├── .gitattributes ├── .gitignore ├── .zenodo.json ├── DataCorrectionsComputation ├── ComputePoissonDataCorrections.sh ├── EstimateGATESTIRNorm.sh ├── EstimateRandomsFromDelayed.sh ├── README.md └── forward_projector_proj_matrix_ray_tracing.par ├── ExamplePhantoms ├── GATEMacros │ ├── AttenuationCylindrical.mac │ ├── AttenuationSpherical.mac │ ├── SourceCylindrical.mac │ ├── SourcePoint.mac │ ├── SourceSpherical.mac │ ├── VoxelisedAttenuation.mac │ └── VoxelisedSource.mac ├── README.md └── STIRparFiles │ ├── D690FOVCylinder.par │ ├── EmptyAttenuation.par │ ├── SourceSingleCentralVoxel.par │ ├── ThreePointActivity.par │ ├── generate_atten_cylinder.par │ └── generate_uniform_cylinder.par ├── ExampleReconstruction ├── ExampleReconstruction.sh ├── OSEM.par └── README.md ├── ExampleScanners ├── D690 │ ├── STIRScanner_D690_0_segment.hs │ ├── STIRScanner_D690_full_segment.hs │ ├── digitiser_D690.mac │ ├── geometry_D690.mac │ └── root_header_template.hroot ├── README.md └── mMR │ ├── STIR_scanner.hs │ ├── digitiser_mMR.mac │ ├── geometry_mMR.mac │ └── root_header_template.hroot ├── LICENSE.md ├── README.md ├── VoxelisedSimulation ├── CheckGeometry.mac ├── CheckGeometry.sh ├── DebuggingScripts │ ├── DebugUnlistRoot.sh │ └── README.md ├── ExampleSTIR-GATE.sh ├── GATESubMacros │ ├── AttenuationConv.dat │ ├── GATEOutput.mac │ ├── GateMaterials.db │ ├── PhantomActivity.mac │ ├── PhantomAttenuation.mac │ ├── README.md │ ├── SetupDmap.mac │ ├── cuts.mac │ ├── physics.mac │ └── visualisation.mac ├── JobGATESimulationCS.sh ├── JobGATESimulationMyriad.sh ├── MainGATE.mac ├── README.md ├── RunGATE.sh ├── SetupSimulation.sh ├── SubScripts │ ├── CombineSourceMaps.sh │ ├── CreateXCATImages │ │ ├── CreateXCATImage.sh │ │ ├── README.md │ │ ├── create_XCAT.par │ │ └── input_image_atn_1.hv │ ├── GenerateSTIRGATEImages.sh │ ├── GetAttenuationTranslation.sh │ ├── GetSourcePosition.sh │ ├── PrepareScannerFiles.sh │ ├── README.md │ ├── STIR2GATE_interfile.sh │ ├── SumData.sh │ └── 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