How do I cut out an area that I've created a boundary to?

I've created a boundary around the lungs in this image & I would like to show just the area inside the boundar. How would I do this?

I've tried subracting it from the original image but had no luck. Any help would be greatly appreciated.

http://i45.tinypic.com/2z3nja1.jpg

this is the code so far

I = imread('Image1.png');                   %%Read in image
C = I(90:400,40:460);                       %%Crop out unnecessary parts
thresholded = C < 150;                      %%Threshold to isolate lung tissue
clearThresh = imclearborder(thresholded);  %%Remove artifacts attached to border
BW = bwareaopen(clearThresh,100);           %%Remove objects less than 40 pixels in size
dim = size(BW);                             %%Boundary trace one of the lungs
col = round(dim(2)/2)-130;
row = find(BW(:,col), 1 );
boundary = bwtraceboundary(BW,[row ,col],'N');
imshow(C)                                   %%Display Boundary on original image
hold on;
plot(boundary(:,2),boundary(:,1),'r','LineWidth',3);
BW_filled = imfill(BW,'holes');             %%Boundary Trace the second lung
boundaries = bwboundaries(BW_filled);
for k = 1:2
  b = boundaries{k};
  plot(b(:,2),b(:,1),'g','LineWidth',3);
end

Answer 1

[Image Analyst]

Close. Here, try this:

clc;    % Clear the command window.
close all;  % Close all figures (except those of imtool.)
imtool close all;  % Close all imtool figures.
clear;  % Erase all existing variables.
workspace;  % Make sure the workspace panel is showing.
format longg;
format compact;
fontSize = 20;

% Change the current folder to the folder of this m-file.
if(~isdeployed)
  cd(fileparts(which(mfilename)));
end
  
% Check that user has the Image Processing Toolbox installed.
hasIPT = license('test', 'image_toolbox');
if ~hasIPT
  % User does not have the toolbox installed.
  message = sprintf('Sorry, but you do not seem to have the Image Processing Toolbox.\nDo you want to try to continue anyway?');
  reply = questdlg(message, 'Toolbox missing', 'Yes', 'No', 'Yes');
  if strcmpi(reply, 'No')
    % User said No, so exit.
    return;
  end
end

% Read in a demo image.
folder = 'C:\Users\Student\Documents\Temporary';
baseFileName = '2z3nja1.jpg';
% Get the full filename, with path prepended.
fullFileName = fullfile(folder, baseFileName);
% Check if file exists.
if ~exist(fullFileName, 'file')
  % File doesn't exist -- didn't find it there.  Check the search path for it.
  fullFileName = baseFileName; % No path this time.
  if ~exist(fullFileName, 'file')
    % Still didn't find it.  Alert user.
    errorMessage = sprintf('Error: %s does not exist in the search path folders.', fullFileName);
    uiwait(warndlg(errorMessage));
    return;
  end
end
grayImage = rgb2gray(imread(fullFileName));
% Get the dimensions of the image.  
% numberOfColorBands should be = 1.
[rows columns numberOfColorBands] = size(grayImage);
% Display the original gray scale image.
subplot(2, 2, 1);
imshow(grayImage, []);
title('Original Grayscale Image', 'FontSize', fontSize);
% Enlarge figure to full screen.
set(gcf, 'units','normalized','outerposition',[0 0 1 1]);
% Give a name to the title bar.
set(gcf,'name','Demo by ImageAnalyst','numbertitle','off') 

% Let's compute and display the histogram.
[pixelCount grayLevels] = imhist(grayImage);
subplot(2, 2, 2); 
bar(pixelCount);
grid on;
title('Histogram of original image', 'FontSize', fontSize);
xlim([0 grayLevels(end)]); % Scale x axis manually.

% Find border and mask it off
binaryImage = grayImage == 255;
% Display the image.
subplot(2, 2, 3);
imshow(binaryImage, []);
title('Original Binary Image', 'FontSize', fontSize);
% Get just hte border pixels.
borderImage = logical(binaryImage - imclearborder(binaryImage));
% Move the outer edge in a little bit.
borderImage = imdilate(borderImage, true(7));
% Display the image.
subplot(2, 2, 4);
imshow(borderImage, []);
title('Border Pixels Image', 'FontSize', fontSize);

% Start a new figure.
figure;
% Enlarge figure to full screen.
set(gcf, 'units','normalized','outerposition',[0 0 1 1]);
% Give a name to the title bar.
set(gcf,'name','Demo by ImageAnalyst','numbertitle','off') 
% Erase border pixels.
grayImage(borderImage) = 0;
% Display the image.
subplot(2, 2, 1);
imshow(grayImage, []);
title('Masked Image', 'FontSize', fontSize);

% Threshold for dark pixels.
binaryImage3 = (grayImage > 0) & (grayImage < 125); % Threshold to isolate lung tissue

% Get the two largest blobs.
[labeledImage numberOfBlobs] = bwlabel(binaryImage3);
blobMeasurements = regionprops(labeledImage, 'Area');
allAreas = [blobMeasurements.Area];
[sortedAreas sortIndices] = sort(allAreas, 'descend');
% Get a list of the blobs that meet our criteria and we need to keep. 
keeperIndexes = [sortIndices(1), sortIndices(2)]; 
% Extract only those blobs that meet our criteria, and 
% eliminate those blobs that don't meet our criteria. 
% Note how we use ismember() to do this.
keeperBlobsImage = ismember(labeledImage, keeperIndexes); 
% Binarize and fill holes.
binaryImage3 = imfill(keeperBlobsImage>0, 'holes');
% Display the image.
subplot(2, 2, 2);
imshow(binaryImage3, []);
title('Two Largest Regions', 'FontSize', fontSize);
% Re-label with only the keeper blobs kept.
labeledImage = bwlabel(keeperBlobsImage, 8);     % Label each blob so we can make measurements of it

% Find outer boundaries and trace over image.
% bwboundaries() returns a cell array, where each cell contains the row/column coordinates for an object in the image.
% Plot the borders of two largest regions returned by bwboundaries.
subplot(2, 2, 3); 
imshow(grayImage, []);
title('Outlines, from bwboundaries()', 'FontSize', fontSize);
hold on;
boundaries = bwboundaries(binaryImage3);  
numberOfBoundaries = size(boundaries);
for k = 1 : numberOfBoundaries
  thisBoundary = boundaries{k};
  plot(thisBoundary(:,2), thisBoundary(:,1), 'g', 'LineWidth', 2);
end
hold off;

% Now let's extract out just the lungs.
maskedImage = zeros(rows, columns, 'uint8'); % Initialize.
maskedImage(binaryImage3) = grayImage(binaryImage3);
subplot(2, 2, 4); 
imshow(maskedImage, []);
title('Lungs Masked', 'FontSize', fontSize);

Answer 2

[Sean de Wolski]

doc poly2mask

To turn your boundaries into a mask that can then me elementwise multiplied by the image to show just what's inside.