JordanSilverman: Formatting changes and tweaks of information contained

2017-09-26T09:54:16Z

Formatting changes and tweaks of information contained

SimonJolly: Created page with "== Introduction == This tutorial is based on the GEANT4 DICOM example originally developed by Louis Archambault, Luc Beaulieu and Vincent Hu..."

2017-09-20T13:44:51Z

Created page with "== Introduction == This tutorial is based on the GEANT4 DICOM example originally developed by Louis Archambault, Luc Beaulieu and Vincent Hu..."

New page

== Introduction ==

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.

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'''.

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].

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

This is one of the DICOM files used in the tutorial.

== How to run the tutorial ==

; Connect to the HEP cluster and create folder DICOMFolder in your area

<pre style="color: #800000; background-color: #dcdcdc">
ssh -X username@plus1.hep.ucl.ac.uk

username@plus1.hep.ucl.ac.uk's password: type your password here

[username@plus1 ~]$ mkdir DICOMFolder

[username@plus1 ~]$ cd DICOMFolder
</pre>

; Setup your environment

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DICOMFolder]$ source /unix/pbt/software/dev/bin/pbt-dev.sh
</pre>

; Copy the code to your working directory and rename it

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DICOMFolder]$ cp -r /unix/pbt/tutorials/advanced/DICOM .

[username@plus1 DICOMFolder]$ mv DICOM DICOM_source
</pre>

; Inside /home/username/DICOMFolder/ create a directory

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DICOMFolder]$ mkdir DICOM_build
</pre>

; To compile the code enter this directory and run cmake and make

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DICOMFolder]$ cd DICOM_build

[username@plus1 DICOM_build]$ cmake -DGeant4_DIR=/unix/pbt/software/dev /home/username/DICOMFolder/DICOM_source

[username@plus1 DICOM_build]$ make
</pre>

; Run macro run.mac

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DICOM_build]$ ./DICOM run.mac
</pre>

== How to analyze data ==

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.

=== Text files ===

The macro run.mac produces a text file '''dicom.out''' which includes the dose deposition in several voxels.

=== Run with different settings ===

; Chose among several voxelization algorithms

* G4RegularNavigation :

'''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".

* G4NestedParameterization :

To run with this voxelization algorithm you need to set the variable '''DICOM_NESTED_PARAM'''

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DICOM_build]$ export DICOM_NESTED_PARAM=1
</pre>

You can check if it is set correctly by typing in the command line

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DICOM_build]$ env
</pre>

Then, compile and run the code:

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DICOM_build]$ make

[username@plus1 DICOM_build]$ ./DICOM run.mac
</pre>

* G4SmartVoxel / G4VoxelNavigation :

Using smart voxels required a huge amount of memory. At /home/username/DICOMFolder/DICOM_source/src/DicomRegularDetectorConstruction.cc set

<pre style="color: #800000; background-color: #dcdcdc">
patient_phys->SetRegularStructureId(0);
</pre>

compile and run the code:

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DICOM_build]$ make

[username@plus1 DICOM_build]$ ./DICOM run.mac
</pre>

; Change the type, energy and position of the incident particle

At /home/username/DICOMFolder/DICOM_source/src/DicomPrimaryGeneratorAction.cc change the following lines:

<pre style="color: #800000; background-color: #dcdcdc">
G4ParticleDefinition* particle = particleTable->FindParticle(particleName="e-");

fParticleGun->SetParticleEnergy(100.*MeV);

fParticleGun->SetParticlePosition(G4ThreeVector(0.,0.,0.));
</pre>

You can chose among several particles like "gamma", "e+", "alpha" and "He3". Then, compile and run the code

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DICOM_build]$ make

[username@plus1 DICOM_build]$ ./DICOM run.mac
</pre>

=== Visualisation ===

Run the visualisation macro vis.mac

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DICOM_build]$ ./DICOM vis.mac
</pre>

which will produce .prim file. You can open this file in DAWN

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DICOM_build]$ dawn g4_00.prim
</pre>

This will create 3D image showing the patient geometry and the incident electron beam. The image is big and it takes time to open:

http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DICOM/g4_03.eps

== Files ==

[[List of computed tomography files with brief description]]

Software/Geant4/Tutorials/Advanced/Computed Tomography - Revision history

JordanSilverman: Formatting changes and tweaks of information contained

SimonJolly: Created page with "== Introduction == This tutorial is based on the GEANT4 DICOM example originally developed by Louis Archambault, Luc Beaulieu and Vincent Hu..."