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raw dicom in matlab
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 13 Jun 2017 20:35:14 +0200
parents 5ffea09f47a3
children 86e92d0cc53e
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1 Interfacing with Matlab and Octave
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2 ==================================
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3
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4 Thanks to the REST API of Orthanc, it is easy to access DICOM images
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5 from Matlab or Octave, as depicted in the following sample image:
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6
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7 .. image:: ../images/Matlab.png
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8 :align: center
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9 :width: 470px
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10
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11 Both Matlab and Octave have access to HTTP servers thanks to their
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12 built-in `urlread() function
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13 <http://nl.mathworks.com/help/matlab/ref/urlread.html>`__. Once must
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14 simply install a Matlab/Octave library to decode JSON files. The
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15 `JSONLab toolkit <https://github.com/fangq/jsonlab>`__ works perfectly
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16 to this end.
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17
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18 .. highlight:: matlab
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19
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20 Using JSONlab, the following code will download and display a DICOM image::
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21
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22 SERIES = 'ae164c84-e5bd0366-ba937a6d-65414092-f294d6b6';
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23 URL = 'http://demo.orthanc-server.com/';
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24
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25 # Get information about the instances in this DICOM series
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26 instances = loadjson(urlread([ URL '/series/' SERIES '/instances' ]));
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28 # Select one slice from the series
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29 instance = instances{1}.ID
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30
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31 # Decode the slice with Orthanc thanks to the "/matlab" URI
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32 slice = eval(urlread([ URL '/instances/' instance '/matlab' ]));
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33
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34 # Compute the maximum value in this slice
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35 max(max(slice))
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36
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37 # Display the slice
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38 imagesc(slice)
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39
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40 # Annotate the graph with the patient name and ID
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41 tags = loadjson(urlread([ URL '/instances/' instance '/tags?simplify' ]));
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42 title([ 'This is a slice from patient ' tags.PatientID ' (' tags.PatientName ')' ])
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44
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45 Opening the raw DICOM file
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46 --------------------------
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47
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48 Here is another sample Matlab/Octave script explaining how to download
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49 the raw DICOM file corresponding to one given instance stored in
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50 Orthanc, then decode this DICOM file using Matlab/Octave::
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51
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52 SERIES = 'ae164c84-e5bd0366-ba937a6d-65414092-f294d6b6';
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53 URL = 'http://demo.orthanc-server.com/';
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54
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55 # Get information about the instances in this DICOM series
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56 instances = loadjson(urlread([ URL '/series/' SERIES '/instances' ]));
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57
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58 # Select one slice from the series
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59 instance = instances{1}.ID
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60
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61 # Download the raw DICOM file and store it as a file named "instance.dcm"
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62 urlwrite([ URL '/instances/' instance '/file' ], 'instance.dcm');
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63
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64 if exist('OCTAVE_VERSION', 'builtin') ~= 0
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65 # If running Octave instead of Matlab, load the "dicom" package from Octave Forge
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66 pkg load image
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67 pkg load dicom
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68 endif
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69
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70 # Decode the downloaded DICOM file
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71 im = dicomread('instance.dcm');
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72 imagesc(im)
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74 .. highlight:: bash
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75
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76 **Note:** If running Octave, you will have to manually install the
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77 `dicom package from Octave Forge
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78 <https://octave.sourceforge.io/dicom/index.html>`__. Download the
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79 source code of the package, make sure the ``libgdcm2-dev`` and
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80 ``octave-image`` packages are installed (for Ubuntu 16.04), then type
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81 the following command to install the ``dicom`` package::
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82
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83 $ octave --no-gui --eval "pkg install ./dicom-0.2.0.tar.gz"