Direct generation of random events using SimSET
Author: Robert Harrison
Date: May 2007
Overview
To simulate random events directly (as opposed to generating them from singles rates
using the Rij = 2SiSj formula) one needs a list of all detected photons ordered by and
stamped with their detection times. This is quite different from SimSET’s ‘native’ mode:
SimSET generates decays voxel-by-voxel (not in time-order) and when simulating PET
always stopped tracking a photon when its annihilation partner wasn’t detected.
Furthermore, importance sampling options are not compatible with direct generation of
randoms, indeed, the decays and photons all need to have weight 1.
The new SimSET randoms software addresses these problems by splitting the simulation
into a four-step process: first a list-mode (history) file is created for the detected photons
without pruning of unmatched photons; a new program called timesort sorts the list by
detection time (using a new field added to the decay record); a new program addrandoms
scans this list with a time window adding random events and deleting single events and
triple events; the resulting list-mode file is then processed through the binning module.
This document describes each of the above steps.
Note that this process requires lots of free disk space: simulating a clinically realistic
number of events will require hundreds of gigabytes of free disk space.
The directory test1user gives an example of how to simulate randoms. The script
runPET3d.sh runs all the necessary software. The following descriptions refer to some of
the parameter files used by the software.
Creating a list-mode file for randoms generation
(See PET3d.phgin and PET3d.detparms.)
The list-mode file used for randoms generation is the standard list-mode file created by
the detector module. The list-mode file name is given in the detector parameters file:
STR history_file = "PET3d.dethist"
The randoms software only works with the standard history file format, so the line giving
custom history parameters should be omitted or set to the empty string:
STR history_params_file = ""
The run file must also be changed. To support PET tracking both with and without the
tracking of unmatched singles, we have added two new options:
BOOL simulate_SPECT
= false
BOOL simulate_PET_coincidences_only = false
BOOL simulate_PET_coincidences_plus_singles = true
In previous versions setting “simulate_SPECT = false” automatically made the
simulation a PET simulation. Now one must specify whether one wants to simulate only
those photons that have an annihilation partner (“simulate_PET_coincidences_only =
true”, much more efficient when randoms generation is not desired) or all photons
including unmatched singles (“simulate_PET_coincidences_plus_singles = true”,
necessary when simulating randoms). Exactly one of these three options must be set true
in every simulation.
The binning parameters file name can be left blank: if filled in, the simulated data will be
binned without randoms.
STR bin_params_file = ""
(A separate run through the binning module after randoms have been added to the listmode data will create the binned data with randoms.)
To allow for the generation of photons and events with a uniform weight of 1, we have
added an option for SimSET to compute the number of decays to simulate from the
activity distribution and scan time. (Previously the user specifed the number of decays,
the activity, and the scan time – there was one piece of redundant information,
necessitating the use of weights even when importance sampling was not used.) The scan
time input has also been changed to a real number – this allows the user to set up very
short runs (e.g., 0.01 scan time) to check they have set everything up correctly.
In addition, all the importance sampling features must be set to false
(simulate_stratification, simulate_forced_detection, and forced_non_absorbtion in the run
file and do_forced_interaction in the detector parameters file).
Outside of the above changes, the run and detector parameter files can be identical to
those used before. The simulation is run as before to create the detected list-mode file:
phg PET3d.phgin
Sort by detection time
(See PET3d.tsparms.)
We have created a new program to sort the list mode data by detection time, timesort. It
requires only three parameters:
# INPUT HISTORY FILE
STR history_file = "PET3d.dethist"
# SORTED (OUTPUT) HISTORY FILE
STR sorted_history_file = "PET3d.dethist.srtd"
# BUFFER MEMORY SIZE (IN MEGABYTES)
INT buffer_size = 200
The first parameter must give the same file name given for the list-mode file in the
detector parameters file. The second is the output file name for the sorted listmode data.
The third is the size buffer used for the sub-sorting of the data: 200 megabytes is a good
size as long as it doesn’t cause memory problems on your system, e.g., if you only have
500MB RAM you may wish to reduce this to 50.
Once the file is created, timesort is run by:
timesort –d -r PET3d.tsparms
(The “-d” specifies that a detector history file will be used as input. “-r” causes
PET3d.dethist to be deleted after the time-sorted file is created – a little cleaning up.)
Add random events
(See PET3d.randparms.)
We have created a new program to add randoms to time-sorted list-mode files,
addrandoms. It requires 4 parameters:
#
detector_type can be
#
dual-headed or cylindrical
ENUM detector_type = cylindrical
#
STR
Time-sorted input history file
history_file = "PET3d.dethist.srtd"
# Output history file for the new randoms-added data.
STR randoms_history_file = "PET3d.randhist"
# Coincidence timing window in nanoseconds.
REAL coincidence_timing_window_in_ns = 5
The detector type must be dual-headed or cylindrical. (We have not yet passed one of our
tests for the dual-headed detector – I am pretty sure that this is a problem in the test
definition and not the program, but still have less confidence in that detector.) The second
parameter must be the file name for the output from the timesort program. The third
parameter is a file name for the output from addrandoms, a list-mode file with randoms
added to it (and with all other singles and all triples removed). The fourth parameter gives
the desired timing window in nanoseconds. Every detected photon opens a window this
long. If exactly one other photon arrives within the window, a true event (if the second
photon is from the same decay) or random event (if its from a different decay) is added to
the output list-mode file. If two or more other photons arrive within the window, the
photons are discarded.
addrandoms is run by:
addrandoms PET3d.randparms
Binning the randoms-added list-mode data
(See PET3d.dethistin, PET3d.detrandparms, and PET3d.binparms.)
Binning of the randoms-added data uses the same function that has always been used to
bin list-mode files. However, there are some new binning options, and one has to make
sure to bin the right list-mode file (the one produced by addrandoms).
PET3d.dethistin can be a copy of PET3d.phgin, except with a new file name for the
detector parameters file and a name for the binning parameters file:
STR detector_params_file = "PET3d.detrandparms"
STR bin_params_file = "PET3d.binparms"
PET3d.detrandparms points to the randoms-added list-mode data:
STR history_file = "PET3d.randhist"
Otherwise it should be exactly like the detector parameters file (PET3d.detparms).
PET3d.binparms has two new parameters, “accept_randoms” and
“scatterRandomParam”. To include randoms in the binned data, one must set
BOOL accept_randoms = true
scatterRandomParam defines a new array of options for binning trues/randoms/scatter. It
replaces the parameter “scatterParam”. scatterRandomParam controls how the trues,
scatter and randoms get binned. The options are described in the parameter file. The most
popular options will probably be: scatterRandomParam = 0, which causes trues, scatter,
and randoms to all be binned together (as they are in actual scans); scatterRandomParam
= 1, which creates separate bins for trues and scatter (i.e., if the user has selected
distance-angle binning, there will be separate distance-angle arrays for true and scatter
events); and scatterRandomParam = 6, which creates separate bins for trues, scatter, and
randoms.