CancerRisk extension

Repository for code related to Cancer Risk project

Authors:

• Isaac Meyer
• Alejandro Bertolet
• Harald Paganetti

SEER data

This extension uses statistics from SEER (Surveillance, Epidemiology and End Results) Program to estimate risks in relation to each organ. This information is included in cvs files that are provided with this extension. All these files need to be included in the same directory, and its full path needs to be specified in the parameter file as follows:

• s:Sc/CancerRisk/DataDirectory = "/Users/.../SEERData/"

How to use it

To include the cancer risk prediction as an outcome of the calculation, please include "CancerRisk" within the options in the parameter sv:Sc/OAR/OutcomeModelName (OAR represents the name of each organ at risk for which outcome is desired). This process needs to be done for each OAR to be considered. Dose-volume histogram needs to be calculated for each OAR of interest. For each OAR, it is possible to specify the parameter set used for outcome (BEIR or Schneider). It is assumed by default the Schneider set. To change to BEIR, it is optional to use the following parameter for each OAR:

• s:Sc/OAR/CancerRisk/ParameterSet = "BEIR" (otherwise Schneider set will be used).

The name of the OAR needs to be specified: s:Sc/OAR/OrganName. This is used to seek for the specific SEER parameters for that organs. The available data include: "brain", "breast", "colonrectum", "esophagus", "kidneys", "laryinx", "liver", "lung", "lungbronchus", "pancreas", "pharynx", "prostateovary", "stomach", "testesuterus", "thyroid", "urinarybladder". Plase make sure that you use one of these exact strings.

The rest of parameters, however, need to be specified only once. It is optional to specify the following parameters:

• s:Sc/CancerRisk/CancerModel = "carcinoma" or "sarcoma". If not specified, it will use models for carcinoma.
• s:Sc/CancerRisk/PatientName. If not specified, it will use "Patient1". This is used to produce output files.

It is mandatory to specify the following parameters:

• s:Sc/CancerRisk/Sex = "male" or "female".
• i:Sc/CancerRisk/AttainedAge = attained age of the patient.
• i:Sc/CancerRisk/AgeAtExposure = age at which patient received radiation.
• i:Sc/CancerRisk/NumberOfFractions = number of fractions for the treatment.

MRCP Phantoms and scoring

If instead of calculating on a patient, a MRCP tetrahedron-based phantom is preferred, this can be loaded using the classes in the module "MRCP". Phantoms need to be defined as geometry components in the parameter file (Type="TsMRCP"), and the directory where the files .node, .ele and .material provided by IRCP are located needs to be specified (see example "15F_SOBP_Liver.txt"). A specific class of scorer is needed for MRCP phantoms by specifying (Quantity="TsMRCPScorer"). By default, dose to water is computed, but other material can be used to calculate the dose by using the parameter Material. For each organ involved it is necessary to add a new scorer, specifying the list parameter Organ=1 "Name", where Name should be one (or more) of the materials listed in the .material file of the MRCP phantom, e.g., "Liver" or "Stomach_contents". This will restrict the dose considered only to the organ(s) of interest.

Installation and Examples

Installing TOPAS with extension

1. Clone OpenTOPAS repo v4.0.0
   git clone -b v4.0.0 https://github.com/OpenTOPAS/OpenTOPAS
2. Clone the cancerrisk extension
   git clone --recurse-submodules https://github.com/OpenTOPAS/OpenTOPAS-CancerRisk
3. Install Geant4v11.1.2 following https://opentopas.github.io/installation.html
4. Build TOPAS with cmake, possible build script below (change directories as appropriate)

#!/bin/bash

FLAVOR="CancerRisk"
BUILDDIR="build_$FLAVOR"
rm -rf $BUILDDIR
mkdir $BUILDDIR
cd $BUILDDIR

export Geant4_DIR=/Applications/geant4-v11.1.2-install
cmake -DTOPAS_TYPE=public \
      -DTOPAS_EXTENSIONS_DIR="../../OpenTOPAS-CancerRisk" \
      -DCMAKE_INSTALL_PREFIX="../topas-install-$FLAVOR" \
      ../
make -j12 install 

Running example example/AF_SOBP_Liver

1. Check that the environment variable $TOPAS_G4_DATA is appropriately set
2. Set appropriate path to ICRP 145 phantom data for parameter Ge/MeshPhantom/PhantomDirector

Installing python wrapper

The python wrapper requires generating a TOPAS shared library.

1. Add the following to OpenTOPAS/extensions/CMakeLists.txt.in:

   add_library( extensions_shared SHARED
   TsExtensionManager.cc
   TsExtensionManager.hh
   )
   target_link_libraries(extensions_shared
       main
       parameter
       chemistry
       geometry
       extensions
       graphics
       material
       physics
       variance
       filtering
       scoring
       outcome
       io
       sequence
       primary
       gdcmMSFF 
       ${Geant4_LIBRARIES}
   )
   

2. Set the environment variable $TOPAS_CANCER_RISK_BUILD_DIR
3. The python module can be installed by running pip install -e . in the TOPAS-CancerRisk/python folder
4. The DVH processing example in TOPAS-CancerRisk/python/examples/ can be run after running TOPAS on the example/AF_SOBP_Liver example

Issues

Please use the issues tab on github to report problems or request features