Computed tomography

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== Introduction ==
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== <span style="color:#000080"> Introduction </span> ==
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This tutorial will based on the DICOM GEANT4 example originally developed by Louis Archambault, Luc Beaulieu and Vincent Hubert-Tremblay. In this example a DICOM file is converted to a simple ASCII file, where the Hounsfield numbers are converted to materials and densities so that it can be used by GEANT4. It also creates a GEANT4 geometry based on the DICOM file information using the '''G4PhantomParameterisation'''.  
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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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== Setting up the environment ==
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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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; Connect to HEP cluster and create folder DICOMFolder in your area
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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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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'''.
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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 used in the tutorial.
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== <span style="color:#000080"> How to run the tutorial </span> ==
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; Connect to the HEP cluster and create folder DICOMFolder in your area
<pre style="color: #800000; background-color: #dcdcdc">
<pre style="color: #800000; background-color: #dcdcdc">
ssh -X username@plus1.hep.ucl.ac.uk  
ssh -X username@plus1.hep.ucl.ac.uk  
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password: type your password here
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username@plus1.hep.ucl.ac.uk's password: type your password here
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cd /home/username/
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[username@plus1 ~]$ mkdir DICOMFolder
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mkdir DICOMFolder
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[username@plus1 ~]$ cd DICOMFolder   
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cd DICOMFolder   
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</pre>
</pre>
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<pre style="color: #800000; background-color: #dcdcdc">
<pre style="color: #800000; background-color: #dcdcdc">
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source /unix/pbt/software/dev/bin/pbt-dev.sh   
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[username@plus1 DICOMFolder]$ source /unix/pbt/software/dev/bin/pbt-dev.sh   
</pre>
</pre>
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== <span style="color:#000080"> How to get the code </span> ==
 
; Copy the code to your working directory and rename it
; Copy the code to your working directory and rename it
<pre style="color: #800000; background-color: #dcdcdc">
<pre style="color: #800000; background-color: #dcdcdc">
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cp -r /unix/pbt/tutorials/basic/DICOM .
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[username@plus1 DICOMFolder]$ cp -r /unix/pbt/tutorials/advanced/DICOM .
    
    
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mv DICOM DICOM_source
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[username@plus1 DICOMFolder]$ mv DICOM DICOM_source
</pre>
</pre>
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== <span style="color:#000080"> How to run the code </span> ==
 
; Inside /home/username/DICOMFolder/ create a directory
; Inside /home/username/DICOMFolder/ create a directory
<pre style="color: #800000; background-color: #dcdcdc">
<pre style="color: #800000; background-color: #dcdcdc">
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mkdir DICOM_build   
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[username@plus1 DICOMFolder]$ mkdir DICOM_build   
</pre>
</pre>
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<pre style="color: #800000; background-color: #dcdcdc">
<pre style="color: #800000; background-color: #dcdcdc">
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cd DICOM_build  
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[username@plus1 DICOMFolder]$ cd DICOM_build  
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cmake -DGeant4_DIR=/unix/pbt/software/dev /home/username/DICOMFolder/DICOM_source  
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[username@plus1 DICOM_build]$ cmake -DGeant4_DIR=/unix/pbt/software/dev /home/username/DICOMFolder/DICOM_source  
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make   
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[username@plus1 DICOM_build]$ make   
</pre>
</pre>
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; Run macro run.mac.
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; Run macro run.mac
<pre style="color: #800000; background-color: #dcdcdc">
<pre style="color: #800000; background-color: #dcdcdc">
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./DICOM run.mac
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[username@plus1 DICOM_build]$ ./DICOM run.mac
</pre>
</pre>
== <span style="color:#000080"> How to analyze data </span> ==
== <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'''
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<pre style="color: #800000; background-color: #dcdcdc">
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[username@plus1 DICOM_build]$ export DICOM_NESTED_PARAM=1
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</pre>
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You can check if it is set correctly by typing in the command line
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<pre style="color: #800000; background-color: #dcdcdc">
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[username@plus1 DICOM_build]$ env
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</pre>
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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>
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* <span style="color:#ff0000"> G4SmartVoxel / G4VoxelNavigation </span>:
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Using smart voxels required a huge amount of memory. At /home/username/DICOMFolder/DICOM_source/src/DicomRegularDetectorConstruction.cc set
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<pre style="color: #800000; background-color: #dcdcdc">
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patient_phys->SetRegularStructureId(0);
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</pre>
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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>
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; Change the type, energy and position of the incident particle
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At /home/username/DICOMFolder/DICOM_source/src/DicomPrimaryGeneratorAction.cc change the following lines:
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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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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>
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=== <span style="color:#000080"> Visualisation </span> ===
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Run the visualisation macro vis.mac
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<pre style="color: #800000; background-color: #dcdcdc">
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[username@plus1 DICOM_build]$ ./DICOM vis.mac
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</pre>
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which will produce .prim file. You can open this file in DAWN
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<pre style="color: #800000; background-color: #dcdcdc">
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[username@plus1 DICOM_build]$ dawn g4_00.prim
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</pre>
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This will create 3D image showing the patient geometry and the incident electron beam. The image is big and it takes time to open:
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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

Retrieved from "https://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/index.php/Computed_tomography"
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