How can I convert Dicom directory (series of dicom images) to 3D volume image?

Question

I have almost 80 dicom images in a folder. Now, I want to convert these series of dicom images to a 3d volume.

Below is the code which loads MRI data, forms counter slices and then generates 3d volume. But, it loads inbuilt MRI images.

How can I change this program to load dicom images from my folder and display 3d volume??

load mri
D = squeeze(D);
%figure
colormap(map)
image_num = 8;
image(D(:,:,image_num))
axis image
x = xlim;
y = ylim;
cm = brighten(jet(length(map)),-.5);
figure
colormap(cm)
contourslice(D,[],[],image_num)
axis ij
xlim(x)
ylim(y)
daspect([1,1,1])
figure
colormap(cm)
contourslice(D,[],[],[1,12,19,27],8);
view(3);
axis tight
figure
colormap(map)
Ds = smooth3(D);
hiso = patch(isosurface(Ds,5),...
   'FaceColor',[1,.75,.65],...
   'EdgeColor','none');
   isonormals(Ds,hiso)
hcap = patch(isocaps(D,5),...
   'FaceColor','interp',...
   'EdgeColor','none');
view(35,30) 
axis tight 
daspect([1,1,.4])
lightangle(45,30);
lighting gouraud
hcap.AmbientStrength = 0.6;
hiso.SpecularColorReflectance = 0;
hiso.SpecularExponent = 50;

score 0 · Accepted Answer · answered Nov 16 '15 at 05:08

we can use fullfile which returns a string containing the full path to the file. and dir which returns a list of files and folders that match the string name. When name is a folder, dir lists the contents of the folder. Specify name using absolute or relative path names. name can include wildcards (*). and rest of the things are well commented in program.

    clear all;
    close all;
    clc;
    fileFolder = fullfile('series 9');
    files = dir ( fullfile (fileFolder, '*.dcm'));
    fileNames = {files.name};

    %examine file header (metadata , from dicom stack)

    info = dicominfo(fullfile(fileFolder,fileNames{1}));

    %extract size info from metadata
    voxel_size = [info.PixelSpacing;info.SliceThickness];

    %read one file to get size
    I = dicomread(fullfile(fileFolder,fileNames{1}));
    classI = class(I);
    sizeI = size(I);
    numImages = length(fileNames);

    %read slice images populate 3d matrix
    hWaitBar = waitbar(0,'reading dicom files');

    %create array
    mri= zeros(sizeI(1),sizeI(2), numImages , classI );
    for i=length(fileNames):-1:1
        fname = fullfile(fileFolder, fileNames{i});
        mri(:,:,i) = uint16(dicomread(fname));
        waitbar((length(fileNames)-i+1)/length(fileNames))
    end

    delete(hWaitBar);

How can I convert Dicom directory (series of dicom images) to 3D volume image?

1 Answers1