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


See also




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Created at: 2007-05-21
Updated at: 2016-08-06
Written by: Vesa Oikonen, Jarkko Johansson, Tuula Tolvanen