MATLAB: How to save an average voxel values from multiple ROIs in a dicom slice

dicomdigital image processing

I want to extract an average voxel values form each ROIs drawn on dicom slice. How can I do that? Using the following code I read the dicom slice, then draw 4 rois, now I want to save the ROI intensty statistics such as the average, minimum, maximum and standard deviation in voxel values within the ROI. How to complete the code below to get that done? 
close all; clear;  clc;
%% load and read dicom slice
info_ct = dicominfo('37.100.dcm');
Height = info_ct.Height;
Width = info_ct.Width;
slope = info_ct.RescaleSlope;
intercept = info_ct.RescaleIntercept;
ct_matrix = slope * double(dicomread(info_ct)) + intercept; % respect slope and intercept
%% Now, draw 4 ROIs on dicom slice
figure
N = 4;
I = imshow(ct_matrix(:,:,1), [-800 1000]);
% Define the Region of Interest
e = drawcircle(gca, 'Label', '1'); % draw 1 ROI
f = drawcircle(gca, 'Label', '2'); % draw 2 ROI
g = drawcircle(gca, 'Label', '3'); % draw 3 ROI
h = drawcircle(gca, 'Label', '4'); % draw 4 ROI
% Create a Mask
BW1 = createMask(e, I);  % 1s at ROI and 0s everywhere
BW1 = double(BW1);
BW2 = createMask(f, I); 
BW2 = double(BW2);
BW3 = createMask(g, I); 
BW3 = double(BW3);
BW4 = createMask(h, I); 
BW4 = double(BW4);
....

Best Answer

BW1 = createMask(e, I);
Data=I(BW1);
Now you can calculate the statistics you need.
I would suggest using a struct array:
% Generate example data (yes, it is an MRI, but the code works)
D=load('mri');D=double(D.D);
ct_matrix= ( D/max(D(:)) *1800 ) -800;
f=figure(1);clf(f)
N = 4;
IM=ct_matrix(:,:,1);
I = imshow(IM, [-800 1000]);
set(f,'WindowState','maximized')
% Define the Region of Interests
H=cell(N,1);
for n = 1:N
    H{n} = drawcircle(gca, 'FaceAlpha', 0.05, 'Label', sprintf('%d',n));
end
% Extract parameters
output=struct;
for n = 1:N
    BW = createMask(H{n}, IM);
    data = IM(BW);
    %or:
    % BW = createMask(H{n}, I.CData);
    % data = I.CData(BW);
    output(n).mean = mean(data);
    output(n).SD = std(data);
end
Related Question