title: Matlab - Fixing white noise on DICOM stack
body: <p>I loaded <a href="https://www.dropbox.com/sh/jy4nr9zm58dfuly/4HR-CWk7qw" rel="nofollow noreferrer">this dicom stack of images</a> following the instructions on <a href="http://www.mathworks.com/videos/medical-imaging-analysis-and-visualization-71066.html" rel="nofollow noreferrer">this tutorial video</a>. </p>
  
  <p>I wrote the following code</p>
  
  <pre><code> clear all; close all; clc; imtool close all; 
  
    %loads the full dicom stack
    fileFolder = fullfile (pwd, 'dicom_test'); %se debe estar al mismo nivel de la carpeta 
    files = dir (fullfile(fileFolder, '*.dcm'));
    fileNames = (files.name);
  
    %%examine file header (metadata, from DICOM stack)
    info = dicominfo (fullfile (fileFolder, fileNames)); %%fileNames{1} or fileName[1] both fail
  
    %extract size info from metadata
    voxel_size = [info.PixelSpacing; info.SliceThickness]';
  
    %read one file to get size
    I = dicomread(fullfile(fileFolder, fileNames));
    classI = class(I);
    sizeI  = size(I);
    numImages = length (fileNames);
  
    %read slice images; populate 3D matrix
    bWaitBar = waitbar (0, 'reading DICOM files');
  
    %create array to store the images
    mri = zeros(sizeI(1), sizeI(2), numImages, classI);
  
    %load the images into the mri array 
    for i=length(fileNames): -1:1
        fname = fullfile(fileFolder, fileNames);
        mri(:,:,i) = uint16(dicomread(fname));
        waitbar((length(fileNames)-i+1)/length(fileNames));
    end
  
  
    delete (bWaitBar);
  
  
    %explore dataset as a montage
    % imtool close all
    minMRI = min(mri(:)); %min is 0 %%variables no usadas
    maxMRI = max(mri(:)); %max is 332 %%variables no usadas
    montage (reshape(uint16(mri),[size(mri,1), size(mri,2), 1, size(mri,3)]));
    set (gca, 'clim', [0,100]); % got this value by call to imcontrast
  </code></pre>
  
  <p>I got this noisy visualization of the stack: </p>
  
  <p><img src="https://i.stack.imgur.com/W0QYq.jpg" alt="enter image description here"></p>
  
  <p>How can I fix it to show proper contrast? </p>