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Division of Nuclear Medicine SimSET- |
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You have successfully installed the SimSET package, and read the overview chapter. You now want to start simulating. Unfortunately, using SimSET is somewhat more complex than editing a word-processing document or programming in PERL! You will need to read most of this user guide before you can start getting meaningful results. This section outlines the steps you need to take to get a simulation going.
A note about Parameter Files
All the modules used in SimSET are configurable by the user, and configuration is achieved by editing ascii text files called parameter files. There is a parameter file for each module. Parameter files consist of entries in the following format:
DATA_TYPE parameter_name = value For example,
BOOL simulate_SPECT = TRUE Where possible, parameter names have been chosen to reveal something meaningful about the parameter, and example parameter files and step-by-step instructions on how to chose appropriate parameter values are included in each chapter.
Basically, there are two steps to this process:
This involves further editing of the PHG run-time parameters file. Since the object geometry has already been specified, there remain three parameter categories to be dealt with:
Full instructions on setting up each parameter are given in the Photon History Generator chapter. Note that it is not necessary to simulate either collimators or detectors - for a simple simulation of the flux through the target cylinder, all that remains to be done is to configure the binning module. However, if you do want to simulate either collimators and/or detectors, their respective parameter files must also be configured (and specified in the PHG run-time parameters file).
The first task is to choose an appropriate collimator model from the following:
Simple PET
Monte Carlo PET
UNC SPECT
Monte Carlo slat collimators (for dual-head coincidence imaging, DHCI)The Simple PET option just uses perfectly absorbing end-plates. It is very easy to configure, and is often a good choice for PVI (3D PET). For 2D PET, the Monte Carlo option is needed. This is based on Chris Thompson's PETSIM model - it is very flexible in terms of septa geometry, but is commensurately more complex to configure. For SPECT, collimators are modelled using software predominantly developed at UNC (by the Tsui/Frey group then at the University of North Carolina, now at Johns Hopkins). Parallel, fan-beam or cone-beam collimators can be selected. A quite flexible Monte Carlo slat collimator module is provided for DHCI.
Having chosen the appropriate collimator model, the collimator parameters file must be edited to specify the exact collimator geometry. Step-by-step instructions for this can be found in the Collimator module chapter. Multiple collimators may also be simulated from one PHG run using the tomograph file feature.
At this time there are 5 supported detector models:
Simple (PET and SPECT) - just performs Gaussian energy blurring
Planar (SPECT)
DHCI (Dual-Head Coincidence Imaging)
Cylidrical PET
Block detectorsStep-by-step instructions for specifying detector geometry and properties in the detector parameters file can be found in the Detector module chapter. Multiple detectors may also be simulated from one PHG run using the tomograph file feature.
Detected photon data generated by the simulation (with or without detectors and/or collimators) is histogrammed and written out by the binning module, which has it's own parameters file. In the binning module parameters file you specify whether you want the data written as sinograms, projections for 3D-RP or in other formats. You also specify whether photons should be binned according to energy and scattering history. Full instructions for configuring the binning module can be found in the Binning chapter. [You can bin in up to 12 different ways at once if you wish - simply specify up to 12 binning parameter files in the PHG run-time parameters file. NOTE, we are currently having problems with the multiple binning file feature--you may need to use multiple tomograph files instead.]
To run the simulation enter the following command at the UNIX prompt:
phg your_phg_params_file <return>
The phg binary will then read your parameters file and begin the simulation. The screen output produced during the simulation is useful diagnostic information and should be noted.
The PHG, the collimator module, the detector module and the binning module can all create photon history files if desired. These contain records for each photon processed by that module. History files can be re-processed after simulation by the "downstream" modules (i.e., the collimator, detector, and binning modules for PHG history files; the detector and binning modules for collimator history files; etc) to finish simulating the history data.
The standard history file can become unmanageably long (100's of Gbytes) for a long simulation, so provision has been made for the user to chose which photon properties are written out. This customization process is achieved by means of a history parameters file. More information can be found in the History files chapter.
The history file format is fairly simple (see the file headers page and the History files chapter), so it is a reasonably straight-forward process to write your own binning code, if the options provided in the binning module do not suit your needs.
The collimator module, the detector module, and binning module contain hooks to which you can attach your own code. Further information on this can be found in the relevant chapters.
Finally, make sure that you keep up with the news section while you are using SimSET. Important information on bug fixes and updates is regularly posted there.
Last revised by: Robert Harrison Revision date: 7 January 2014