1. SLAC Geant4 Tutorial 2009 J. Perl
DICOM and gMocren
Geant4 v9.2p02
Joseph Perl, SLAC
6 November 2009
SLAC Geant4 Tutorial J. Perl

2. SLAC Geant4 Tutorial 2009 J. Perl
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 J. Perl

3. SLAC Geant4 Tutorial 2009 J. Perl
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 J. Perl

4. SLAC Geant4 Tutorial 2009 J. Perl
DICOM Navigation
G4NestedParameterization 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 J. Perl

5. Dealing with Different Slice Thicknesses
Nested 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 J. Perl

6. SLAC Geant4 Tutorial 2009 J. Perl
OCTREE
G4NestedParameterization 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 J. Perl

7. SLAC Geant4 Tutorial 2009 J. Perl
DICOM Example
geant4/examples/extended/medical/DICOM
See the README
6 November 2009
SLAC Geant4 Tutorial J. Perl

8. SLAC Geant4 Tutorial 2009 J. Perl
gMocren
Great 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 but offered freely to all Geant4 users
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 J. Perl

9. gMocren : A Visualization Tool
gMocren and utility software are freely available.
3D (ray casting)
2D (MPR)
Opacity curve and color map editor
Supported system :
- Windows 2k/XP or PC Linux OS
- Pentium 4 or faster
- more than 1 GB (recommend)
free hand or templates with WW&WL editing
Particle trajectories
Calculated dose distribution
Opacity curve and color map editor
Functionality Requirements :
color mapping
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.
contour plot
6 November 2009
SLAC Geant4 Tutorial J. Perl

10. Sample Data available for Download
6 November 2009
SLAC Geant4 Tutorial J. Perl

11. SLAC Geant4 Tutorial 2009 J. Perl
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 J. Perl

12. SLAC Geant4 Tutorial 2009 J. Perl
Live Demo
6 November 2009
SLAC Geant4 Tutorial J. Perl