Gabriele Cosmo
117 lines
5.5 KiB
Markdown
117 lines
5.5 KiB
Markdown
/\page Examples_DICOM Category "medical/DICOM"
|
|
|
|
# Geant4 DICOM Examples
|
|
|
|
The DICOM applications were originally developed by the Geant4 users: \n
|
|
Louis Archambault,(1)Luc Beaulieu, (2)Vincent Hubert-Tremblay.
|
|
|
|
- (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](http://dicom.offis.de/dcmtk.php.en), 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](DICOM1/README) and [DICOM2 README](DICOM2/README) respectively.
|