offsets = p.offsets{1};
end
else
if(~isempty(data))
offsets = offsets_ + data.b0(index,min(size(data.b0,2),j)) + study.b0_shift(1);
else
offsets = offsets_;
end
end
N = length(p.mt_angles);
M = length(offsets);
Mxy = zeros(M,N);
if(dual_flag == 0)
for i = 1:N
rates = cw_rfrate(p.pulses{i}, p.T2(2), offsets, lineshape);
for j = 1:M
Sf{i}.values(j) = get_value_i(cache{i}, p.mt_angles(i),...
offsets(j), p.T2(1));
if(strncmp(p.model, 'mtspgr_dp', 9))
[Mz_, Mxy(j,i)] = feval(p.model, p.angle(i), p.kf, p.f, p.TR(i), p.T1,...
[Sf{i}.values(j) 1], rates(j), p.T2(2), ...
offsets(j)*2*pi);
elseif(strncmp(p.model, 'mtspgr_rp', 9))
[Mz_, Mxy(j,i)] = feval(p.model, p.angle(i), p.kf, p.f, p.TR(i), ...
p.T1, [Sf{i}.values(j) 1], rates(j), p.T2(2), ...
offsets(j)*2*pi, p.tau(i));
elseif(strncmp(p.model, 'mtspgr_frp', 10))
[P, avgP] = lookup_power (p.pulses{i});
[Mz_, Mxy(j,i)] = feval(p.model, p.angle(i), p.kf, p.f, p.TR(i), p.T1,...
[1 1], rates(j), p.T2, ...
offsets(j)*2*pi, p.tau(i), avgP);
else
[Mz_, Mxy(j,i)] = feval(p.model, p.angle(i), p.kf, p.f, p.TR(i), p.T1, ...
[Sf{i}.values(j) 1], rates(j));
end
Mz(j,i) = Mz_(1,1);
if(sim_flag)
BW = 1.2e-3*10e-3*42.57e6*5120/1024;
excite = gaussian_hann(p.angle(i), 1024e-6, 0, p.TR(i), BW);
pulse = set_offset(p.pulses{i}, offsets(j));
if(strcmp(p.model, 'mtspgr_dp') | strcmp(p.model, 'mtspgr_rp3') | ...
strcmp(p.model, 'mtspgr_frp3'))
disp('warning: flexible lineshape not implemented for 3 pool simulation');
sim = 'dipolar_3pool';
M0 = [0 0 1 p.f 0]*Mz(j,i);
else
sim = thermal_2pool_flex(lineshape);
M0 = [0 0 1 p.f]*Mz(j,i);
end
[t, m] = sim_mtspgr(M0, pulse, excite, p.T1, p.T2, p.f, p.kf, ...
p.TR(i), sim, 100, eps);
Mxy_sim(j,i) = norm(m(length(t),1:2));
Mz_sim(j,i) = m(length(t),3);
end
end
end
else
for i = 1:N
rates(1,:) = cw_rfrate(p.pulses{i}, p.T2(2), offsets, lineshape);
rates(2,:) = cw_rfrate(p.pulses{i}, p.T2(4), offsets, lineshape);
for j = 1:M
Sf(1) = get_value_i(cache{i}, p.mt_angles(i), offsets(j), p.T2(1));
Sf(2) = get_value_i(cache{i}, p.mt_angles(i), offsets(j), p.T2(3));
% f = p.P(2)/(1-p.P(2));
% [Mz_, Mxy(j,i)] = mtspgr_rp2_opt(p.angle(i), p.K(2), f, ...
% p.TR(i), 1./p.R1(1:2), [Sf{i}.values(j) 1], rates_a(j), p.T2(2), ...
% offsets(j)*2*pi, p.tau(i));
[Mz_, Mxy(j,i)] = mtspgr_rp2_dual(p.angle(i), p.TR(i), p.R1, p.T2,...
[], p.P, p.K, Sf, rates(:,j), [], p.tau(i), p.mix);
Mz(j,i) = Mz_(1,1)+Mz_(3,1);
if(sim_flag)
BW = 1.2e-3*10e-3*42.57e6*5120/1024;
excite = gaussian_hann(p.angle(i), 1024e-6, 0, p.TR(i), BW);
pulse = set_offset(p.pulses{i}, offsets(j));
sim = thermal_4pool_flex(lineshape);
% M0 = [0 0 p.P(1)*(1-p.P(2)) p.P(1)*p.P(2) 0 0 p.P(2)*(1-p.P(3)) p.P(2)*p.P(3)]'* ...
% Mz(j,i);
M0 = [0 0 Mz_(1) Mz_(2) 0 0 Mz_(3) Mz_(4)];
[t, m] = sim_mtspgr_dual(M0, pulse, excite, p.R1, p.T2, p.T1d, ...
p.P, p.K, p.TR(i), sim, 100, eps);
Mxy_sim(j,i,1) = norm(m(length(t),1:2));
Mxy_sim(j,i,2) = norm(m(length(t),5:6));
Mz_sim(j,i,1) = m(length(t),3);
Mz_sim(j,i,2) = m(length(t),7);
end
end
end
end
% plot curves with data
colors = ['kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk'];
if(~isempty(data))
Z = p.beta(1)*abs(Mxy(:,1));
semilogx(voxel_data.samples{1}(1,:), voxel_data.samples{1}(2,:), [colors(1) '.'], voxel_data.samples{1}(1,:), voxel_data.samples{1}(2,:), [colors(1) '--'], offsets', Z, 'b-' )
hold on
for j = 2:length(p.offsets)
Z = p.beta(j)*abs(Mxy(:,j));
semilogx(voxel_data.samples{j}(1,:), voxel_data.samples{j}(2,:), [colors(j) '.'], voxel_data.samples{j}(1,:), voxel_data.samples{j}(2,:), [colors(j) '--'], offsets', Z, 'b-')
end
if(nargin < 7 | isempty(offsets_))
n = 0;
e2 = 0;
for j = 1:length(p.offsets)
Z = p.beta(j)*abs(Mxy(:,j));
n = n+length(Z);
if(length(Z) == length(voxel_data.samples{j}(2,:)))
e2 = e2 + sum((Z' - voxel_data.samples{j}(2,:)).^2);
else
disp('Warning: error in fit cannot be calculated')
end
end
p.e2 = e2/n;
end
else
Z = abs(Mxy)*diag(p.beta);
semilogx(offsets', Z, 'r-' )
end
if(sim_flag)
hold on
if(dual_flag == 0)
semilogx( offsets', Mxy_sim*diag(1./Mxy_sim(size(Mxy_sim,1),:)), 'r-.' )
else
mixed = Mxy_sim(:,:,1)*fits.mix(1) + Mxy_sim(:,:,2)*fits.mix(2);
mixed = mixed*diag(1./(mixed(size(mixed,1),:)));
semilogx( offsets', mixed, 'k-');
% semilogx( offsets', Mxy_sim(:,:,1)*diag(1./Mxy_sim(size(Mxy_sim,1),:,1)), 'b-' )
% semilogx( offsets', Mxy_sim(:,:,2)*diag(1./Mxy_sim(size(Mxy_sim,1),:,2)), 'k-' )
end
end
hold off
axis([min(500,min(offsets)) max(1e5,max(offsets)) 0 1.1])
xlabel('frequency offset (Hz)')
ylabel('MTw signal')
function p0 = create_try(fits, study, index)
%
% function p0 = create_try(fits, study, index)
%
% Create initial guess at parameters
p0.kf = fits.kf(index);
p0.f = fits.f(index);
p0.T1 = 1./fits.R1(index,:);
if(isfield(fits, 'T1d'))
p0.T1(3) = fits.T1d(index);
end
p0.T2 = fits.T2(index,:);
p0 = create_try_common(p0, fits, study, index);
return
function p0 = create_try_dual(fits, study, index)
%
% function p0 = create_try(fits, study, index)
%
% Create initial guess at parameters
p0.K = fits.K(index,:);
p0.P = fits.P(index,:);
p0.R1 = fits.R1(index,:);
if(isfield(fits, 'T1d') & ~isempty(fits.T1d))
p0.T1d = fits.T1d(index);
else
p0.T1d = [];
end
p0.T2 = fits.T2(index,:);
p0.mix = fits.mix;
p0 = create_try_common(p0, fits, study, index);
return
function p0 = create_try_common(p0, fits, study, index)
%
% function p0 = create_try_common(p0, fits, study, index)
%
% Create initial guess at parameters
p0.beta = ones(1,length(study.nominal_offsets));;
p0.offsets = study.nominal_offsets;
% given in pulse sequence
if(isfield(study, 'flip'))
p0.angle = study.flip;
else
p0.angle = 10*ones(1,length(study.nominal_angles)); % degrees
end
if(isfield(study, 'TR'))
p0.TR = study.TR;
else
p0.TR = 50e-3*ones(1,length(study.nominal_angles)); % ms
end
p0.model = fits.model;
if(isfield(study, 'pulse_duration'))
p0.mt_duration = study.pulse_duration;
else
p0.mt_duration = 10240e-6*ones(1,length(study.nominal_angles)); % s
end
if(strcmp(study.pulse_type,'gaussian_hann'))
p0.mt_bw = 200*10240e-6./p0.mt_duration; % Hz
end
if(strcmp(study.pulse_type,'fermi'))
p0.s = 15*ones(1,length(study.nominal_angles)); % Hz
end
return