Mercurial > hg > orthanc-book
comparison Sphinx/source/faq/matlab.rst @ 103:af1e13dac7e6
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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| 102:5ffea09f47a3 | 103:af1e13dac7e6 |
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| 38 imagesc(slice) | 38 imagesc(slice) |
| 39 | 39 |
| 40 # Annotate the graph with the patient name and ID | 40 # Annotate the graph with the patient name and ID |
| 41 tags = loadjson(urlread([ URL '/instances/' instance '/tags?simplify' ])); | 41 tags = loadjson(urlread([ URL '/instances/' instance '/tags?simplify' ])); |
| 42 title([ 'This is a slice from patient ' tags.PatientID ' (' tags.PatientName ')' ]) | 42 title([ 'This is a slice from patient ' tags.PatientID ' (' tags.PatientName ')' ]) |
| 43 | |
| 44 | |
| 45 Opening the raw DICOM file | |
| 46 -------------------------- | |
| 47 | |
| 48 Here is another sample Matlab/Octave script explaining how to download | |
| 49 the raw DICOM file corresponding to one given instance stored in | |
| 50 Orthanc, then decode this DICOM file using Matlab/Octave:: | |
| 51 | |
| 52 SERIES = 'ae164c84-e5bd0366-ba937a6d-65414092-f294d6b6'; | |
| 53 URL = 'http://demo.orthanc-server.com/'; | |
| 54 | |
| 55 # Get information about the instances in this DICOM series | |
| 56 instances = loadjson(urlread([ URL '/series/' SERIES '/instances' ])); | |
| 57 | |
| 58 # Select one slice from the series | |
| 59 instance = instances{1}.ID | |
| 60 | |
| 61 # Download the raw DICOM file and store it as a file named "instance.dcm" | |
| 62 urlwrite([ URL '/instances/' instance '/file' ], 'instance.dcm'); | |
| 63 | |
| 64 if exist('OCTAVE_VERSION', 'builtin') ~= 0 | |
| 65 # If running Octave instead of Matlab, load the "dicom" package from Octave Forge | |
| 66 pkg load image | |
| 67 pkg load dicom | |
| 68 endif | |
| 69 | |
| 70 # Decode the downloaded DICOM file | |
| 71 im = dicomread('instance.dcm'); | |
| 72 imagesc(im) | |
| 73 | |
| 74 .. highlight:: bash | |
| 75 | |
| 76 **Note:** If running Octave, you will have to manually install the | |
| 77 `dicom package from Octave Forge | |
| 78 <https://octave.sourceforge.io/dicom/index.html>`__. Download the | |
| 79 source code of the package, make sure the ``libgdcm2-dev`` and | |
| 80 ``octave-image`` packages are installed (for Ubuntu 16.04), then type | |
| 81 the following command to install the ``dicom`` package:: | |
| 82 | |
| 83 $ octave --no-gui --eval "pkg install ./dicom-0.2.0.tar.gz" |