Geant4 User's Guide for Application Developers Version: geant4 10.1
6 November 2009SLAC Geant4 Tutorial 2009 J. Perl1 DICOM and gMocren Geant4 v9.2p02 Joseph Perl,...
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Transcript of 6 November 2009SLAC Geant4 Tutorial 2009 J. Perl1 DICOM and gMocren Geant4 v9.2p02 Joseph Perl,...
6 November 2009 SLAC Geant4 Tutorial 2009 J. Perl 1
DICOM and gMocrenGeant4 v9.2p02
Joseph Perl, SLAC
6 November 2009 SLAC Geant4 Tutorial 2009 J. Perl 2
Patient Geometry Patient Geometry presents a challenge for Geant4.
Remember that Geant4 was originally developed for a very different environment:
• HEP: constructive solid geometry
• Med Phys: constructive solid geometry + imported voxel data (DICOM)– different strategies for geometry and navigators
6 November 2009 SLAC Geant4 Tutorial 2009 J. Perl 3
DICOM Issues• Memory
– Improved parameterizations such as G4NestedParameterization bring typical DICOM memory footprints down from 1GB to 25MB
• Speed– Has been slower than EGSnrc by factor of 2 to 10 depending who
you talk to
– Responded with specialized navigators for Voxel geometries• fast navigator work goes back to Paganetti years ago• compressed voxel parameterization examples go back as far as
OCTREE, by Vincent Hubert-Tremblay and Louis Archambault• latest Geant4 releases contain official solution, G4RegularNavigation
• Visualization– gMocren
• from the Japanese effort shown earlier
6 November 2009 SLAC Geant4 Tutorial 2009 J. Perl 4
DICOM NavigationG4NestedParameterization and G4RegularParameterization are both reasonable options for handling large numbers of voxels with reasonable speed and memory
• Bring typical DICOM memory footprints down from 1GB to 25MB
• G4RegularNavigation
– A navigator that takes advantage of regularity of voxel geometries
– See DICOM example for details
– Option to skip boundaries if next voxel is of same material type
• First release did not correctly handle dose sharing when skipping boundaries
• Corrected in most recent beta release
6 November 2009 SLAC Geant4 Tutorial 2009 J. Perl 5
Dealing with Different Slice ThicknessesNested and Regular parameterizations assume all voxels are same shape.
• Workaround for fact that in CT not all slices are same thickness: Build as three separate adjoining main volumes
– One with thick slices
– One with thinner slices
– Another with thick slices
6 November 2009 SLAC Geant4 Tutorial 2009 J. Perl 6
OCTREEG4NestedParameterization and G4RegularParameteization assume all voxels are same shape.
In some cases, this requirements cannot be met
• such as when Brachytherapy seeds are included in the volume
Use other speedup techniques
• such as OCTREE which works by grouping adjoining voxels of same material into larger super-voxels before starting simulation
6 November 2009 SLAC Geant4 Tutorial 2009 J. Perl 7
DICOM Examplegeant4/examples/extended/medical/DICOM
See the README
6 November 2009 SLAC Geant4 Tutorial 2009 J. Perl 8
gMocrenGreat tool available for volume visualization
• From JST/CREST project (Japan) to improve Geant4 for medical physics
• Able to visualize:
– Volume data(including overlay of more than one set)
– Trajectories
– Geometry
• Runs on:
– Windows and Linux
– Mac will likely happen soon
– Based on a commercial package butoffered freely to all Geant4 users
– http://geant4.kek.jp/gMocren
– Installation is straightforward, follow the Download link on the above page
• First run gMocren’s one-click installer
• Then, inside C:\Program Files\gMocren\gtk, you will find the one-click installer for gtk
6 November 2009 SLAC Geant4 Tutorial 2009 J. Perl 9
http://geant4.kek.jp/gMocren/
Calculated dose Calculated dose distributiondistribution
color mapping
contour plot
Particle Particle trajectoriestrajectories
Opacity curve and color Opacity curve and color map editormap editor
free hand or templates with WW&WL editing
Supported system : - Windows 2k/XP or PC Linux OS - Pentium 4 or faster - more than 1 GB (recommend)
Supported system : - Windows 2k/XP or PC Linux OS - Pentium 4 or faster - more than 1 GB (recommend)
3D (ray casting)
2D (MPR)
Opacity curve and color map editor
gMocren and utility software are freely available.
gMocren and utility software are freely available.
Functionality Functionality Requirements Requirements ::
•To visualize- the modality image used by the simulation,- the calculated dose distribution and- the particle trajectories- in an agreeable speed•Transfer function editor•Multi-platform
•To visualize- the modality image used by the simulation,- the calculated dose distribution and- the particle trajectories- in an agreeable speed•Transfer function editor•Multi-platform
Trajectory information in the simulation is available.
gMocren : A Visualization ToolgMocren : A Visualization Tool
6 November 2009 SLAC Geant4 Tutorial 2009 J. Perl 10
Sample Data available for Download
6 November 2009 SLAC Geant4 Tutorial 2009 J. Perl 11
gMocren File Driver• Currently:
– to make gMocren files, you have to capture output “by hand” in your user code and export it as a gMocren file.
– gMocren tutorial explains how to do this
• In Release 9.3:
– ability to create gMocren files will become a standard part of the Geant4 Visualization system.
– /vis/open gMocrenFile
– /vis/scene/add/psHits
– /vis/viewer/flush
– many other options available with /score/draw ... commands
However you generate the gMocren input file,the actual gMocren visualization application is the same.
6 November 2009 SLAC Geant4 Tutorial 2009 J. Perl 12
Live Demo