I want to freehand draw on an image and crop everything inside and outside of where I drew.

I wrote a code to freehand draw on a circle to crop out everything inside and outside and it's running through and not giving me any errors but the end result is just 3 white figures.

 clc;
clear;
close all;
J=imread('M004L_SI_06_ORO.png'); %specify picture
h_im=imshow(J)
%%Draw contours onto the phase image to isolate the vessel wall. 
%You will be prompted to draw for the number of "imfreehand" commands below.
% Draw in this order: lumen, intima, EEL
       message_1=sprintf('Draw Lumen');
        uiwait(msgbox(message_1));
        Lumen = imfreehand(gca,'Closed','True');
        message_2=sprintf('Draw Intima');
        uiwait(msgbox(message_2));
        Intima = imfreehand(gca,'Closed','True'); 
        message_3=sprintf('Draw EEL');
        uiwait(msgbox(message_3));
        EEL = imfreehand(gca,'Closed','True');
        %%Obtain x-y coordinates
        Lumenxy=Lumen.getPosition;
        Intimaxy=Intima.getPosition;
        EELxy=EEL.getPosition;

        %%Create a binary image ("mask") 

       LumenImage =Lumen.createMask();                                    
       IntimaImage = Intima.createMask(); 
        if size(EELxy,1) < 20
            EELimage = [];
        else
            EELimage = EEL.createMask(); 
        end
        %%Set to "white" (or >255) all positions on the inside (lumen) and outside of the vessel wall 
        Intimafinal1(IntimaImage == 0) = 999;     % Set the outside of contour 1 to zero and inside of contour 2 to zero (leaving only the area in-between the contours)
        Intimafinal1(LumenImage == 1) = 999;

        if isempty(EELimage) == 0
            Efinal2(EELimage == 0) = 999;
            Efinal2(IntimaImage == 1) = 999;
        end

        %%Check final image
        figure2 = figure('PaperType','A','Color',[1 1 1],'units','normalized','outerposition',[0 0 1 1]);

        hold on;

        imshow(Intimafinal1,[0.25 0.4],'InitialMagnification','fit');

        if isempty(EELimage) == 0
            figure3 = figure('PaperType','A','Color',[1 1 1],'units','normalized','outerposition',[0 0 1 1]);

            hold on;

            imshow(Efinal2,[0.25 0.4],'InitialMagnification','fit');
            hold off;
        end
figure

Answer 1

[Image Analyst]

See attached demo that does this.

[Serena Tenhumberg]

Hey so just to clarify, the picture that I attached is a picture of a blood vessel. We are looking to quantify the amount of stain "the red pixels" between the lumen and the intima. When looking at this picture, the lumen is the area in the center of the picture with a weird shape that has mostly white pixels with a few red pixels. The intima is the area a little outside of this where there is an interior blue line that goes around in a whole circle of the vessel. We are trying to find a way to crop in between these two areas and turn the rest of the pixels into black or white. In the code I sent you we use imfreehand to draw the regions of the blood vessel we want. In the end result we want to have a donut shaped ROI. Is there anyway we could use it with a color image? Let me know what you think. Thanks again.

[Image Analyst]

Yes, just call imfreehand twice and create a mask. A true one for the outer ring, and an inner mask that zeros out that part of the outer mask. Easy. Let me know if you can't figure it out.

[Serena Tenhumberg]

Yes, I figured that out pretty easily. My next dilemma is to have the final image in color. When I edit the code to be in color, the inside mask ends up being a teal color or a red color depending on what I write. Do you know why this would be happening? I tried using a png file as well, with no luck. Thank you.