How to calculate the total pixel value in volume segmentation

Dear all,

I have code below. How to calculate the total counts (represent the pixel value) in every volume segmentation P

All the image attached.

% For binary images (png format, each pixel just have value 1 and 0.)
clc
clear all
close all
dataSetDir = fullfile('C:\Users\Akmal\Downloads\1.2.840.113619.2.280.2.1.6032022125618360.139679786-20220425T063142Z-001\1.2.840.113619.2.280.2.1.6032022125618360.139679786');
imageDir = fullfile(dataSetDir,'gradieweigbwaftersegmentationpngTCEswari');
imds = imageDatastore(imageDir);
for i = 1:45
    subplot(13,11,i)
    I = readimage(imds,i);
    % binary
    Is{i} = logical(I);
    imshow3D(I)
end
% For 3D images spect
myFolder = ('C:\Users\Akmal\Downloads\1.2.840.113619.2.280.2.1.6032022125618360.139679786-20220425T063142Z-001\1.2.840.113619.2.280.2.1.6032022125618360.139679786\dcmeswariint16128x128');
filePattern = fullfile(myFolder, '*.dcm'); % Change to whatever pattern you need.
theFiles = dir(filePattern);
for K = 1 : length(theFiles)
    baseFileName = theFiles(K).name;
    fullFileName = fullfile(theFiles(K).folder, baseFileName);
    fprintf(1, 'Now reading %s\n', fullFileName);
    % Now do whatever you want with this file name,
    % such as reading it in as an image array with imread()
    P(:,:,K) = dicomread(fullFileName);
    P(:,:,K) = (P(:,:,K))  .* int16( Is{K} );
    %     P(:,:,K) = double(uint8(K).*uint8(Is{K}));
end

[mohd akmal masud]

Tq Sir. Its Work!!

Answer 1

[DGM]

I'm not quite sure if this is what you're after, but this:

pnz = nnz(P);

will give you the total number of nonzero elements in the pagewise intersection of P and Is.

So it's not necessarily the volume of Is, but the intersection of the two volumes.

[mohd akmal masud]

Dear DGM,

My image P as below, where all the volume segmentation have the pixel value.

if I use you code pnz = nnz(P); , the asnwer is 589.

589 its look like give the total number pixel for all the six volume segmentation.

What I need is the total pixel value for each volume. As picture, there are index (represent the pixel value), I need the total pixel value for it volume.

[DGM]

Not exactly sure if you're after the volumes of the objects in Is or the sum of the regions in P intersecting those volumes. Either way, this calculates both.

It makes sense to arrange Is as a 3D array instead of as a cell array.

% For binary images (png format, each pixel just have value 1 and 0.)
dataSetDir = fullfile('');
imageDir = fullfile(dataSetDir,'gradieweigbwaftersegmentationpngTCEswari');
imds = imageDatastore(imageDir);

Is = false(128,128,45); % preallocate
for i = 1:45
    %subplot(13,11,i)
    I = readimage(imds,i);
    % binary
    Is(:,:,i) = logical(I);
    %imshow3D(I)
end

% For 3D images spect
myFolder = ('dcmeswariint16128x128');
filePattern = fullfile(myFolder, '*.dcm'); % Change to whatever pattern you need.
theFiles = dir(filePattern);
P = zeros(128,128,45,'int16'); % preallocate
for K = 1 : length(theFiles)
    baseFileName = theFiles(K).name;
    fullFileName = fullfile(theFiles(K).folder, baseFileName);
    %fprintf(1, 'Now reading %s\n', fullFileName);
    % Now do whatever you want with this file name,
    % such as reading it in as an image array with imread()
    P(:,:,K) = dicomread(fullFileName);
    % this shouldn't be needed unless it's for something else
    %P(:,:,K) = (P(:,:,K))  .* int16( Is(:,:,K) ); 
end

% calculate things
CC = bwconncomp(Is); % default uses 26-connectivity (a full 3x3x3 nhood) for 3D images
volumes = cellfun(@numel,CC.PixelIdxList) % the volumes of the objects in Is
volumesums = zeros(CC.NumObjects,1); % sum of pixel values in P as selected by Is
for k = 1:CC.NumObjects
    volumesums(k) = sum(P(CC.PixelIdxList{k}));
end
volumesums

Answer 2

[Image Analyst]

Use regionprops3 and ask for 'Volume'.

[mohd akmal masud]

Dear Image Analyst,

I dont want volume, but total pixel value inside the volume.

[Image Analyst]

Get the MeanIntensity (one of regionprops3 measurements) and multiply it by the Volume. This will give you the "Total Integrated Graly Level" inside the volume.

[mohd akmal masud]

I see..Okay thank you Image Analyst.