(1) Centre Hospitalier Universitaire de Quebec (CHUQ), \n Hotel-Dieu de Quebec, departement de Radio-oncologie \n 11 cote du palais. Quebec, QC, Canada, G1R 2J6 \n tel (418) 525-4444 #6720 \n fax (418) 691 5268 \n web : thomson.phy.ulaval.ca/phys_med \n
(2) Universite Laval, Quebec (QC) Canada

It has since been deeply reviewed by Pedro Arce in December 2007. \n Very small changes by Stephane Chauvie in January 2008. \n Stephane Chauvie, Oct 2009: changed Physics list; changes in DICOM read. \n Stephane Chauvie and Andrea Armando; June 2010 adapted for reading whatever DICOM file \n Jonathan Madsen, Nov 2013: updated DICOM to utilize multithreading now available in Geant4.10 \n

Introduction

This example consists of the following applications:

\ref ExampleDICOM1
\ref ExampleDICOM2

with two libraries that implement capabilities common to both applications:

G4DicomCore: providing the core Geant4 application structure.
G4DicomReader: Optional utility library to read DICOM files and RT structure in DICOM format, as well as RT plans. It uses the DCMTK library, which must be installed if you wish to use this capability.
- Requires DCMTK 3.6.1 or newer, with the dcmrt package available.

Both application can optionally use the DICOM Digital Head developed by S. Guatelli (susanna@uow.edu.au) and V. Giacometti. This digital model is documented in: Giacometti, V., Guatelli, S., Bazalova-Carter, M., Rosenfeld, A.B., Schulte, R.W., "Development of a high resolution voxelised head phantom for medical physics applications", (2017) Physica Medica, 33, pp. 182-188.

Compiling the libraries and applications

A standard Geant4 example CMakeLists.txt is provided, and thus the project may be configured and built using:

$ cmake -DCMAKE_PREFIX_PATH=/path/to/geant4-install -S. -Bbuild
$ cmake --build ./build

Note that this assumes you run cmake in the top level DICOM directory.

To build the applications and libraries with support for reading DICOM files using DCMTK, run cmake as

$ cmake \
  -DCMAKE_PREFIX_PATH=/path/to/geant4-install \
  -DG4DICOM_USE_DCMTK=ON \
  -S. -Bbuild 
$ cmake --build ./build

This requires that you have DCMTK v3.6.1 or newer with the dcmrt package installed. If CMake has problems located the install of DCMTK, add its install path to the CMAKE_PREFIX_PATH argument, e.g.

$ cmake \
  -DCMAKE_PREFIX_PATH="/path/to/geant4-install;/path/to/dcmtk-install" \
  -DG4DICOM_USE_DCMTK=ON \
  -S. -Bbuild 
$ cmake --build ./build

To enable use of the DICOM Digital Head model, run cmake as:

$ cmake \
  -DCMAKE_PREFIX_PATH=/path/to/geant4-install \
  -DG4DICOM_USE_HEAD=ON \
  -S. -Bbuild 
$ cmake --build ./build

This requires a working network connection in order to download the model from the Geant4 website.

Running the applications

Both applications can have their runtime behaviour configured using a series on environment variables:

DICOM_CHANGE_MATERIAL_DENSITY
- set to the minimum density difference before making a separate material
- e.g. if DenseBone is from > 1.496 to <= 1.654 and DICOM_CHANGE_MATERIAL_DENSITY=0.079 then DenseBone would be separated into DenseBone > 1.496 to <= 1.575 and DenseBone > 1.575 to <= 1.654
DICOM_PARTIAL_PARAM
- set to 1 to build the partial build instead of regular or nested construction (see section 9)
DICOM_NESTED_PARAM
- set to 1 to build the nested construction (see section 9; overridden by DICOM_PARTIAL_PARAM)
DICOM_NTHREADS
- To set the number of threads (only when Geant4 itself has been built with multithreading capability)
- Needs to be set to the number of desired threads, e.g. DICOM_NTHREADS=8 (default is 4 threads)
DICOM_USE_HEAD
- set to 1 (export DICOM_USE_HEAD=1) to use the digital head phantom documented in Giacometti, V., Guatelli, S., Bazalova-Carter, M., Rosenfeld, A.B., Schulte, R.W., "Development of a high resolution voxelised head phantom for medical physics applications", (2017) Physica Medica, 33, pp. 182-188. To use this option, the DICOM library needs to be downloaded. This is distributed with the other Geant4 data files on the Geant4 Download site. For convenience of use, it is suggested to have the DICOM library directory in the DICOM Geant4 extended example or in the directory containing the DICOM executable. When using this option,
  1. export DICOM_USE_HEAD=1
  2. export DICOM_PATH=path/to/DICOM1.1/DICOM_HEAD - to use the full DICOM HEAD project or export DICOM_PATH=path/to/DICOM1.1/DICOM_HEAD_TEST - to use 4 DICOM files of the DICOM HEAD project. This option is useful for testing purposes.
  3. THE DICOM_HEAD uses the OLD version of the Metadata files (see point 4a) Note 1: The Conversion of Hounsfield numbers to materials (point 5) is not used. The material is associated to the voxel in the Detector Construction without using the calibration curve.This happens because the DICOM project has already been segmented and cleaned from artefacts (see publication).

Detailed information on the capabilities of, and how to run, the DICOM1 and DICOM2 applications are available in the DICOM1 README and DICOM2 README respectively.