Processing ABSS data
Researcher has to pre-process the arterial blood data collected using an on-line detector with "blood pump") (*.alg, *.bld, *.txt or *.blo.lis files), before using it as the input in his/her data analyses. This page contains instructions on what needs to be done and how to do that.
As a rule, there are tracer specific (and sometimes both tracer and organ specific) software (scripts) which do most of the required steps, and new scripts can be written when needed, based on the general step-by-step instructions given below.
Scripts can be downloaded from gitlab.utu.fi/vesoik/inputbatch; but no downloads are necessary inside TPC/hospital network, since the scripts can be executed from command-line by giving the name of the script.
Scripts as such are useful only Windows computers in TPC/hospital network, because of dependencies on other software and network folders containing calibration data. Outside TPC, the necessary software must be downloaded and installed separately.
1. ABSS file format conversion, calibration, and correction for radioactive decay
If you need to do the preprocessing steps (calibration, decay correction, file format conversion) to the ABSS data by yourself, use absscal in Windows, macOS, or Linux command prompt window with the following command-line options and arguments:
- with option
-cthe location and name of datafile containing the calibration coefficients,
- to correct the data for radioactive decay,
-decay, and specify the isotope code (below),
-iwith isotope code (again) to select the correct calibration coefficient and branching ratio,
- optionally, the name of the output file may be specified with option
- the name of the raw ABSS data file.
As an example, an oxygen-15 labeled tracer data might be processed with this command in Windows command prompt window:
absscal -c=S:\Lab\plasma\bsampler_calibration\pump_cal.dat -decay=on -i=O-15 -o=uo268blo.kbq uo268.bld
If you copy the calibration file (
pump_cal.dat) to your own data directory,
make sure that it contains an up-to-date calibration coefficient for all of your studies, because
PET physicists can update only the original calibration file in
2. Dispersion correction
Correction for dispersion in the ABSS assembly and possibly in vasculature is necessary in 15O studies, and may be useful with other radiopharmaceuticals if the peak shape of the input curve is important in the analysis method.
3. Blood curve must be converted to plasma
The blood and plasma curves of most tracers are different, and for most analysis models the plasma curve is needed as input function. Therefore the blood curve must be converted to plasma curve. This is never needed for 15O tracers.
4. ABSS and manual sample data must be combined
This catenation of the two TACs can be accomplished with taccat.
There is often an overlap in ABSS and manual samples, and in those cases
will automatically ignore the end of ABSS. This can be changed with options.
In some cases it may be necessary to select and remove the overlapping samples manually in
a text editor.
Manual blood samples are pre-processed by the
personnel of blood laboratory, and the necessary corrections for manually sampled blood and plasma
TACs are made to the data before the data files are copied
to PETPACS or
When you have the combined plasma TAC, you can proceed with the processing of the input curve as usual.
5. Metabolite correction
[15O]O2 and [13N]NH4+ studies may require metabolite correction. However, some model analysis software make these corrections automatically; look for the specific analysis program documentation.
6. Delay time correction
The difference between the tracer arrival times to tissue (PET measurement) and blood sampling site (ABSS) may have to be corrected (delay correction). Result of delay time correction must always be controlled visually!
These command-line tools are used by the scripts, but can be used separately, if needed. These programs are available for both Windows and Linux.
- Processing on-line detector data, calibration and decay correction: absscal
- Applying or removing decay correction: tacdecay
- Dispersion correction: disp4dft
- Time delay correction: fitdelay
- Manual delay correction: tactime
- Converting blood TACs to plasma TACs: b2plasma
Updated at: 2019-12-03
Created at: 2006-05-23
Written by: Vesa Oikonen