File format of Scanditronics/GEMS on-line detector raw data
Specifications
The data collected using the ABSS ("blood pumps" with on-line detectors) is saved in
ASCII files named as *.bld or *blo.lis. The format is specified by the
manufacturer of the devices, except for the header lines, starting with #; these lines are written
by in-house programs. These lines must specify at least the date of study in a format shown in
the example below, because the applied calibration coefficients are selected based on this date.
Into the oldest data files the date has to be added
manually.
The data columns are:
- Count collection start time as seconds from the beginning of the day
- Time (sec) from the start of this study
- Measurement interval, i.e. count collection time (sec)
- Coincidence counts from the first pair of detectors
- Single counts collected by the first detector of the first pair
- Single counts collected by the second detector of the first pair
- Coincidence counts from the second pair of detectors
- Single counts collected by the first detector of the second pair
- Single counts collected by the second detector of the second pair
- Aux counts (always zero in our measurements)
Example #1: GEMS on-line detector raw data file from a [15O]O2 study
# Protocol: /usr/PET/frq/frqflow5.prt # Patient: ut193 # Isotope half-life: 2.05 # Start Interv 1st detector pair 2nd detector pair AUX # time time coinc singl1 singl2 coinc singl1 singl2 counts # 2002-06-25 12:59:04 ut193 2.050000 1.230000 1.400000 1.400000 1.400000 1.400000 46834.0 0.0 1.0 5 877 783 15 1505 1864 0 46835.0 1.0 1.0 3 719 511 13 1103 1254 0 46836.0 2.0 1.0 4 650 503 8 1005 1166 0 46837.0 3.0 1.0 3 632 468 8 1006 1094 0 46838.0 4.0 1.0 2 639 511 6 1005 1063 0 46839.0 5.0 1.0 4 589 461 9 987 1030 0 46840.0 6.0 1.0 3 543 431 5 1012 1015 0 46841.0 7.0 1.0 3 613 479 8 995 1126 0 46842.0 8.0 1.0 2 621 441 8 928 1079 0 46843.0 9.0 1.0 3 655 495 6 915 1105 0 46844.0 10.0 1.0 9 658 504 8 973 1106 0 46845.0 11.0 1.0 19 731 557 25 1023 1150 0 46846.0 12.0 1.0 92 955 810 74 1215 1273 0 46847.0 13.0 1.0 165 1229 1105 166 1544 1547 0 46848.0 14.0 1.0 237 1484 1316 220 1647 1704 0 46849.0 15.0 1.0 287 1750 1604 338 1988 2067 0 46850.0 16.0 1.0 353 1978 1811 366 2128 2216 0 46851.0 17.0 1.0 406 2151 1952 424 2279 2336 0 46852.0 18.0 1.0 360 2183 2052 459 2351 2435 0 46853.0 19.0 1.0 410 2269 2073 475 2424 2561 0 ...
Example #2: GEMS on-line detector raw data file after control software was updated to an in-house program
# GEMS Automated Blood Measurement System
# Protocol: 180 1
# Patient: tf04042018_2
# Isotope half-life: 109.8
# Start Interv 1st detector pair 2nd detector pair AUX
# time time coinc singl1 singl2 coinc singl1 singl2 counts
# 2018-04-04 11:31:33
41493.5 0.0 1.0 283 849 931 230 877 652 0
41494.5 1.0 1.0 259 851 823 237 824 694 0
41495.5 2.0 1.0 289 897 909 231 912 682 0
...
Example #3: Scanditronics on-line detector raw data file from a [15O]O2 study
The first column contains the time in seconds since the epoch in local time.
# Scanditronics Automated Blood Measurement System # Protocol: 400 1 # Start Interv 1st detector pair 2nd detector pair AUX # time time coinc singl1 singl2 coinc singl1 singl2 counts # 2002-02-06 11:01:35 1012986129.0 1.0 1.0 0 114 152 5 634 333 0 1012986130.0 2.0 1.0 0 133 176 6 668 332 0 1012986131.0 3.0 1.0 3 134 182 5 680 350 0 1012986132.0 4.0 1.0 2 132 183 4 742 309 0 1012986133.0 5.0 1.0 3 184 263 10 793 437 0 1012986134.0 6.0 1.0 3 188 227 20 866 461 0 1012986135.0 7.0 1.0 16 196 276 17 823 478 0 1012986136.0 8.0 1.0 20 232 300 18 944 504 0 1012986137.0 9.0 1.0 20 244 338 39 1083 579 0 1012986138.0 10.0 1.0 41 345 446 58 1204 606 0 1012986139.0 11.0 1.0 63 397 471 81 1322 773 0 1012986140.0 12.0 1.0 68 484 582 96 1444 843 0 1012986141.0 13.0 1.0 102 617 658 126 1645 934 0 1012986142.0 14.0 1.0 131 665 816 172 1864 1097 0 1012986143.0 15.0 1.0 152 873 958 219 2023 1274 0 1012986144.0 16.0 1.0 187 978 1102 264 2385 1447 0 1012986145.0 17.0 1.0 243 1162 1252 334 2680 1620 0 ...
Calibration of data
Each measurement line is calibrated to units kBq/ml by following this procedure. Note that this does not contain correction for physical decay or dispersion. Normally, blo2kbq or absscal can be used for this purpose.
- Calculate the average of coincidence counts (columns #4 and #7)
- Divide the average by measurement duration in seconds (column #3)
- Read the two calibration coefficients from
calibration coefficient file:
- selected detector specific detector-to-gamma counter calibration coefficient: "pump1(ecat)" for *blo.lis files and "pump2(ge)" for *.bld files
- read also the last column, gamma counter-to-pet coefficient, which is common to all on-line detectors
- select calibration that is made just before or on the same day as the blood measurement
- Multiply the two calibration coefficients with each other
- Divide the calibration coefficient by the branching ratio of the radioactive label isotope
- Multiply the count-per-second value from step #2 by the combined calibration coefficient
Sample time for each measurement is calculated as the sum of measurement start time (column #2), and measurement duration (column #3) divided by 2, i.e. the middle point of each measurement. There are separate instructions for correcting data for the physical decay.
Problems with on-line detector raw data
"Dead" detector pair
In some cases, either of the pairs can not calculate the coincidences and print zeros the 4th or 7th column in raw data file. This results in blood TAC files that are about one-half of the normal curves. If you suspect or have found out that this has happened, contact Tuula Tolvanen (or try to use abssfch).
Interrupted and remade study
If the same study has been started again because of some failure in the first try, it may happen that on-line detector raw data consists of the start of the interrupted study, and directly after it, the data from the successful second try. In this case, you can read the raw data file in a text editor, remove there the data belonging to the first study, and then save the data again in ASCII file, and then continue the analysis as usual. However, you should make a backup copy of the original raw data file before editing it.
Scanditronics data collected before Oct 1998
The original VAX software was used to run the Scanditronics on-line sampler at ECAT 931 before Oct 4, 1998. Data files from that time do not contain any title lines and are in VAX format, which can not be processed by the recent software releases. If you need to re-analyze old data, please try to use previously calibrated blood data.
Scanner and blood sampler in different time
In early 2006, the time in PET-CT was not yet the same as in other equipments (computer clocks were not synchronized). The different time must be corrected to the online sampler data, before it is processed further.
If PET scan and blood sampler were started simultaneously, the start times in dynamic PET image and in blood sampler data file must be the same. This can be checked using egetstrt and absstime and, if necessary, also corrected using absstime.
Faulty sample times in Scanditronics data
Sample times (first columns) are wrong in Scanditronics data collected with bsampler 2.2.0. However, the measurement start time in file header is correct. blo2kbq (and absscal) uses correct sample start time from the header.
Blood sampler curve has a high initial activity
High activity values in the beginning of the blood curve will lead to error later in the time delay correction, and should be corrected either manually with a text editor or with absszero.
Not really problems, but things to be noted:
Scanditronics count collection start time
Count collection start time (column 1), has not been recorded as seconds from the beginning of
the day, but as seconds from 1970-01-01 00:00:00 with certain bsampler releases.
This does not affect the results.
Start time with GEMS on-line sampler
Data that has been collected with GEMS on-line sampler has a date and time in its header section. However, this is NOT the time at when the measurement actually started, but this is the time when the blood collection software began to wait for the actual scan start. If measurement start time is needed, it can be read from the first sample line, the first column.
In Scanditronics data files the start time, if it exists in the header, is the actual start time, and can be used as such.
Tags: ABSS, Scanditronics, Blood, ECAT, File format
Updated at: 2016-12-14
Created at: 2006-10-13
Written by: Vesa Oikonen, Tuula Tolvanen