KrisThielemans / STIR-GATE-Connection

Example files on how to run STIR on GATE data

STIR-GATE-Connection

Author: Robert Twyman
Author: Ludovica Brusaferri
Author: Elise Emond
Author: Francesca Leek
Author: Vesna Cuplov
Author: Kris Thielemans
Copyright (C) 2014-2020 University College London
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0.txt
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

About

The purpose of this project is to provide a simple method to:

• create a GATE compatible voxelised phantom from a STIR parameter files or interfiles using STIR functionality,
• setup and run GATE in cluster array jobs,
• combine and unlist root files into STIR compatible sinograms for reconstruction, and
• compute normalisation factors, scatter correction, and random correction from the measured GATE data using STIR.

See STIR-GATE-Connection/VoxelisedSimulation/README.md for a Tutorial.

New to STIR? Checkout the website (http://stir.sourceforge.net/) and github (https://github.com/UCL/STIR). New to GATE? Checkout their website (http://www.opengatecollaboration.org/) and their incredibly useful UsersGuide (https://opengate.readthedocs.io/en/latest/index.html).

Requirements

This project is reliant on: ROOT, current STIR master branch (https://github.com/UCL/STIR/tree/master) installed with ROOT support, and GATE version 9.0. GATE has dependancy on Geant4 and ROOT. Both STIR install bin and GATE bin must be in your PATH.

STIR-GATE-Connection requires the SGCPATH enviromental variable to be set to this primary directory (containing this README file). Many scripts use this variable when executing sub-scripts.

The project is designed to be run on Linux or Unix (MacOS does normally work) using Shell/Bash/Zsh. Furthermore, the project uses programs, such as sed and awk, for various manipulations.

Directories

• ExamplesOfScannersMacros/: Contains examples of macros for creating a scanner in GATE.
• ExamplesOfPhantomMacros/: Contains examples of macros and STIR parameter files for creating/importing source and attenuation phantoms.
• VoxelisedSimulation/: Main GATE simulation directory.
• ExampleReconstruction/: Contains example scripts for iterative reconstruction using STIR, e.g. OSEM.
• DataCorrectionsComputation/: Contains scripts to compute the data corrections for iterative image reconstruction, including: normalisation and attentuation correction coefficients, plus randoms and scattered estimations of the measured data.

Files

• this_SGC.sh: This script sets the SGCPATH enviromental variable. It also adds SGCPATH to PATH. Additional enviromental variables are added for the major project directories. See script for more details.

Acknowledgements

Additional help with testing an early stage of the macros:

• Catherine Scott (UCL/UCLH)
• Ana Margarida Motta (Universidade de Lisboa)