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Copy pathDTIguicode.m
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DTIguicode.m
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tic
getDicomsgui %uses my script to load an entire Dicom directory.
disp('Calculating tensor...')
noise=evalin('base','noise'); %noise threshold
doFAmap=evalin('base','doFAmap'); %write DICOMs?
dotADC=evalin('base','dotADC');
dolambda1=evalin('base','dolambda1');
dolambda2=evalin('base','dolambda2');
dolambda3=evalin('base','dolambda3');
docm=evalin('base','docm');
counter=evalin('base','counter'); %counter comes from getDicomsgui
extension=evalin('base','extension');
slices=counter/7;
FAmaps=[];
tADCmaps=[];
lambda1_maps=[];
lambda2_maps=[];
lambda3_maps=[];
cmaps=[];
xyzmaps=[];
warning off MATLAB:divideByZero %supress matlab warning
for numslice=1:slices
bo=tensorvol(:,:,numslice,1);%bo=bo'; %transposes the images to correct for getDicoms
b1=tensorvol(:,:,numslice,2);%b1=b1';
b2=tensorvol(:,:,numslice,3);%b2=b2';
b3=tensorvol(:,:,numslice,4);%b3=b3';
b4=tensorvol(:,:,numslice,5);%b4=b4';
b5=tensorvol(:,:,numslice,6);%b5=b5';
b6=tensorvol(:,:,numslice,7);%b6=b6';
ADC101=log(im2double(b1)./im2double(bo))./(-1000); %Calculate ADC maps for each direction
ADC_101=log(im2double(b2)./im2double(bo))./(-1000);
ADC011=log(im2double(b3)./im2double(bo))./(-1000);
ADC01_1=log(im2double(b4)./im2double(bo))./(-1000);
ADC110=log(im2double(b5)./im2double(bo))./(-1000);
ADC_110=log(im2double(b6)./im2double(bo))./(-1000);
transform=[1 1 0 2 0 0;1 0 1 0 2 0;0 1 1 0 0 2;1 1 0 -2 0 0;1 0 1 0 -2 0;0 1 1 0 0 -2]; %the transformation matrix to obtain tensor elements
xx=zeros(256); %Create empty tensor elements
yy=zeros(256);
zz=zeros(256);
xy=zeros(256);
xz=zeros(256);
yz=zeros(256);
lambda1=zeros(256); %create empty images
lambda2=zeros(256);
lambda3=zeros(256);
r=zeros(256);
g=zeros(256);
b=zeros(256);
FAmap=zeros(256);
tADC=zeros(256);
for i=1:256 %Fill in tensor elements pixel by pixel.
for j=1:256
if (bo(i,j)>noise) %noise threshold. Change this to zero if you want the whole image to be calculated (takes longer)
ADCm=[ADC110(i,j);ADC101(i,j);ADC011(i,j);ADC_110(i,j);ADC_101(i,j);ADC01_1(i,j)]; %see Hedehus, http://www-radiology.stanford.edu/majh/
ADCe=inv(transform)*ADCm;
xx(i,j)=ADCe(1,1); %get tensor elements
yy(i,j)=ADCe(2,1);
zz(i,j)=ADCe(3,1);
xy(i,j)=ADCe(4,1);
xz(i,j)=ADCe(5,1);
yz(i,j)=ADCe(6,1);
ten=[xx(i,j) xy(i,j) xz(i,j);xy(i,j) yy(i,j) yz(i,j);xz(i,j) yz(i,j) zz(i,j)]; %the tensor itself
[V,D]=eig(ten);
D=eig(ten); %get eigenvalues
D=abs(D);
E=D; %get the eigenvalues before re-ordering
D=sort(D); %sort the eigenvalues (upwards)
e1=D(3,1);e1=e1*2;
e2=D(2,1);e2=e2*2;
e3=D(1,1);e3=e3*2;
lambda1(i,j)=e1;
lambda2(i,j)=e2;
lambda3(i,j)=e3;
%V=abs(V); %get the x,y,z components of e3
largest=find(E==D(3,1)); %find the value of the largest eigenvalue in the original matrix
sz=length(largest);
r(i,j)=V(1,largest(sz)); %in order to get its corresponding eigenvector components in x, y and z
g(i,j)=V(2,largest(sz));
b(i,j)=V(3,largest(sz));
trace=(e1+e2+e3)/3;
%FA=(sqrt(3/2)*sqrt((1/3)*((e1-e2)^2+(e2-e3)^2+(e3-e1)^2)))/(sqrt(e1^2+e2^2+e3^3)); %Another formula for FA
FA=(sqrt(3*((e1-trace)^2+(e2-trace)^2+(e3-trace)^2)))/(sqrt(2*(e1^2+e2^2+e3^2))); %Le Bihan 2001
tADC(i,j)=trace;
FAmap(i,j)=FA;
end;
end;
end;
rgb=cat(3,r,g,b);
xyz=cat(3,r,(g*-1),b);
FAmap3=cat(3,FAmap,FAmap,FAmap); %needed to combine with the colormap, need 3D.
cm=abs(rgb).*FAmap3; %FA weighting for colormap. Has absolute values for vector components
%eval (['rgb' num2str(numslice) '=rgb;']);
%nameofmap=['rgb' num2str(numslice)];
%assignin('base',nameofmap,rgb);
FAmaps=cat(3,FAmaps,FAmap);
tADCmaps=cat(3,tADCmaps,tADC);
lambda1_maps=cat(3,lambda1_maps,lambda1);
lambda2_maps=cat(3,lambda2_maps,lambda2);
lambda3_maps=cat(3,lambda3_maps,lambda3);
cmaps=cat(4,cmaps,cm);
xyzmaps=cat(4,xyzmaps,xyz);
%eval (['xyz' num2str(numslice) '=rgb;']); %xyz is the same as cm (colormap) but without abs. But, apparently, doesn't make a difference.
%nameofmap=['xyz' num2str(numslice)];
%assignin('base',nameofmap,rgb);
%image (cm);axis image
%eval (['FA' num2str(numslice) '=FAmap;']);
%nameofmap=['FA' num2str(numslice)];
%assignin('base',nameofmap,FAmap);
if (doFAmap==1)
number=num2str(numslice); %FOUR LINES FOR FILE WRITING, REPEAT FOR THE OTHER IMAGES
st1='FA';st2='.dcm';
nameforfile=[st1 number st2];
dicomwrite(FAmap,nameforfile);
disp('writing FA map to DICOM file')
end
%eval (['tADC' num2str(numslice) '=tADC;']);
%nameofmap=['tADC' num2str(numslice)];
%assignin('base',nameofmap,tADC);
if (dotADC==1)
number=num2str(numslice); %FOUR LINES FOR FILE WRITING, REPEAT FOR THE OTHER IMAGES
st1='tADC';st2='.dcm';
nameforfile=[st1 number st2];
dicomwrite(tADC,nameforfile);
disp('writing tADC map to DICOM file')
end
%eval (['lambda1' num2str(numslice) '=lambda1;']);
%nameofmap=['lambda1_' num2str(numslice)];
%assignin('base',nameofmap,lambda1);
if (dolambda1==1)
number=num2str(numslice); %FOUR LINES FOR FILE WRITING, REPEAT FOR THE OTHER IMAGES
st1='lambda1_';st2='.dcm';
nameforfile=[st1 number st2];
dicomwrite(lambda1,nameforfile);
disp('writing lambda1 map to DICOM file')
end
%eval (['lambda2' num2str(numslice) '=lambda2;']);
%nameofmap=['lambda2_' num2str(numslice)];
%assignin('base',nameofmap,lambda2);
if (dolambda2==1)
number=num2str(numslice); %FOUR LINES FOR FILE WRITING, REPEAT FOR THE OTHER IMAGES
st1='lambda2_';st2='.dcm';
nameforfile=[st1 number st2];
dicomwrite(lambda2,nameforfile);
disp('writing lambda2 map to DICOM file')
end
%eval (['lambda3' num2str(numslice) '=lambda3;']);
%nameofmap=['lambda3_' num2str(numslice)];
%assignin('base',nameofmap,lambda3);
if (dolambda3==1)
number=num2str(numslice); %FOUR LINES FOR FILE WRITING, REPEAT FOR THE OTHER IMAGES
st1='lambda3_';st2='.dcm';
nameforfile=[st1 number st2];
dicomwrite(lambda3,nameforfile);
disp('writing lambda3 map to DICOM file')
end
%eval (['cm' num2str(numslice) '=cm;']);
%nameofmap=['cm' num2str(numslice)];
%assignin('base',nameofmap,cm);
if (docm==1)
number=num2str(numslice); %FOUR LINES FOR FILE WRITING, REPEAT FOR THE OTHER IMAGES
st1='cm';st2='.dcm';
nameforfile=[st1 number st2];
dicomwrite(cm,nameforfile);
disp('writing colormap to DICOM file')
end
mes=[num2str(numslice) ' of ' num2str(slices) ' finished'];
disp(mes)
end
%assignin('base','ten',ten)
clear FA FAmap tADC lambda1 lambda2 lambda3 cm FAmap3 rgb bo b1 b2 b3 b4 b5 b6 ADC101 ADC_101 ADC011;
clear ADC01_1 ADC110 ADC_110 r g b xx yy zz xy xz yz trace ten tensorvol transform ADCe ADCm D V;
assignin('base','tensorvol',0)
assignin('base','FAmaps',FAmaps);
assignin('base','tADCmaps',tADCmaps);
assignin('base','lambda1_maps',lambda1_maps);
assignin('base','lambda2_maps',lambda2_maps);
assignin('base','lambda3_maps',lambda3_maps);
assignin('base','cmaps',cmaps);
assignin('base','xyzmaps',xyzmaps);
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