DICOM and gMocren

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DICOM and gMocren
Geant4 v9.2p02
Joseph Perl, SLAC
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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

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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

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DICOM Navigation

• G4NestedParameterization and G4RegularParameteriza
  tion 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

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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

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OCTREE

• G4NestedParameterization and G4RegularParameteizat
  ion 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

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DICOM Example
geant4/examples/extended/medical/DICOM See the
README
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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 butoffered freely
  to all Geant4 users
• http//geant4.kek.jp/gMocren
• Installation is straightforward, follow the
  Download link on the above page
• First run gMocrens one-click installer
• Then, inside C\Program Files\gMocren\gtk, you
  will find the one-click installer for gtk

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http//geant4.kek.jp/gMocren/
gMocren A Visualization Tool
gMocren and utility software are freely
available.
Opacity curve and color map editor
3D (ray casting)
2D (MPR)
Supported system - Windows 2k/XP or PC Linux
OS - Pentium 4 or faster - more than 1 GB
(recommend)
free hand or templates with WWWL 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
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Sample Data available for Download
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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.

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Live Demo