GateContrib

(Warning: this is yet a tentative & experimental Gate sub-project. Contributions and suggestions welcome)

Gate, based on Geant4 library, allows to perform various Monte-Carlo simulations in the field of medical physics. Gate can be used in numerous ways and for a lot of different applications. This repository contains Gate simulation examples, mostly provided by users, in order to help sharing knowledge.

Warning - This repository contains data (binary files), stored with git-lfs extension. Find below a step-by-step tutorial to install git-lfs:

1. Download the Git LFS extension for versioning large files
2. Untar, install and set up the Git command line extension
   tar -xzf git-lfs-linux-amd64-2.0.1.tar.gz
cd git-lfs-2.0.1
sudo ./install.sh
   If your installation was succesful, your terminal should display the following message:
   Git LFS initialized
   Note that you only have to set up Git LFS once.

3. Clone the Gate user-oriented repository as usual
   git clone https://github.com/OpenGATE/GateContrib.git
   Note that the git lfs clone https://github.com/OpenGATE/GateContrib.git command operates exactly like git clone and takes all the same arguments, but has one important difference: it's a lot faster! Depending on the number of files you have it can be more than 10x faster in fact.
   The output of the executing commande should be:
   Cloning into 'GateContrib'...
remote: Counting objects: 21076, done.
remote: Compressing objects: 100% (61/61), done.
remote: Total 21076 (delta 36), reused 0 (delta 0), pack-reused 21012
Receiving objects: 100% (21076/21076), 13.96 MiB | 3.76 MiB/s, done.
Resolving deltas: 100% (14211/14211), done.
Checking connectivity... done.
Downloading dosimetry/Radiotherapy/example10/data/phantom.raw (3.25 MB)
Downloading dosimetry/Radiotherapy/example2/data/patient-2mm.raw (3.36 MB)
...
Checking out files: 100% (549/549), done.
   

Warning - This is user-oriented, the provided examples are not tested and may not work. The OpenGate collaboration is not responsible of any contents.

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How to contribute ?

• Prepare your example as a pull-request. Clone this repository in your github account, commit your example in your cloned repository, then ask us to integrate your proposal via the "New pull request" button.
• Your simulation must be in a separate folder. You can put it in the folder imaging or dosimetry or misc.
• Example must contains:
  • a readme.md file that describe the example, the authors, the date and Gate version
  • 3 folders mac/ data/ output/. The first will contains all macros (.mac files), the second all data files needed as input for the simulations. Results should be written in the output/ folder.
  • Simulation should be run by a command such as Gate mac/main.mac
• It is also possible to contribute via analysis tools. If you developed a killer python script or C++ code useful for Gate simulation, feel free to share it here !

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http://www.opengatecollaboration.org

References collaboration papers:

• 2004 http://www.ncbi.nlm.nih.gov/pubmed/15552416
• 2011 http://www.ncbi.nlm.nih.gov/pubmed/21248393
• 2014 http://www.ncbi.nlm.nih.gov/pubmed/24877844