I have performed image segmentation on dicom brain tumor images. now i want to extract rest of the region except the tumor region.

hello , can any one help me with this, actually i want to work on the NROI portion/ larger section of brain image after extracting the tumor using image segmentation. i am using the below code.

Im=imread('C:\Coding\Brain-Tumor-Detection-using-Image-Processing-master\5.jpg');
figure, imshow(Im); title('Brain MRI Image');
I = imresize(Im,[256,256]);
Im=I;
I= rgb2gray(I);
I= im2bw(I,.6);%binarising with thresold .6
figure, imshow(I);title('Thresholded Image');
% hy = fspecial('sobel');
% hx = hy';
% Iy = imfilter(double(I), hy, 'replicate');
% Ix = imfilter(double(I), hx, 'replicate');
% gradmag = sqrt(Ix.^2 + Iy.^2);
% L = watershed(gradmag);
% Lrgb = label2rgb(L);
% figure, imshow(Lrgb), title('Watershed segmented image ')
se = strel('disk', 20);
Io = imopen(I, se);
Ie = imerode(I, se);
Iobr = imreconstruct(Ie, I);
Iobrd = imdilate(Iobr, se);
Iobrcbr = imreconstruct(imcomplement(Iobrd), imcomplement(Iobr));
Iobrcbr = imcomplement(Iobrcbr);
I2 = I;
fgm = imregionalmax(Iobrcbr);
I2(fgm) = 255;
se2 = strel(ones(5,5));
fgm2 = imclose(fgm, se2);
fgm3 = imerode(fgm2, se2);
fgm4 = bwareaopen(fgm3, 20);
I3 = I;
bw = im2bw(Iobrcbr);
figure
imshow(bw), title('only tumor')
bw2=bwperim(bw);
figure
imshow(bw2)
D=imfuse(Im,bw);
D=rgb2gray(D);
imshow(D)
% labeledImage = bwlabel(I, 8);     % Label each blob so we can make measurements of it
% coloredLabels = label2rgb (labeledImage, 'hsv', 'k', 'shuffle'); % pseudo random color labels
% coloredLabels=rgb2gray(coloredLabels);
% biggestLabel = ismember(I, sortIndexes(1));
% binaryImage = biggestLabel > 0;
% maskedImage = grayImage;
% maskedImage(~binaryImage) = 0;
% figure
% imshow(coloredLabels);
% ME = 1 - (nnz(~I & ~bw) + nnz(I & bw))/(numel(I));
% c=ones(size(Im,1),size(Im,2),3);
% c(:,:,2)=1;
% figure,imshow(Im)
%  hold all
%  h=imshow(c);
%   set(h,'AlphaData',bw)

I got the result tumor sementaed image which is ROI of original image. now i want to extract rest of the image except tumor as output in last image. please help me with this. Thank you

Answer 1

[Image Analyst]

You forgot to attach your image so we can't try your code. And using non-descriptive variable names and no comments certainly doesn't help. But assuming bw is your (badly named) tumor mask and I is your (badly-named) gray scale image, you can get the non-tumor part of the image like

tumorAlone = I; % Initialize
tumorAlone(~bw) = 0; % Erase outside the tumor.
nonTumorAlone = I; % Initialize
nonTumorAlone(bw) = 0; % Erase inside the tumor to get gray scale image outside the tumor mask.

[Suniti Singh]

sir i am attaching the image (I) and also the tumor extracted as (bw). I want to extract rest of the image except tumor as image shown in right side of last image attached . So i can further work on rest of the image section except tumor. kindly help me. thank you for your reply.

[Image Analyst]

I'm not sure why the code I gave you doesn't work.

tumorAlone = I; % Initialize
tumorAlone(~bw) = 0; % Erase outside the tumor.
nonTumorAlone = I; % Initialize
nonTumorAlone(bw) = 0; % Erase inside the tumor to get gray scale image outside the tumor mask.

Please explain why this is not working for you. Note that the image in the bottom row is different than the image in the top row. Are you sure you're using the right arrays?

[yanqi liu]

Im=imread('https://www.mathworks.com/matlabcentral/answers/uploaded_files/899640/I.jpeg');
figure, imshow(Im); title('Brain MRI Image');

I = imresize(Im,[256,256]);
Im=I;
I= rgb2gray(I);
I= im2bw(I,.6);%binarising with thresold .6
figure, imshow(I);title('Thresholded Image');

% hy = fspecial('sobel');
% hx = hy';
% Iy = imfilter(double(I), hy, 'replicate');
% Ix = imfilter(double(I), hx, 'replicate');
% gradmag = sqrt(Ix.^2 + Iy.^2);
% L = watershed(gradmag);
% Lrgb = label2rgb(L);
% figure, imshow(Lrgb), title('Watershed segmented image ')
se = strel('disk', 20);
Io = imopen(I, se);
Ie = imerode(I, se);
Iobr = imreconstruct(Ie, I);
Iobrd = imdilate(Iobr, se);
Iobrcbr = imreconstruct(imcomplement(Iobrd), imcomplement(Iobr));
Iobrcbr = imcomplement(Iobrcbr);
I2 = I;
fgm = imregionalmax(Iobrcbr);
I2(fgm) = 255;
se2 = strel(ones(5,5));
fgm2 = imclose(fgm, se2);
fgm3 = imerode(fgm2, se2);
fgm4 = bwareaopen(fgm3, 20);
I3 = I;
bw = im2bw(Iobrcbr);

Warning: The input image is already binary.

figure
imshow(bw), title('only tumor')

tumorAlone = Im(:,:,1); % Initialize
tumorAlone(~bw) = 0; % Erase outside the tumor.
nonTumorAlone = Im(:,:,1); % Initialize
nonTumorAlone(bw) = 0; % Erase inside the tumor to get gray scale image outside the tumor mask.

figure
imshow(tumorAlone)

figure
imshow(nonTumorAlone)

[Suniti Singh]

Thank you so much sir. I got my required result.

[Image Analyst]

Then can you click on the "Accept this answer" link? Thanks in advance. 🙂