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segmentation by marking points around the region

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Elysi Cochin
Elysi Cochin 2012-12-17
评论： Image Analyst 2018-6-28
please can someone help me with a sample code of medical image segmentation by the method of marking points around the region to be segmented..... i marked few points around the region but dont know how to proceed.... please could someone reply.....

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采纳的回答

Image Analyst
Image Analyst 2012-12-17
Use roipoly() or roipolyold() and then poly2mask().
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zainab srabony
zainab srabony 2018-6-28
can anyone help me to find the function of mri brain image segmentation?

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更多回答（2 个）

Image Analyst
Image Analyst 2012-12-18
See this demo:
% Demo to have the user freehand draw an irregular shape over
% a gray scale image, have it extract only that part to a new image,
% and to calculate the mean intensity value of the image within that shape.
% Also calculates the perimeter, centroid, and center of mass (weighted centroid).
% Change the current folder to the folder of this m-file.
if(~isdeployed)
cd(fileparts(which(mfilename)));
end
clc; % Clear command window.
clear; % Delete all variables.
close all; % Close all figure windows except those created by imtool.
imtool close all; % Close all figure windows created by imtool.
workspace; % Make sure the workspace panel is showing.
fontSize = 16;
% Read in a standard MATLAB gray scale demo image.
folder = fullfile(matlabroot, '\toolbox\images\imdemos');
baseFileName = 'cameraman.tif';
% 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 = imread(fullFileName);
imshow(grayImage, []);
axis on;
title('Original Grayscale Image', 'FontSize', fontSize);
set(gcf, 'Position', get(0,'Screensize')); % Maximize figure.
message = sprintf('Left click and hold to begin drawing.\nSimply lift the mouse button to finish');
uiwait(msgbox(message));
hFH = imfreehand();
% Create a binary image ("mask") from the ROI object.
binaryImage = hFH.createMask();
xy = hFH.getPosition;
% Now make it smaller so we can show more images.
subplot(2, 3, 1);
imshow(grayImage, []);
axis on;
drawnow;
title('Original Grayscale Image', 'FontSize', fontSize);
% Display the freehand mask.
subplot(2, 3, 2);
imshow(binaryImage);
axis on;
title('Binary mask of the region', 'FontSize', fontSize);
% Label the binary image and computer the centroid and center of mass.
labeledImage = bwlabel(binaryImage);
measurements = regionprops(binaryImage, grayImage, ...
'area', 'Centroid', 'WeightedCentroid', 'Perimeter');
area = measurements.Area
centroid = measurements.Centroid
centerOfMass = measurements.WeightedCentroid
perimeter = measurements.Perimeter
% Calculate the area, in pixels, that they drew.
numberOfPixels1 = sum(binaryImage(:))
% Another way to calculate it that takes fractional pixels into account.
numberOfPixels2 = bwarea(binaryImage)
% Get coordinates of the boundary of the freehand drawn region.
structBoundaries = bwboundaries(binaryImage);
xy=structBoundaries{1}; % Get n by 2 array of x,y coordinates.
x = xy(:, 2); % Columns.
y = xy(:, 1); % Rows.
subplot(2, 3, 1); % Plot over original image.
hold on; % Don't blow away the image.
plot(x, y, 'LineWidth', 2);
drawnow; % Force it to draw immediately.
% Burn line into image by setting it to 255 wherever the mask is true.
burnedImage = grayImage;
burnedImage(binaryImage) = 255;
% Display the image with the mask "burned in."
subplot(2, 3, 3);
imshow(burnedImage);
axis on;
caption = sprintf('New image with\nmask burned into image');
title(caption, 'FontSize', fontSize);
% Mask the image and display it.
% Will keep only the part of the image that's inside the mask, zero outside mask.
blackMaskedImage = grayImage;
blackMaskedImage(~binaryImage) = 0;
subplot(2, 3, 4);
imshow(blackMaskedImage);
axis on;
title('Masked Outside Region', 'FontSize', fontSize);
% Calculate the mean
meanGL = mean(blackMaskedImage(binaryImage));
% Put up crosses at the centriod and center of mass
hold on;
plot(centroid(1), centroid(2), 'r+', 'MarkerSize', 30, 'LineWidth', 2);
plot(centerOfMass(1), centerOfMass(2), 'g+', 'MarkerSize', 20, 'LineWidth', 2);
% Now do the same but blacken inside the region.
insideMasked = grayImage;
insideMasked(binaryImage) = 0;
subplot(2, 3, 5);
imshow(insideMasked);
axis on;
title('Masked Inside Region', 'FontSize', fontSize);
% Now crop the image.
leftColumn = min(x);
rightColumn = max(x);
topLine = min(y);
bottomLine = max(y);
width = rightColumn - leftColumn + 1;
height = bottomLine - topLine + 1;
croppedImage = imcrop(blackMaskedImage, [leftColumn, topLine, width, height]);
% Display cropped image.
subplot(2, 3, 6);
imshow(croppedImage);
axis on;
title('Cropped Image', 'FontSize', fontSize);
% Put up crosses at the centriod and center of mass
hold on;
plot(centroid(1)-leftColumn, centroid(2)-topLine, 'r+', 'MarkerSize', 30, 'LineWidth', 2);
plot(centerOfMass(1)-leftColumn, centerOfMass(2)-topLine, 'g+', 'MarkerSize', 20, 'LineWidth', 2);
% Report results.
message = sprintf('Mean value within drawn area = %.3f\nNumber of pixels = %d\nArea in pixels = %.2f\nperimeter = %.2f\nCentroid at (x,y) = (%.1f, %.1f)\nCenter of Mass at (x,y) = (%.1f, %.1f)\nRed crosshairs at centroid.\nGreen crosshairs at center of mass.', ...
meanGL, numberOfPixels1, numberOfPixels2, perimeter, ...
centroid(1), centroid(2), centerOfMass(1), centerOfMass(2));
msgbox(message);
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Aaron Smith
Aaron Smith 2017-7-13
编辑：Aaron Smith 2017-7-13
I did not set the size of my image. I know that it has 1024 rows as the image is x 1024 but I did not have a line of code like the one you detailed above. The code, spliced with yours and with the (rows, columns) line included looks like:
Folder = uigetdir('C:\Users\c13459232\Documents\MATLAB'); % selecta folder from which to select files
File = uigetfile(Folder); % select a file
Image = imread(File); % Read image
imshow(Image) % generate the image in a figure
again = true;
finalImage = false(rows, columns);
while again
thisRegion = roipoly;
% Add this in to the main one
finalImage = finalImage | thisRegion;
promptMessage = sprintf('Do you want to add another region?');
titleBarCaption = 'Continue?';
buttonText = questdlg(promptMessage, titleBarCaption, 'Yes', 'No', 'Yes');
if contains(buttonText, 'No', 'IgnoreCase', true)
again = false;
end
end
By distinct I mean that each ROI blob needs to be looked at separately. I am going to calculate the sum inside each ROI and tabulate them essentially as region 1, region 2, region 3...
When I added the line you suggested it generated an error: Undefined function 'contains' for input arguments of type 'char'. This could be due to contains being introduced in 2016. strfind is an alternative but it has a different output as far as I can tell.
Image Analyst
Image Analyst 2017-7-13
Use
if strcmpi(buttonText, 'No')
To analyze all the blobs, if you want one of the measurements done by regionprops(), just pass in a labeled version of final image:
labeledImage = bwlabel(finalImage);
props = regionprops(labeledImage, 'all');
This will give you a structure with all kinds of measurements about each individual blob. You can get them out into a single array if you want, for example to get all the areas:
allAreas = [props.Area];
If you want the sum of all the gray levels instead of the sum of pixels (i.e. pixel count), use 'MeanIntensity' and pass in the gray scale image also:
props = regionprops(labeledImage, grayImage, 'Area', 'MeanIntensity');

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GRAN BADSHAH
GRAN BADSHAH 2013-2-16
Thank you sir i found yours this algorithm / explanation very much helpful regarding my work to define ROI of a medical image and then get it as a separate image.
  2 个评论
Meshooo
Meshooo 2014-3-24
Hi, I would like to know why the size or the rectangle"BW" and "hpoly" are different in the following similar case
x = [4 10 10 4 4];
y = [4 4 10 10 4];
BW = poly2mask(x,y,20,20); %binary image
B = bwboundaries(BW);
b = B{1};
X = b(:, 1);
Y = b(:, 2);
hpoly = roipoly(BW,Y,X);
figure, imshow(BW)
figure, imshow(hpoly)
Any idea?
Thank you.
Meshoo
Image Analyst
Image Analyst 2014-3-24
This doesn't seem to be related to Elysi's original question, so please post this as your own question in a separate discussion.

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