I'm trying to covert 2d DICOM MRI images to 3D using Matlab. I am able to get the images to the 3D space but it shows up flat in the z-axis.

This is my code so far below

%% SPECIFY DIRECTORY

clear all

close all

fileFolder = fullfile('/Users/anugrahsajan/Documents/capstone/matlab/digest_article');

files = dir(fullfile(fileFolder, '*.dcm'));

fileNames = {files.name};

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%% EXAMINE FILE HEADER

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

voxel_size = {info.PixelSpacing; info.SliceThickness};

numImages = length(fileNames);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%% READ SLICE IMAGES AND POLULATE 3D MATRIX

hWaitBar = waitbar(0,'Reading Dicom Images');

% Preallocate the 256-by-256-by-1-by-20 image array.

mri = repmat(int16(0), [256 256 20]);

L = repmat(int16(0), [256 256 20]);

mrinew = repmat(int16(0), [256 256 20]);

% Read the series of images.

for i=1:20

if i > 9

fname = sprintf('/Users/anugrahsajan/Documents/capstone/Lab1 - BrainMRI1/brain_0%01d.dcm',i);

mri(:,:,i) = uint16(dicomread(fname));

else

fname = sprintf('/Users/anugrahsajan/Documents/capstone/Lab1 - BrainMRI1/brain_00%1d.dcm',i);

mri(:,:,i) = uint16(dicomread(fname));

end

waitbar(i/numImages)

end

delete(hWaitBar)

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%% SEGMENT OUT THE REGION OF INTEREST (BRAIN)

% This section will take the mri images in the variable mri and try to segment out the

% skull and brain by running the images through regprop function

hWaitBar = waitbar(0,'Segmenting Dicom Images');

for i = 1:numImages

L(:,:,i)=regprop(mri(:,:,i));

mrinew(:,:,i) = mri(:,:,i).*L(:,:,i);

waitbar(i/numImages)

end

delete(hWaitBar)

montage(mrinew,'DisplayRange',[])

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%% View one specific MRI image in the motage

% This section will take one image from the MRI images so I can analyze it

% further in the later code through imtool

im = mrinew(:,:,10);

max_level = double(max(im(:)));

imt = imtool(im,[0,max_level]);

% close the image tool

imtool close all

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%% Threshold based on intensities and row/columns

%isolate brain mass based on the intensities found in the imtool

lb = 370; % set up lower bound value

ub = 580; % set up upper bound value

mriadjust = mrinew; % create a copy of the dataset

mriadjust(mriadjust <= lb) = 0; % segment out pixels w/ intensities lower than ub

mriadjust(mriadjust >= ub) = 0; % segment out pixels w/ intensities greater than lb

%mriadjust(1:70,:,:)= 0; % segment out pixels that are not in the rows 1-70

bw = logical(mriadjust); %binary conversion

figure

imshow(bw(:,:,10));

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%% Morphological opening

% this section gets rid of the reminder of small islands and objects

% remaining

nhood = ones([7 7 3]);

bw = imopen(bw,nhood);

figure

imshow(bw(:,:,10))

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%% ISOLATE THE LARGEST REGION

% Use the regionprops MATLAB function to identify and isolate the largest

% remaining object in the image which should be the brain

L = bwlabeln(bw); %label the objects in the image

stats = regionprops(L,'Area','Perimeter'); %use the regionprops function to gather info on the objects

A = [stats.Area]; % copy the area informaton about the objects to the variable A

biggest = find(A == max(A)); % find the object with the largest area in the image

mriadjust(L ~= biggest) = 0; % any object that is not the largest object gets removed

imA = imadjust(mriadjust(:,:,10));

figure

imshow(imA);

bw = int16(bw); % covert the logical values to int values

for i=1:20

mrinew(:,:,i) = mrinew(:,:,i).*bw(:,:,i); % multiply the mrinew by the mask bw to get segmented image of the brain

end

montage(mrinew,'DisplayRange',[])

%% Export to 3D

M = isosurface(bw,1/2);

tr=triangulation(M.faces,M.vertices);

figure('color','w'), h=trimesh(tr); axis equal

% now write to STL

stlwrite(tr, 'spinalSegmentation.stl');

Regprop function

function [tumor] = regprop(img)

%This code will take the DICOM images fed into it through the variable 'y'

%and then segment out the region of interest.

bw = (img > 0.7*255); %thresholded to remove background and white/gray matter

lbl = bwlabel(bw); %labelled regions

props = regionprops(lbl, 'Solidity', 'Area');

% solidity is the percentage "filled" of an area. For the skull,

%the solidity will be really low.

solidity = [props.Solidity];

area = [ props.Area];

hiSolid= solidity > 0.2; %get only high solidity objects

maxArea = max( area(hiSolid));

tumorLabel = find( area==maxArea); %label of tumor

tumor = ismember(lbl, tumorLabel); %b/w image of tumor

%imshow(tumor); %this isolates tumor

end

This is the dataset I am working with.

This how the dataset looks at the end of the program. I know I can segment it a little bit better but my main problem now is that it looks really flat in the 3D space.

On volumeViewer I can play around with the X-axis values but it starts to look really pixelated and stretched out.

Is there anything I can do to make sure that the 3D diagram does not come out flat or really pixelated/stretched when I vew it in volumeSegmenter?

[Simon Chan]

What are the PixelSpacing and SliceThickness of the images? Suspect the slice thickness is much greater than the pixel size in xy plane.

[Anurah Sajan]

Do you know as to how I could acquire that information? Would it be through dicominfo? I don't know how I can find the pixel spacing and slice thickness just for the xy plane. Howerever, when I ran dicominfo through the dataset it said the pixel spacing is [0.859375;0.859375] and the slice thickness is 5 for all the images. All the images are in DICOM format.

[yanqi liu]

yes，sir，can you zip your folder “digest_article” and upload it，so we can analysis it

[Anurah Sajan]

Lab1-BrainMRI1 is the dataset I am currently using. The digest article is just another folder to be honest.