Computed tomography

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== <span style="color:#000080"> Introduction </span> ==
== <span style="color:#000080"> Introduction </span> ==
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This tutorial is based on the GEANT4 DICOM example originally developed by Louis Archambault, Luc Beaulieu and Vincent Hubert-Tremblay. In this example a list of DICOM files (.dcm) are converted to ASCII files (.g4dcm) and binary (.g4bin) that can be read by GEANT4. Each of these files corresponds to a Z slice. Then, the .g4dcm (.g4bin) files are merged into one unique volume and used by GEANT4 to construct patient geometry and materials.
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This tutorial is based on the GEANT4 DICOM example originally developed by Louis Archambault, Luc Beaulieu and Vincent Hubert-Tremblay. In this example a list of DICOM files (.dcm) are converted to ASCII files (.g4dcm) and binary files (.g4bin) that can be read by GEANT4. Each of these files corresponds to a Z Computed tomography (CT) slice. Then, the .g4dcm (.g4bin) files are merged into one volume.  
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The geometry is constructed by voxelizing the volume. There are four navigation algorithms used to create the voxel geometry: '''G4RegularNavigation''', '''G4VNestedParameterisation''', '''G4SmartVoxel'''/'''G4VoxelNavigation''' and '''G4PVReplica'''.   
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The geometry is constructed by voxelizing this volume. There are four navigation algorithms used to create the voxel geometry: '''G4RegularNavigation''', '''G4VNestedParameterisation''', '''G4SmartVoxel'''/'''G4VoxelNavigation''' and '''G4PVReplica'''.   
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The material is constructed by converting the pixel values (Hounsfield numbers) from the DICOM images to densities using  
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The material for this volume is constructed by converting the pixel values (Hounsfield numbers) from the DICOM images to densities using the [http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DICOM/CT2Density.dat Hounsfield scale]. Then, the densities are converted to material types according to this [http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DICOM/Materials.txt table].
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the [http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DICOM/CT2Density.dat Hounsfield scale]. Then, the densities are converted to material types according to this [http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DICOM/Materials.txt table].
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A simple monenergetic electron beam is simulated using '''G4ParticleGun''' class. The output of the tutorial is a text file with dose deposition in several voxels. The dose is scored using classes '''G4VSensitiveDetector''' and '''G4THitsMap'''.  
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A simple monenergetic electron beam is simulated using '''G4ParticleGun''' class. The output of the tutorial is a text file with dose deposition in several voxels. The dose is scored using classes '''G4MutiFunctionalDetector''', '''G4VPrimitiveScorer''', '''G4PSDoseDeposit3D''' and '''G4THitsMap'''.  
http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DICOM/dicom.png
http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DICOM/dicom.png
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This is one of the DICOM files that is used in the tutorial.
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This is one of the DICOM files used in the tutorial.
== <span style="color:#000080"> How to run the tutorial </span> ==
== <span style="color:#000080"> How to run the tutorial </span> ==
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</pre>
</pre>
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; Before running the code you can chose among several voxelization algorithms. 
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; Run macro run.mac
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* Using <span style="color:#ff0000"> G4RegularNavigation </span>:
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It is a special algorithm to navigate in a regular voxelized geometry. This algorithm skips frontiers between voxels when they have the same material i.e. "replacing group of voxels with a smaller number of larger voxels". '''G4RegularNavigation''' class is the default class for this tutorial. To run with the default settings simply run macro run.mac.
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<pre style="color: #800000; background-color: #dcdcdc">
<pre style="color: #800000; background-color: #dcdcdc">
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</pre>
</pre>
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* Using <span style="color:#ff0000"> G4NestedParameterization </span>:
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== <span style="color:#000080"> How to analyze data </span> ==
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This is a [http://geant4.web.cern.ch/geant4/UserDocumentation/Doxygen/examples_doc/html/ExampleDICOM.html link] to the official DICOM tutorial explanation notes. We recommend to read it before proceeding with this tutorial.
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=== <span style="color:#000080"> Text files </span> ===
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The macro run.mac produces a text file '''dicom.out''' which includes the dose deposition in several voxels.
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=== <span style="color:#000080"> Run with different settings </span> ===
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; Chose among several voxelization algorithms
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* <span style="color:#ff0000"> G4RegularNavigation </span>:
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'''G4RegularNavigation''' class is the default class for this tutorial. This algorithm skips frontiers between voxels when they have the same material i.e. "replacing group of voxels with a smaller number of larger voxels". 
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* <span style="color:#ff0000"> G4NestedParameterization </span>:
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To run with this voxelization algorithm you need to set the variable '''DICOM_NESTED_PARAM'''
<pre style="color: #800000; background-color: #dcdcdc">
<pre style="color: #800000; background-color: #dcdcdc">
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</pre>
</pre>
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You can check if this variable is set correctly by typing in the command line
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You can check if it is set correctly by typing in the command line
<pre style="color: #800000; background-color: #dcdcdc">
<pre style="color: #800000; background-color: #dcdcdc">
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</pre>
</pre>
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Then, run the code:
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Then, compile and run the code:
<pre style="color: #800000; background-color: #dcdcdc">
<pre style="color: #800000; background-color: #dcdcdc">
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[username@plus1 DICOM_build]$ make
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[username@plus1 DICOM_build]$ ./DICOM run.mac
[username@plus1 DICOM_build]$ ./DICOM run.mac
</pre>
</pre>
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* Usinging <span style="color:#ff0000"> G4SmartVoxel / G4VoxelNavigation </span>:
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* <span style="color:#ff0000"> G4SmartVoxel / G4VoxelNavigation </span>:
Using smart voxels required a huge amount of memory. At /home/username/DICOMFolder/DICOM_source/src/DicomRegularDetectorConstruction.cc set
Using smart voxels required a huge amount of memory. At /home/username/DICOMFolder/DICOM_source/src/DicomRegularDetectorConstruction.cc set
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</pre>
</pre>
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== <span style="color:#000080"> How to analyze data </span> ==
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; Change the type, energy and position of the incident particle
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This is a [http://geant4.web.cern.ch/geant4/UserDocumentation/Doxygen/examples_doc/html/ExampleDICOM.html link] to the official DICOM explanation notes. We recommend to read it before proceeding with this tutorial.
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At /home/username/DICOMFolder/DICOM_source/src/DicomPrimaryGeneratorAction.cc change the following lines:
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=== <span style="color:#000080"> Text files </span> ===
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<pre style="color: #800000; background-color: #dcdcdc">
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G4ParticleDefinition* particle = particleTable->FindParticle(particleName="e-");
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The macro run.mac produces a text file which includes the dose deposition in several voxels.
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fParticleGun->SetParticleEnergy(100.*MeV);
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fParticleGun->SetParticlePosition(G4ThreeVector(0.,0.,0.));
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</pre> 
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You can chose among several particles like "gamma", "e+", "alpha" and "He3". Then, compile and run the code
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<pre style="color: #800000; background-color: #dcdcdc">
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[username@plus1 DICOM_build]$ make
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[username@plus1 DICOM_build]$ ./DICOM run.mac
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</pre>
=== <span style="color:#000080"> Visualisation </span> ===
=== <span style="color:#000080"> Visualisation </span> ===
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http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DICOM/g4_03.eps
http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DICOM/g4_03.eps
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== <span style="color:#000080"> Files </span> ==
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[[List of computed tomography files with brief description]]

Latest revision as of 15:40, 2 September 2014

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