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    <p>If I understand you correctly, you have a binary image of the boundary of the kidney and now need to set the inside of the boundary to 1s. To do this, you can use the <a href="http://www.mathworks.com/help/toolbox/images/ref/imfill.html" rel="nofollow">imfill()</a> function with the 'holes' setting on. </p> <pre><code>BW2 = imfill(BW,'holes'); </code></pre> <p>EDIT: Looking at the code, it seems that it does what you want already. </p> <pre><code>% Outputs: % J: Binary mask (with the same size as the input image) indicating % 1 (true) for associated pixel/voxel and 0 (false) for outside </code></pre> <p>so you just need to get the second output as well:</p> <pre><code> IR=imread('nfliver5.jpg'); figure, imshow(IR), hold all [poly im] = regionGrowing(IR,[],15,1200); % click somewhere inside the liver imshow(im,[]) </code></pre> <p>Now <code>im</code> is a binary image with your segmented region. </p> <p>EDIT2: </p> <p>Once you have the binary image <code>im</code>, you can simply use element-wise multiplication to remove all parts of the orignal image outside the segmented region.</p> <pre><code>SEG = IR.*im; imshow(SEG,[]) </code></pre> <p>EDIT3:</p> <p>For 3D images, you need to specify the coordinates manually, and not by using the mouse. This is because the mouse only gives us 2 coordinates (x and y) and you need 3 (x,y and z). So just find the coordinates you need by looking at the image, and then choosing an appropriate z coordinate.</p> <pre><code>%Example coordinates, coordinates = [100 100 5] poly = regionGrowing(squeeze(IR), coordinates, 60, Inf, [], true, false); </code></pre>
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    1. POExtracting image region within boundary
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    1. POExtracting image region within boundary
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    1. COThanks Gaul. But when I try this, I get only the same input as output.I wrote as BW=imread('nfliver5.jpg');BW2=imfill(BW,'holes'); Then i displayed the images.where nfliver5.jpg is the output image within boundary. Actually I need only the region surrounded by the white boundary and have to remove the remaining part of image that is outside the boundary.
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    2. COFor imfill to work it has to be a binary image, but never mind. The algorithm already does this for you. Look at my edited answer.
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    3. COU are right. but kindly check out the following pdf http://www.ijcaonline.org/casct/number1/SPE34T.pdf .See the output images Fig 6 and Fig 7 in it. Now am getting an output similar to that shown in Fig 6(using region growing). What I need is the Fig 7. Because I need to further process it to extract tumor also(just like Fig 8). Kindly help.
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