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.

Available scripts

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.

Step-by-step instructions

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:

  1. with option -c the location and name of datafile containing the calibration coefficients,
  2. to correct the data for radioactive decay, use option -decay, and specify the isotope code (below),
  3. option -i with isotope code (again) to select the correct calibration coefficient and branching ratio,
  4. optionally, the name of the output file may be specified with option -o,
  5. 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 \pet-storage disk system.

Detailed information on how on-line detector raw data is processed is given with the raw data file format descriptions for Scanditronics/GEMS, and Allogg ABSS #1 and ABSS #2.

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 tracers 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

After the ABSS raw data is converted to plasma TAC, it usually has to be combined with the plasma TAC measured from manual blood samples (in 15O studies usually only ABSS is used).

This catenation of the two TACs can be accomplished with dftcat.

There is often an overlap in ABSS and manual samples, and in those cases dftcat 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 S:\Lab\plasma\.

When you have the combined plasma TAC, you can proceed with the processing of the input curve as usual.

5. Metabolite correction

Metabolite correction of the plasma or blood curve is required for most of the tracers, but not for the most commonly used tracers [18F]FDG and [15O]H2O.

[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!

Low-level software

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.

See also:



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Created at: 2006-05-23
Updated at: 2017-10-26
Written by: Vesa Oikonen