Count rate data
What is count-rate data?
"Count-rate" (CR) data file contains the true counts per second collected by the PET scanner during each second of the scanning. It is used for time-delay correction. However, CR data may not be suitable for time-delay correction, if scanned area contains large blood pools where injected tracer arrives quickly, such as heart, lungs, abdominal aorta, subclavian vein and superior vena cava.
CR data is stored in an ASCII text file with two columns, time (s) and true
count rate (units may differ). In Turku PET Centre, CR curves are corrected for
physical decay. The filename extension is usually
.cr
, .head
("head curve"), or *.hc
.
However, the count-rate data is originally saved in different formats by the PET scanners and may need to be converted to this format before use.
Where does CR data come from?
Count-rate data is (optionally) saved during PET scanning, or can be later saved from collected list-mode data. Count rate data files are stored with the images in PETPACS.
HR+
Count-rate data is routinely saved in all PET studies beginning in the autumn 2005.
Count-rate data ("head-curve") in HR+ is originally saved in format like this:
time prompt delayed p_rate d_rate dtime frame singles 1050 148 131 0 0 0 1 184302 3066 1165 1084 504 472 1 1 622488 4133 2060 1889 838 754 1 1 622488 5866 3858 3715 1037 1053 0 2 0 6916 5260 5010 1335 1233 3 2 1284090 ...
Before any use, this data must be converted to normal count-rate data format using tocr. However, batch files and scripts for processing blood and plasma curves may do this step automatically for the often used tracers.
HRRT
Head-curve files (*.hc
) are stored with the PET images
(for example, History\ra128_em_static_lm.hc), and they are also located in
pet-storage disk in folder HRRT\rawdata.
Data is originally in comma-separated table format, like this:
Singles,Randoms,Prompts,Time(ms) 1913508,4936,5580,761 2017637,6025,6437,1975 2570950,28844,29498,3299 3133375,59768,60599,4545 4867737,67194,67184,5587 ...
Be sure to use the correct *.hc
file (usually the one largest
in size), which contains counts at about 1 sec frequency, and not the ones
which contain count data from PET frames.
Before any use, this data must be converted to normal count-rate data format using tocr. However, batch files and scripts for processing blood and plasma curves may do this step automatically for the often used tracers.
PET-CT
Not considered yet.
GE Advance
In Turku PET Centre, when images are extracted from GE Advance database
in ECAT 6.3 format, the CR data is also extracted (program crexport
via dbExtr), and written in the same directory than the PET image with extra
extension .cr
.
The CR data is corrected for physical
decay and dead-time. Originally the .cr
file does not contain
the time column, which must be added before any use, with
addtimes;
however, many software do this automatically.
ECAT 931
Count-rate data was written in the same directory as the dynamic PET image
with extension *.head
; the files did not originally contain the
time column, which may have to be added with
addtimes;
however, many software do this automatically, and some very old software may
work only if there is no time column.
If CR data is not available
Count-rate curve can be replaced in time delay fitting with regional TACs or "head curve", an average TAC from the dynamic image or sinogram made with imghead, in case that PET time frames are short enough (10-15 s or less) in the beginning of the PET scan. As the last resort, you can draw a large ROI on the dynamic image, calculate its TAC, and use that as "head curve", or compute mean TAC of regional TACs previously saved in a TTAC file.
Software for processing CR data
- Add time column into count-rate file
- Create a "head curve" if count-rate file does not exist
- Make a SVG graph for viewing the count-rate curve; count-rate curve can be scaled to fit better in the same graph.
See also
Tags: Countrate, Delay correction, Count
Updated at: 2016-08-06
Created at: 2007-05-21
Written by: Vesa Oikonen, Jarkko Johansson, Tuula Tolvanen