Computed tomography - Revision history

IlinaMediaWiki at 15:40, 2 September 2014

2014-09-02T15:40:36Z

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	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

-	This is one of the DICOM files ~~that is~~ used in the tutorial.	+	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> ==

IlinaMediaWiki at 13:48, 2 September 2014

2014-09-02T13:48:22Z

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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
		+
		+	== <span style="color:#000080"> Files </span> ==
		+
		+	[[List of computed tomography files with brief description]]

IlinaMediaWiki at 16:07, 1 September 2014

2014-09-01T16:07:04Z

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	== <span style="color:#000080"> How to analyze data </span> ==		== <span style="color:#000080"> How to analyze data </span> ==

-	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.	+	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.

	=== <span style="color:#000080"> Text files </span> ===		=== <span style="color:#000080"> Text files </span> ===

IlinaMediaWiki at 12:17, 1 September 2014

2014-09-01T12:17:24Z

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	== <span style="color:#000080"> Introduction </span> ==		== <span style="color:#000080"> Introduction </span> ==

-	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~~.	+	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 ~~the~~ volume. There are four navigation algorithms used to create the voxel geometry: '''G4RegularNavigation''', '''G4VNestedParameterisation''', '''G4SmartVoxel'''/'''G4VoxelNavigation''' and '''G4PVReplica'''.	+	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 is constructed by converting the pixel values (Hounsfield numbers) from the DICOM images to densities using	+	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].
-	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'''.		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'''.

IlinaMediaWiki at 10:35, 1 September 2014

2014-09-01T10:35:44Z

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	</pre>		</pre>

-	; ~~Before running the code you can chose among several voxelization algorithms.~~	+	; Run macro run.mac
-		+
-	* Using <span style="color:#ff0000"> G4RegularNavigation </span>:	+
-		+
-	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.	+

	<pre style="color: #800000; background-color: #dcdcdc">		<pre style="color: #800000; background-color: #dcdcdc">
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	</pre>		</pre>

-	* ~~Using~~ <span style="color:#ff0000"> G4NestedParameterization </span>:	+	== <span style="color:#000080"> How to analyze data </span> ==
		+
		+	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.
		+
		+	=== <span style="color:#000080"> Text files </span> ===
		+
		+	The macro run.mac produces a text file '''dicom.out''' which includes the dose deposition in several voxels.
		+
		+	=== <span style="color:#000080"> Run with different settings </span> ===
		+
		+	; Chose among several voxelization algorithms
		+
		+	* <span style="color:#ff0000"> G4RegularNavigation </span>:
		+
		+	'''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".
		+
		+	* <span style="color:#ff0000"> G4NestedParameterization </span>:
		+
		+	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>

-	You can check if ~~this variable~~ is set correctly by typing in the command line	+	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>

-	Then, run the code:	+	Then, compile and run the code:

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

-	* ~~Usinging~~ <span style="color:#ff0000"> G4SmartVoxel / G4VoxelNavigation </span>:	+	* <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>

-	~~== <span style="color:#000080"> How to analyze data </span> ==~~	+	; Change the type, energy and position of the incident particle

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

-	~~===~~ <~~span~~ style="color:#~~000080~~"> ~~Text files </span~~> ===	+	<pre style="color: #800000; background-color: #dcdcdc">
		+	G4ParticleDefinition* particle = particleTable->FindParticle(particleName="e-");

-	~~The macro run~~.~~mac produces a text file which includes the dose deposition in~~ several ~~voxels~~.	+	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>

	=== <span style="color:#000080"> Visualisation </span> ===		=== <span style="color:#000080"> Visualisation </span> ===

IlinaMediaWiki at 09:53, 1 September 2014

2014-09-01T09:53:08Z

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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].		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''' and '''G4THitsMap'''.	+	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

IlinaMediaWiki at 09:39, 1 September 2014

2014-09-01T09:39:37Z

← Older revision		Revision as of 09:39, 1 September 2014
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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].		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 '''~~G4VSensitiveDetector~~''' and '''G4THitsMap'''.	+	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''' 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

IlinaMediaWiki at 09:20, 1 September 2014

2014-09-01T09:20:35Z

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	</pre>		</pre>

-	You can check if ~~you set~~ this ~~environment~~ variable correctly by typing in the command line	+	You can check if this variable is set correctly by typing in the command line

	<pre style="color: #800000; background-color: #dcdcdc">		<pre style="color: #800000; background-color: #dcdcdc">

IlinaMediaWiki at 09:19, 1 September 2014

2014-09-01T09:19:12Z

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	* Using <span style="color:#ff0000"> G4RegularNavigation </span>:		* Using <span style="color:#ff0000"> G4RegularNavigation </span>:

-	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 ~~setup~~ for this tutorial. To run with the default settings simply run macro run.mac.	+	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.

	<pre style="color: #800000; background-color: #dcdcdc">		<pre style="color: #800000; background-color: #dcdcdc">

IlinaMediaWiki at 09:17, 1 September 2014

2014-09-01T09:17:01Z

← Older revision		Revision as of 09:17, 1 September 2014
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	* Using <span style="color:#ff0000"> G4RegularNavigation </span>:		* Using <span style="color:#ff0000"> G4RegularNavigation </span>:

-	It is a special algorithm to navigate in a regular voxelized geometry. This algorithm ~~skip~~ 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 setup for this tutorial. To run with the default settings simply run macro run.mac.	+	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 setup for this tutorial. To run with the default settings simply run macro run.mac.

	<pre style="color: #800000; background-color: #dcdcdc">		<pre style="color: #800000; background-color: #dcdcdc">