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DICOM and gMocren

Geant4 v9.2p02. DICOM and gMocren. Joseph Perl, SLAC. Patient Geometry . Patient Geometry presents a challenge for Geant4. Remember that Geant4 was originally developed for a very different environment: HEP: constructive solid geometry

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DICOM and gMocren

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

  4. 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 SLAC Geant4 Tutorial 2009 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 SLAC Geant4 Tutorial 2009 J. Perl

  6. 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 SLAC Geant4 Tutorial 2009 J. Perl

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

  8. 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 gMocren’s one-click installer • Then, inside C:\Program Files\gMocren\gtk, you will find the one-click installer for gtk SLAC Geant4 Tutorial 2009 J. Perl

  9. gMocren : A Visualization Tool http://geant4.kek.jp/gMocren/ 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 SLAC Geant4 Tutorial 2009 J. Perl

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

  12. Live Demo SLAC Geant4 Tutorial 2009 J. Perl

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