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Gunn1997_nifti_mask.m
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Gunn1997_nifti_mask.m
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function parametric_images = Gunn1997_nifti_mask(theta3_lb,theta3_ub,nBases,decaytime,refTAC,frametimes,filenamedyn,maskfilename,outputdir)
frameMid = 0.5.*(frametimes(:,1)+frametimes(:,2));
%frameMid = frametimes(:,2);
frameDur = frametimes(:,2)-frametimes(:,1);
lambda = log(2)/decaytime;%C-11 decay constant: 20.4 min
decayRemove = 2.^-(frameMid/decaytime);
dynhdr = spm_vol_nifti(filenamedyn);
dynVol = nifti(filenamedyn);
if dynhdr.private.dat.dim(4) ~= length(frameMid)
error(['Number of frame times ' num2str(length(frameMid)) ...
' does not match number of dynamic frames in image ' ...
num2str(dynhdr.private.dat.dim(4))]);
end
%masking
maskhdr = spm_vol_nifti(maskfilename);
maskVol = nifti(maskfilename);
MASK = zeros(maskhdr.dim);
MASK(:,:,:) = maskVol.dat(:,:,:);
idxmask = find(MASK > 0);
%calculate weights
tots = zeros(length(frameMid),1);
DYNframe = zeros(dynhdr.dim);
for f=1:length(frameMid), %calculate mean framewise
helper_img = dynVol.dat(:,:,:,f);
helper_img(isnan(helper_img)) = 0;
DYNframe(:,:,:) = helper_img;
tots(f) = decayRemove(f)*sum(DYNframe(:));
end
clear idxmask;
clear DYNframe
weights = (frameDur.^2)./tots;
weights(isinf(weights)) = 0; %if frame mean==0;
%weights = ones(length(frameMid),1); %no weights
W = diag(sqrt(weights));
% compute basis functions: Cr @ exp(-theta3*t)
nFrames = size(frametimes, 1);
B = zeros([nFrames nBases]); % the basis functions
%theta3 = linspace(theta3_lb,theta3_ub,nBases);
bases_lb=log(theta3_lb)/log(10);
bases_ub=log(theta3_ub)/log(10);
theta3 = logspace(bases_lb, bases_ub, nBases);
% evaluate input function Cr
Cr = decayRemove.*refTAC;
interp_refdata = pchip([0 ; frameMid],[0 ; Cr]);
inTol = 1e-4; %integration tolerance
trace=0; %quad option
convIntegrand = @(tau, funH, parm, theta3, t, varargin) funH(parm, t - tau, varargin{:}) .* exp(-theta3 * tau);
for i = 1:nBases
% use quad to evaluate the convolution integrals at mid frame time
% Basis function = integral_0^t (Cr(t-tau) * exp(-theta3*tau)) dtau
for j = 1:nFrames
B(j,i) = quad(convIntegrand, 0, frameMid(j), inTol, trace, @ppval, interp_refdata, theta3(i), frameMid(j));
end
end
M = zeros([2*nBases nFrames]);
for i = 1:nBases
A = [Cr B(:,i)];
[Q, R] = qr(W * A);
M(2*(i-1)+[1 2], :) = R \ (Q.');
end
clear A, clear Q, clear R;
Ct = zeros([nFrames nBases]);
theta = zeros([2 nBases]);
BP_img_3D = zeros(maskhdr.dim);
RI_img_3D = zeros(maskhdr.dim);
k2_img_3D = zeros(maskhdr.dim);
theta3_img_3D = zeros(maskhdr.dim);
DYNplane = zeros([dynVol.dat.dim(1) dynVol.dat.dim(2) dynVol.dat.dim(4)]);
fprintf(1,' \nStarting to fit bf-SRTM.\n');
tic
for pl = 1:dynVol.dat.dim(3)
if (mod(pl,10)==0), disp(['fitting plane: ' int2str(pl)]); end;
DYNplane(:,:,:) = dynVol.dat(:,:,pl,:);
% process all TACs from the corresponding plane in one go
[mask_iX,mask_iY] = find(MASK(:,:,pl));
TACs = zeros(nFrames,length(mask_iX));
nTACs = length(mask_iX);
RI = zeros([1 nTACs]);
k2 = zeros([1 nTACs]);
BP = zeros([1 nTACs]);
th3 = zeros([1 nTACs]);
for T = 1:nTACs
CPET = DYNplane(mask_iX(T), mask_iY(T),:);
TACs(:,T)=decayRemove.*CPET(:);
end
TACs(isnan(TACs)) = 0 ; %replace NaNs with zeros
clear CPET
for j = 1:nTACs
H = W * TACs(:, j);
for i = 1:nBases
theta(:,i) = M(2*(i-1)+[1 2], :) * H;
Ct(:,i) = theta(1,i) * Cr + theta(2,i) * B(:,i);
end
RSS = sum(repmat(weights, [1 nBases]) .* ((repmat(TACs(:, j), [1 nBases]) - Ct) .^ 2), 1);
[RI(j),k2(j),BP(j),th3(j)] = bound_srtm_parameters(RSS,theta,theta3,lambda);
end
for T=1:length(mask_iX),
BP_img_3D(mask_iX(T),mask_iY(T),pl) = BP(T);
RI_img_3D(mask_iX(T),mask_iY(T),pl) = RI(T);
k2_img_3D(mask_iX(T),mask_iY(T),pl) = k2(T);
theta3_img_3D(mask_iX(T),mask_iY(T),pl) = th3(T);
end
clear RI k2 BP RSS TACs th3
end
[~,filename] = fileparts(filenamedyn);
parametric_images = cell(3,1);
parametric_images{1} = fullfile(outputdir,[filename '_bfsrtm_BP.nii']);
parametric_images{2} = fullfile(outputdir,[filename '_bfsrtm_R1.nii']);
parametric_images{3} = fullfile(outputdir,[filename '_bfsrtm_k2.nii']);
VO = maskhdr;
VO.dt = [spm_type('int16') spm_platform('bigend')];
VO.pinfo = [Inf Inf Inf]';
VO.fname = parametric_images{1};
spm_write_vol(VO,BP_img_3D);
VO.fname = parametric_images{2};
spm_write_vol(VO,RI_img_3D);
VO.fname = parametric_images{3};
spm_write_vol(VO,k2_img_3D);
VO.fname = fullfile(outputdir,[filename '_bfsrtm_theta3.nii']);
spm_write_vol(VO,theta3_img_3D);
end
function [RI,k2,BP,optim_theta3] = bound_srtm_parameters(RSS,theta,theta3,lambda)
[~,I] = sort(RSS,'ascend');
sorted_theta(1,:) = theta(1,I);
sorted_theta(2,:) = theta(2,I);
sorted_theta3(1,:) = theta3(I);
RI = sorted_theta(1, 1);
k2 = sorted_theta(2, 1) + RI*(sorted_theta3(1) - lambda);
BP = k2 / (sorted_theta3(1) - lambda) - 1;
i = 1;
optim_theta3 = sorted_theta3(i);
% while(BP < -0.2 || BP > 15 || RI <= 0 || RI > 3 || k2 <= 0 || k2 >= 1)
% i = i + 1;
% optim_theta3 = sorted_theta3(i);
% RI = sorted_theta(1, i);
% k2 = sorted_theta(2, i) + RI*(sorted_theta3(i) - lambda);
% BP = k2 / (sorted_theta3(i) - lambda) - 1;
% if(i==length(RSS))
% RI = 0;
% k2 = 0;
% BP = 0;
% break;
% end
% end
end