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0001
0002 # Geant4 DICOM Examples
0003
0004 The DICOM applications were originally developed by the Geant4 users: \n
0005 Louis Archambault,(1)Luc Beaulieu, (2)Vincent Hubert-Tremblay.
0006
0007 - (1) Centre Hospitalier Universitaire de Quebec (CHUQ), \n
0008 Hotel-Dieu de Quebec, departement de Radio-oncologie \n
0009 11 cote du palais. Quebec, QC, Canada, G1R 2J6 \n
0010 tel (418) 525-4444 #6720 \n
0011 fax (418) 691 5268 \n
0012 web : thomson.phy.ulaval.ca/phys_med \n
0013
0014 - (2) Universite Laval, Quebec (QC) Canada
0015
0016 It has since been deeply reviewed by Pedro Arce in December 2007. \n
0017 Very small changes by Stephane Chauvie in January 2008. \n
0018 Stephane Chauvie, Oct 2009: changed Physics list; changes in DICOM read. \n
0019 Stephane Chauvie and Andrea Armando; June 2010 adapted for reading whatever DICOM file \n
0020 Jonathan Madsen, Nov 2013: updated DICOM to utilize multithreading now available in Geant4.10 \n
0021
0022 ## Introduction
0023
0024 This example consists of the following applications:
0025
0026 - DICOM1
0027 - DICOM2
0028
0029 with two libraries that implement capabilities common to both applications:
0030
0031 - G4DicomCore: providing the core Geant4 application structure.
0032 - G4DicomReader: **Optional** utility library to read DICOM files and RT structure in DICOM format, as well as RT plans.
0033 It uses the [DCMTK library](http://dicom.offis.de/dcmtk.php.en), which must be installed if you wish to use this capability.
0034 - Requires DCMTK 3.6.1 or newer, with the `dcmrt` package available.
0035
0036 Both application can optionally use the DICOM Digital Head developed by S. Guatelli (susanna@uow.edu.au) and V. Giacometti.
0037 This digital model is documented in: Giacometti, V., Guatelli, S., Bazalova-Carter, M., Rosenfeld, A.B., Schulte, R.W.,
0038 "Development of a high resolution voxelised head phantom for medical physics applications", (2017) Physica Medica, 33, pp. 182-188.
0039
0040 ## Compiling the libraries and applications
0041
0042 A standard Geant4 example `CMakeLists.txt` is provided, and thus the project may be configured and built using:
0043
0044 ```
0045 $ cmake -DCMAKE_PREFIX_PATH=/path/to/geant4-install -S. -Bbuild
0046 $ cmake --build ./build
0047 ```
0048
0049 Note that this assumes you run `cmake` in the top level `DICOM` directory.
0050
0051 To build the applications and libraries with support for reading DICOM files using DCMTK, run `cmake` as
0052
0053 ```
0054 $ cmake \
0055 -DCMAKE_PREFIX_PATH=/path/to/geant4-install \
0056 -DG4DICOM_USE_DCMTK=ON \
0057 -S. -Bbuild
0058 $ cmake --build ./build
0059 ```
0060
0061 This requires that you have DCMTK v3.6.1 or newer with the `dcmrt` package installed. If CMake has problems
0062 located the install of DCMTK, add its install path to the `CMAKE_PREFIX_PATH` argument, e.g.
0063
0064 ```
0065 $ cmake \
0066 -DCMAKE_PREFIX_PATH="/path/to/geant4-install;/path/to/dcmtk-install" \
0067 -DG4DICOM_USE_DCMTK=ON \
0068 -S. -Bbuild
0069 $ cmake --build ./build
0070 ```
0071
0072 To enable use of the DICOM Digital Head model, run cmake as:
0073
0074 ```
0075 $ cmake \
0076 -DCMAKE_PREFIX_PATH=/path/to/geant4-install \
0077 -DG4DICOM_USE_HEAD=ON \
0078 -S. -Bbuild
0079 $ cmake --build ./build
0080 ```
0081
0082 This requires a working network connection in order to download the model from the Geant4 website.
0083
0084
0085 ## Running the applications
0086
0087 Both applications can have their runtime behaviour configured using a series on environment variables:
0088
0089 - `DICOM_CHANGE_MATERIAL_DENSITY`
0090 - set to the minimum density difference before making a separate material
0091 - e.g. if DenseBone is from > 1.496 to <= 1.654 and `DICOM_CHANGE_MATERIAL_DENSITY=0.079`
0092 then DenseBone would be separated into DenseBone > 1.496 to <= 1.575 and DenseBone > 1.575 to <= 1.654
0093 - `DICOM_PARTIAL_PARAM`
0094 - set to 1 to build the partial build instead of regular or nested construction (see section 9)
0095 - `DICOM_NESTED_PARAM`
0096 - set to 1 to build the nested construction (see section 9; overridden by `DICOM_PARTIAL_PARAM`)
0097 - `DICOM_NTHREADS`
0098 - To set the number of threads (only when Geant4 itself has been built with multithreading capability)
0099 - Needs to be set to the number of desired threads, e.g. `DICOM_NTHREADS=8` (default is 4 threads)
0100 - `DICOM_USE_HEAD`
0101 - 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.,
0102 "Development of a high resolution voxelised head phantom for medical physics applications", (2017) Physica Medica, 33, pp. 182-188.
0103 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.
0104 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.
0105 When using this option,
0106 1) export DICOM_USE_HEAD=1
0107 2) export DICOM_PATH=path/to/DICOM1.1/DICOM_HEAD - to use the full DICOM HEAD project
0108 or
0109 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.
0110 3) THE DICOM_HEAD uses the OLD version of the Metadata files (see point 4a)
0111 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
0112 without using the calibration curve.This happens because the DICOM project has already been segmented and cleaned from artefacts (see publication).
0113
0114 Detailed information on the capabilities of, and how to run, the `DICOM1` and `DICOM2` applications
0115 are available in the [DICOM1 README](DICOM1/README) and [DICOM2 README](DICOM2/README) respectively.
