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THIS DOCUMENTATION IS FOR VERSIONS 1.2.1 AND BELOW. FOR VERSION 2.0 AND UP, SEE https://omega-doc.readthedocs.io/en/latest/. MOST OF THE PET RELATED DOCUMENTATION HERE IS STILL VALID FOR VERSION 2.0 AND UP THOUGH.

Welcome to the OMEGA wiki!

The same documentation can be found in HTML format in the doc-folder and can be viewed in MATLAB documentation under the "Supplemental software" label. You can also manually view it by opening contents.html.

Help contents

Getting started

Basic information on the toolbox. You should read this first.

Installation help

If you are having trouble installing some of the specific features, see this page for more detailed information.

Toolbox overview

This page explains the general workings of the toolbox, i.e. how the toolbox actually works. It also explains some of the technical aspects of the toolbox.

PET Tutorials

This page contains a simple PET tutorial and an advanced example.

CT Tutorials

This page contains tutorial information on the use of CT data.

Function help

This article explains what each variable in the main-files (e.g. gate_main.m) does and also explains what each function in OMEGA actually does. Additional help can be obtained from MATLAB/Octave itself by typing help function_name, e.g. help plotMichelogram.

Extracting GATE scatter, randoms and trues data

This page explains how you can obtain the scatter, randoms and/or trues data from the GATE input.

Useful information

This page contains information that should be useful when starting to use the toolbox. It contains recommendations on choosing the right projector and implementation as well as general tips and things to take into consideration when using OMEGA.

Visualization

This page contains tips and information on how to visualize the reconstructed data.

Using GATE PET data

Contains details on what to take into account when simulating GATE PET data to be used in OMEGA.

Using GATE CT data

Contains details on what to take into account when simulating GATE CT data to be used in OMEGA.

Using TOF data

This page explains how to use and construct TOF data with OMEGA.

Extracting the system matrix

If you want to obtain a system matrix for your PET system, this page explains how that can be achieved. The system matrix is the matrix A in the equation y = Ax, where y are the measurements and x the reconstructed image.

Computing the forward and/or backward projections

This page explains how you can compute the matrix-vector operations y = Ax and x = A^Tz, i.e. forward and backprojections (T is the transpose operator). Any input vectors x and z can be used, while the system matrix A is computed by OMEGA. Contrary to the above system matrix extraction, this can be performed completely matrix free.

Custom detector coordinates and/or list mode reconstruction

This document explains how to perform image reconstruction by using your own input detector coordinates, including detector coordinates obtained from list-mode data.

Using custom gradient-based priors

Here you can find tutorial on how to implement your own gradient-based priors with any or all of the OMEGA MAP-algorithms. Any gradient-based priors implemented in MATLAB/Octave can be input into OMEGA and also computed matrix free.

Using non-cylindrical PET scanners

This short article explains how to use non-cylindrical PET scanners or PET scanners that do not have discrete detectors (e.g. continuous detectors).

Using Inveon PET data

This page explains the contents of the open PET data , how to reconstruct it, and also some recommendations on how to reconstruct it for best results.

Using Inveon CT data

This page explains the contents of the open CT data and how to reconstruct it.

Using Biograph PET data

Here you can find short instructions on how to extract measurement data from the Biograph mCT or Vision list-mode data.

Contributing code to OMEGA

This page explains how you can contribute your own code to OMEGA.

Contact

Contact information.