6 November 2009SLAC Geant4 Tutorial 2009 J. Perl1 DICOM and gMocren Geant4 v9.2p02 Joseph Perl, SLAC.

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