--- a
+++ b/Thoracic Organs Segmentation code/Main.m
@@ -0,0 +1,64 @@
+%Before .m execution add paths
+Path1= cd;  Path1=[Path1,'\OpticalFlow3D'];path(Path1,path);
+Path1 = cd; Path1 = [Path1, '\MAP']; path(Path1, path);
+Path1 = cd; Path1 = [Path1, '\TwoPhaseLevel Sets']; path(Path1, path);
+
+%input images
+%Inhale and Exhale  images
+load InhaleImg.mat;load ExhaleImg.mat;
+
+% InhaleImg=imresize(imread('InhaleImg.jpg'),0.3);
+% ExhaleImg=imresize(imread('ExhaleImg.jpg'),0.3);
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+Img=reshape([InhaleImg;ExhaleImg]',[size(ExhaleImg,2),size(InhaleImg,1),2]);
+
+%Rib Cage Approximation
+Thresh = Histogr(Img);
+
+
+%MaxValue=max(max(max(Img)));
+%Img = rescalingFunction(Img,0.16*MaxValue,MaxValue);
+   
+[RibCage]=RibCageApproximation(Img(:,:,1),Thresh);
+ 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%Feature extraction 
+
+%Optical Flow for the desplacement estimation
+ i1= permute(squeeze(Img(:,:,1)),[1 2 3]);%Inhale Img
+ i2= permute(squeeze(Img(:,:,2)),[1 2 3]);%Exhale Img
+ Displacement = OpticalFlow3D(i1,i2); 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Maximum likelikehood pixel to belong Heart.  
+[J,I] = MaxLikelihood(Img(:,:,1),RibCage,squeeze(Displacement));
+ 
+ 
+
+InnerCurve = DrawCircle(4,I(1),J(1),size(Img,1),size(Img,2),1);
+
+%Level Sets Process
+[phi1,phi2]=TwoPhasesLevelSet(Img(:,:,1),RibCage,InnerCurve);
+
+figure
+ imshow(Img(:,:,1),[]); hold on
+ c1 = contour(phi1,[0 0],'r','LineWidth',2.2);
+ c2 = contour(phi2,[0 0],'g','LineWidth',2);
+ title('Zero Level Set')
+ hold off;
+
+  
+ [I_heart]=find((phi2)<=0);
+ [I_lung]=find((phi1)<=0);
+
+ SegmentOfThorax= zeros(size(Img));
+ SegmentOfThorax(I_heart)=1;
+ SegmentOfThorax(I_lung)=1;
+ SegmentOfThorax= imfill(SegmentOfThorax);
+
+ figure(1)
+ imshow(Img(:,:,1),[]); hold on
+ c = contour(SegmentOfThorax,[0 0],'m','LineWidth',2);
+ hold off
+
+