HOW TO CHANGE BINARY IMAGES TO 3D ARRAY (CONVERT TO 3D DIMENSION)

Hi all, I have 41 binary images.

Anyone know how convert it into 3D?

I means now my binary images just have dimension(let say 256 x 256). Then how to add thickness (as example thickness: 2.332) into that binary images?

So that my binary images now in 3D, (example 256x256x2.332)

Anyone can help me?

[Rik]

You are confusing the position in your array with the position in the world. How is your image 2.3 pixels deep?

What you can do is use ndgrid to create a coordinate grid that stores the coordinates of each voxel center.

[mohd akmal masud]

yah, I think this point. "What you can do is use ndgrid to create a coordinate grid that stores the coordinates of each voxel center."

can you help me?

[Rik]

That depends on what you want to do next. Presumably you want to do some calculations or visualizations. I expect it's more effective to ask how to do those.

For the single task of creating a coordinate grid, the documentation for ndgrid or meshgrid will do.

[mohd akmal masud]

Hir Sir Rik, is it correct I'm used ngrid to create voxel coordinate?

% For binary images
dataSetDir = fullfile('C:\Users\Akmal\Desktop\I-131 256 28.02.2020\I-131 SPECT NEMA VALIDATION 01112019 256X256 26.09.2021 petang');
imageDir = fullfile(dataSetDir,'bnwaftersegmentation');
imds = imageDatastore(imageDir);
for i = 1:41
    %     subplot(6,7,i)
    I = readimage(imds,i);
end
I = ndgrid(:,:,2.332)

is it like that?

[Image Analyst]

No, that just overwrites I every iteration.

[mohd akmal masud]

Hi sir Image Analyst, can you help me, maybe you can write the code?

Please help me sir?

Answer 1

[DGM]

As per Rik's suggestion:

% ...

% assuming that your dicom images and binary images have same page geometry
numframes = 41;
s = [size(P,1) size(P,2)];
maskstack = zeros(s(1),s(2),numframes);
for f = 1:numframes
    if f == 1
        cast(maskstack,class(readimage(imds,f)));
    end
    maskstack(:,:,f) = readimage(imds,f);
end

% build location arrays
[X Y Z] = ndgrid(1:s(1),1:s(2),0:2.332:(numframes-1)*2.332);

Or something like that.

[mohd akmal masud]

yah, dicom images and binary images have same page geometry.

but after that, how to develop it into 4D?

is it like this?

% to view as 4D
p = patch(isosurface(X, Y, Z));
axis equal
set(p,'FaceColor','c','EdgeColor','none');
alpha(p,1)
hold

Answer 2

[Image Analyst]

If you want, just consider your 256x256 image as having a thickness of 2.332 millimeters or centimeters or whatever. There is nothing to do to the image. However if you compute something like area of some region and want the volume in 3-D you have to multiply the area by the square of the lateral pixelsPerMm and then by the z-direction slice spacing of 2.332 to get the volume in mm.

[mohd akmal masud]

yah..you are right sir. that is to get the volume,

but my problem is how to paste the binary image that have value 1 into the origional images (dicom images that have pixel value).

ok let me explain,

let say my origional images is

K = dicomread('image1.dcm');

note: let say the dimension is 256x256x2.332

after i do the segmentation, the binary image become binary images that have value 1 and 0. It is became 2D images because the method of segmentation have to do so.

then, i want mark it, the value 1 is foreground, and the value 0 background. because the origional image (dicom image) have pixel number each voxel.

below is the code that Ihave tried.

% For 3D images
clc
clear all
myFolder = ('C:\Users\Akmal\Desktop\I-131 256 28.02.2020\I-131 SPECT NEMA VALIDATION 01112019 256X256 26.09.2021 petang\dcmoriextract');
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);
end


% For binary images
dataSetDir = fullfile('C:\Users\Akmal\Desktop\I-131 256 28.02.2020\I-131 SPECT NEMA VALIDATION 01112019 256X256 26.09.2021 petang');
imageDir = fullfile(dataSetDir,'bnwaftersegmentation');
imds = imageDatastore(imageDir);
for i = 1:41
    %     subplot(6,7,i)
    I = readimage(imds,i);
end


% to view as 4D
p = patch(isosurface((P(I==1))));
axis equal
set(p,'FaceColor','c','EdgeColor','none');
alpha(p,1)
hold

but ihave problem in my binary images is 2D, so I got error like below

Error using smooth3 (line 51) V must be a 3D array.

THIS IS IMAGE THAT SUPPOSELY I WANT like below

can you help me sir?? Please..

[Image Analyst]

Again, you're overwriting I on each iteration so it will only have the last image in it. I don't see where you're calling smooth3 but if you're passing it I, and if I is only a 2-D array, you'll get that error.