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ANALYSIS OF PET STUDIES. DEMONSTRATION Turku PET Centre 2001-05-08 Vesa Oikonen. BLOOD PUMP Datafiles. Datafiles are found in paths /data/plasma/ecat/*_blo.lis (ECAT) and /data/plasma/ge/patient/*.bld (GE Advance). Datafiles are not calibrated or decay corrected, and they

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analysis of pet studies

ANALYSIS OF PET STUDIES

DEMONSTRATION

Turku PET Centre

2001-05-08 Vesa Oikonen

blood pump datafiles
BLOOD PUMPDatafiles

Datafiles are found in paths

/data/plasma/ecat/*_blo.lis (ECAT) and

/data/plasma/ge/patient/*.bld (GE Advance)

Datafiles are not calibrated or decay corrected, and they

contain all the raw data collected by the detectors:

zelda{vesa}40: more /data/plasma/ecat/s04697_blo.lis

# 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

# 2000-12-08 10:29:33

976264173.0 0.0 1.0 0 11 20 1 61 30 0

976264174.0 1.0 1.0 0 14 23 0 76 37 0

976264175.0 2.0 1.0 1 11 29 1 58 32 0

976264176.0 3.0 1.0 0 40 79 0 169 45 0

976264177.0 4.0 1.0 1 190 330 1 426 179 0

976264178.0 5.0 1.0 3 479 798 2 855 323 0

976264179.0 6.0 1.0 2 648 1027 5 1104 445 0

976264180.0 7.0 1.0 4 841 1369 3 1383 615 0

976264181.0 8.0 1.0 7 982 1658 6 1558 697 0

976264182.0 9.0 1.0 5 1070 1800 2 1954 820 0

976264183.0 10.0 1.0 5 1327 1855 7 2002 887 0

976264184.0 11.0 1.0 2 1372 1908 5 1982 899 0

976264185.0 12.0 1.0 5 1364 1955 7 2113 984 0

blood pump programs for processing data
BLOOD PUMPPrograms for Processing Data

ge_dyn_corr

ge_fcft_input

ge_fdopa_input

ge_flb_input

ge_input_correction

ge_mpa_input

ge_nk1_input

ge_rp_input

...

ecat_dyn_corr

ecat_fcft_input

ecat_fdopa_input

ecat_flb_input

...

manual samples datafiles
MANUAL SAMPLESDatafiles
  • Datafiles are found in path /data/plasma
  • Files are decay corrected and calibrated to kBq/mL
  • Filenames:
  • *ap.kbq = arterial plasma,
  • *ab.kbq = arterial blood,
  • *vp.kbq = venous plasma,
  • *bp.dat = blood/plasma ratio
  • -Example:

# Injection time: 04.10.2000 11:08:25

# Isotope: F-18

# Calibration coefficient: 0.002980

# Activity units: kBq/mL

# Time units: min

0.467 0.000

0.650 20.353

0.833 134.116

1.017 183.610

1.200 186.274

1.367 139.035

1.583 111.311

1.767 91.686

1.933 76.551

...

plasma data correction for metabolites 1
PLASMA DATACorrection for Metabolites #1

The fractions of authentic tracer are written in file:

01.00

10.96

20.89

50.78

100.65

150.5

200.32

300.13

500.04

plasma data correction for metabolites 2
PLASMA DATACorrection for Metabolites #2

A function can be fitted to the fraction data:

plasma data correction for metabolites 3
PLASMA DATACorrection for Metabolites #3

Metabolite corrected plasma curve is calculated with program subtrmet

(or fdmet or fthamet):

zelda{vesa}42: cd /data/test

/data/test

zelda{vesa}43: subtrmet t00001ap.dat t00001ap.rat

Writing file t00001ap.pure.dat...

Writing file t00001ap.met.dat...

zelda{vesa}45: subtrmet t00001ap.dat t00001ap.rat.fit

subtrmet: Warning: fraction outside fit range.

Writing file t00001ap.pure.dat...

Writing file t00001ap.met.dat...

either using fraction

file as such

or function fitted to

the fraction data

pet raw data sinogram or scan file scn
PET RAW DATA”Sinogram” or ”Scan file”, *.scn

-File format: ECAT 931 version 6.3 scan file

-If needed, GE Advance sinograms should be asked for

-ECAT sinograms can be retrieved from DAT tapes; then also

*.nrm and *.atn file should be restored

pet image data img
PET IMAGE DATA*.img

-File format: ECAT 931 version 6.3 image file

-If needed, GE Advance images should be asked for

-ECAT images can be reconstructed from sinograms

(also *.atn and *.nrm files are required)

[18F]FDG

frame

30-60 s

frame

2-3 min

frame

15-20 min

frame

35-40 min

frame

50-55 min

headers main header in image and scan files
HEADERS”Main header” in Image and Scan Files

Main header contains:

-start time of scanning

-patient name; do not distribute!

-calibration unit

-number of planes and frames

zelda{vesa}105: lmhdr ut1101dy1.img

original_file_name = ''

data_type = 2 (short int)

file_type = 2 (image)

scan start = 07.03.2000 11:17:24

isotope_code = 'O-15 ' isotope_halflife = 122.2

radiopharmaceutical = 'H2O -- water'

gantry_tilt = 6.5 gantry_rotation = 0 bed_elevation = 0

axial_fov = 15 transaxial_fov = 55

calibration_factor = 1 calibration_units = 10 (kBq/mL)

study_name = '' patient_id = ''

patient_name = 'Oikonen Vesa'

sex= age= height=173 weigth=74 dexterity=

physician_name = neuro operator_name = thk

study_description = aktivaatio 200MBq

35 planes 1 frames 1 gates 1 bed_pos

init_bed_position = 0

plane_separation = 0.425

user_process_code = ge2cti

headers subheader in image files
HEADERS”Subheader” in Image Files

One subheader for each frame and plane

Subheaders contain:

-start time and duration of the frame

-calibration factor

-voxel size (cm)

zelda{vesa}107: lshdr ut1101dy1.img 1 8

File ut1101dy1.img plane 8 frame 1 gate 1 bed 0

data_type = 2 dimension = 128x128

x_origin = 0 y_origin = 0 recon_scale = 2.00276

quant_scale = 0.000421882 image_min = -7417 image_max = 32766

slice_width = 0.425 pixel_size = 0.234375

frame_start_time = 45 frame_duration = 90 sec

reconstruction start = 00.00.0000 00:00:00

filter_code = 0 image_rotation = 0 intrinsic_tilt = 0

plane_eff_corr_fctr= 0 decay_corr_fctr= 1.64817 loss_corr_fctr= 1

quant_units = 10 (kBq/mL)

ecat_calibration_fctr = 1 well_counter_cal_fctr = 1

annotation = ''

matrix list of image and scan files
MATRIX LISTof Image and Scan Files

zelda{vesa}108: lmlist ut1101dy1.img

matrix pl fr gate bed

1 16842753 1 1 1 0

2 16908289 2 1 1 0

3 16973825 3 1 1 0

4 17039361 4 1 1 0

5 17104897 5 1 1 0

6 17170433 6 1 1 0

7 17235969 7 1 1 0

8 17301505 8 1 1 0

9 17367041 9 1 1 0

10 17432577 10 1 1 0

11 17498113 11 1 1 0

12 17563649 12 1 1 0

13 17629185 13 1 1 0

14 17694721 14 1 1 0

15 17760257 15 1 1 0

To check which planes and

frames really exist in the image

or sinogram:

sum images calculation
”SUM” IMAGESCalculation

Integration:

zelda{vesa}121: cti_int t00001dy1.img 1800 3000 t00001integral.img

integrating...............

zelda{vesa}122: avgframe t00001dy1.img 12 17 t00001avg.img

integrating...............

Averaging (can be multiplied by time later):

arithmetics with image and scan files
ARITHMETICSwith Image and Scan Files

Program calcimg

Addition, Subtraction, Multiplication, Division

between images (or sinograms) or between image

(or sinogram) and a constant

cutting and joining image and scan files
CUTTING AND JOININGImage and Scan Files

Program ctisplit

for extracting specified frames and planes into a new file

Program cticat

for joining images together, e.g. for combining early and late scans

regions of interest roi
REGIONS OF INTEREST*.roi

zelda{vesa}138: more t00316dy1_10.roi

*/data/test/t00316dy1sum.img 3.000000 2.450000 17432577 3 -279691264 330 313 0 0 0 1

put dx///0 16

0 0 -15 -9 -16 -9 -17 -11 -27 0 -37 18 -43 39 -49 64 -50 77 -44 80 -31 65 -17 46 -5 28 2 10 4 6 0 0

*/data/test/t00316dy1sum.img 3.000000 2.450000 17432577 3 0 449 327 0 0 0 2 put sin//

/0 16

0 0 18 -5 20 -5 21 -8 29 0 37 22 42 43 45 67 45 81 39 83 27 66 16 48 6 28 0 10 -1 6 0 0

*/data/test/t00316dy1sum.img 3.000000 2.450000 17432577 3 1152 545 503 0 0 0 3 temp s

in///0 12

0 0 20 17 21 21 11 35 0 49 -17 72 -31 84 -45 55 -32 44 -20 31 0 1 0 0

*/data/test/t00316dy1sum.img 3.000000 2.450000 17432577 3 -65536 222 490 0 0 0 4 temp

dx///0 12

0 0 -17 13 -20 17 -12 33 -3 49 4 73 16 89 37 64 24 49 15 34 1 1 0 0

*/data/test/t00316dy1sum.img 3.000000 2.450000 17432577 0 -279691264 336 557 22 88 0

1 vis dx///0 5

*/data/test/t00316dy1sum.img 3.000000 2.450000 17432577 3 -279691264 427 567 0 0 0 2

vis sin///0 5

0 0 -19 -1 -38 81 -17 86 0 0

Example of a ROI file:

regions of interest calculation of tacs
REGIONS OF INTERESTCalculation of TACs

zelda{vesa}141: img2kbq t00316dy1.img t00316dy1*.roi t00361.roi.kbq

calculated put dx Pl10

calculated put sin Pl10

calculated put dx Pl11

calculated put sin Pl11

calculated temp sin Pl11

calculated temp dx Pl11

calculated vis dx Pl11

calculated vis sin Pl11

calculated cer dx Pl14

calculated cer sin Pl14

calculated cer dx Pl15

calculated cer sin Pl15

Data of 12 ROIs saved in file t00361.roi.kbq

After drawing ROIs, the time-activity curves

(average radioactivity concentration inside ROIs)

can be calculated with program img2kbq

For parametric images, use option -p and give

the result filename with extension *.txt to

save results in an easily printable format

regional tacs file format
REGIONAL TACsFile Format

Files are in ASCII text format. They can be read into Excel, Origin etc.

Example of a TAC file:

DFT1 tumor1 12-lih 13-lih 14-lih lihavg

uo0372 . . . . .

kBq/ml Pl17 Pl12 Pl13 Pl14 .

Time (min) 1.051e+03 5.626e+03 5.626e+03 5.626e+03 5.626e+03

0.25000 9.520e-01 1.687e-01 1.174e-01 2.647e-01 1.836e-01

0.75000 6.104e+00 8.800e-01 1.113e+00 1.240e+00 1.078e+00

1.25000 1.384e+01 2.557e+00 2.609e+00 3.455e+00 2.874e+00

1.75000 1.542e+01 3.377e+00 3.928e+00 3.647e+00 3.650e+00

2.50000 1.461e+01 3.938e+00 3.757e+00 4.587e+00 4.094e+00

3.50000 1.713e+01 4.168e+00 4.582e+00 5.023e+00 4.591e+00

4.50000 1.718e+01 4.969e+00 5.104e+00 5.527e+00 5.200e+00

6.50000 1.502e+01 6.080e+00 6.011e+00 6.492e+00 6.194e+00

9.50000 1.515e+01 6.959e+00 6.851e+00 6.876e+00 6.895e+00

12.50000 1.617e+01 7.141e+00 7.377e+00 7.515e+00 7.344e+00

...

regional gjedde patlak command line version
REGIONAL GJEDDE-PATLAKCommand Line Version

zelda{vesa}212: fit_ki t01205vp.kbq t01205.roi.kbq none 15 60 t01205ki.res

ROI kLoss Ki Ic Time r

cer dx All 0.000e+00 4.040e-02 8.65e-01 52 0.9980

cer sin All 0.000e+00 3.984e-02 8.54e-01 52 0.9981

fro dx All 0.000e+00 4.086e-02 6.95e-01 52 0.9994

fro sin All 0.000e+00 4.127e-02 6.85e-01 52 0.9973

hipp dx All 0.000e+00 2.342e-02 6.03e-01 52 0.9881

hipp sin All 0.000e+00 2.116e-02 6.51e-01 52 0.9951

mfro dx All 0.000e+00 2.898e-02 5.39e-01 52 0.9885

mfro sin All 0.000e+00 3.302e-02 5.90e-01 52 0.9965

put dx All 0.000e+00 4.083e-02 7.65e-01 52 0.9950

put sin All 0.000e+00 3.999e-02 6.79e-01 52 0.9980

sensmo dx All 0.000e+00 3.338e-02 6.08e-01 52 0.9978

sensmo sin All 0.000e+00 3.426e-02 6.34e-01 52 0.9983

zelda{vesa}213:

regional gjedde patlak with k loss
REGIONAL GJEDDE-PATLAKwith kLOSS

zelda{vesa}213: fit_kil t01205vp.kbq t01205.roi.kbq none 15 60 t01205ki.res

ROI kLoss Ki Ic Time r

cer dx All 9.592e-03 5.487e-02 6.21e-01 52 0.9997

cer sin All 9.117e-03 5.330e-02 6.26e-01 52 0.9996

fro dx All 5.446e-03 4.867e-02 5.60e-01 52 0.9999

fro sin All 1.062e-02 5.789e-02 4.06e-01 52 0.9994

hipp dx All 0.000e+00 2.342e-02 6.03e-01 52 0.9881

hipp sin All 1.102e-02 3.005e-02 5.02e-01 52 0.9974

mfro dx All 0.000e+00 2.898e-02 5.39e-01 52 0.9885

mfro sin All 8.489e-03 4.332e-02 4.15e-01 52 0.9978

put dx All 9.974e-03 5.612e-02 5.07e-01 52 0.9969

put sin All 3.772e-03 4.516e-02 5.90e-01 52 0.9983

sensmo dx All 6.971e-03 4.173e-02 4.65e-01 52 0.9987

sensmo sin All 8.050e-03 4.433e-02 4.63e-01 52 0.9995

temp dx All 8.628e-03 4.922e-02 5.06e-01 52 0.9999

temp sin All 7.121e-03 5.020e-02 5.28e-01 52 0.9995

regional logan plot plasma input
REGIONAL LOGAN PLOTPlasma Input

zelda{vesa}220: logan rp0096.roi.kbq rp0096ap.pure.kbq 15 60 logan.res

ROI Plane DV SE IC SE r

caudx All 1.15e+00 1.42e-02 -1.43e+01 6.13e-01 1.000

causin All 1.15e+00 7.32e-03 -1.43e+01 3.16e-01 1.000

cer All 3.32e-01 8.02e-04 -4.23e+00 1.30e-01 1.000

putdx All 1.31e+00 5.57e-03 -1.51e+01 2.11e-01 1.000

putsin All 1.30e+00 1.01e-02 -1.51e+01 3.84e-01 1.000

thadx All 4.82e-01 3.02e-03 -6.73e+00 3.31e-01 1.000

thasin All 4.92e-01 3.98e-03 -6.28e+00 4.20e-01 1.000

cau All 1.15e+00 6.96e-03 -1.43e+01 3.00e-01 1.000

put All 1.31e+00 5.04e-03 -1.52e+01 1.92e-01 1.000

tha All 4.87e-01 2.22e-03 -6.55e+00 2.39e-01 1.000

regional logan plot reference region input
REGIONAL LOGAN PLOTReference Region Input

zelda{vesa}221: logan rp0096.roi.kbq cer 15 60 logan.res

ROI Plane DVR SE IC SE r

caudx All 3.41e+00 3.03e-02 -9.63e+00 4.01e-01 1.000

causin All 3.40e+00 1.16e-02 -9.63e+00 1.54e-01 1.000

putdx All 3.86e+00 1.34e-02 -1.03e+01 1.56e-01 1.000

putsin All 3.85e+00 1.68e-02 -1.03e+01 1.97e-01 1.000

thadx All 1.45e+00 5.80e-03 -2.77e+00 1.95e-01 1.000

thasin All 1.48e+00 5.69e-03 -2.23e+00 1.85e-01 1.000

cau All 3.40e+00 1.41e-02 -9.64e+00 1.87e-01 1.000

put All 3.86e+00 7.91e-03 -1.03e+01 9.23e-02 1.000

tha All 1.47e+00 3.47e-03 -2.52e+00 1.15e-01 1.000

regional binding potential
REGIONAL BINDING POTENTIAL

zelda{vesa}224: fitbp rp0096.roi.kbq cer fitbp.res

ROI Plane R1 k2 BP Time SS/n

caudx All 0.8054 2.329e-01 2.4796 48 6.29e-01

causin All 0.7622 2.361e-01 2.4646 48 3.32e-01

putdx All 0.9161 2.458e-01 2.9638 48 2.77e-01

putsin All 0.9199 2.451e-01 2.9514 48 3.19e-01

thadx All 0.8152 1.705e-01 0.4506 48 2.22e-01

thasin All 0.7650 2.046e-01 0.4855 48 3.07e-01

cau All 0.7837 2.345e-01 2.4720 48 4.38e-01

put All 0.9180 2.454e-01 2.9576 48 2.81e-01

tha All 0.7874 1.892e-01 0.4671 48 2.51e-01

parametric images logan analysis
PARAMETRIC IMAGESLogan Analysis

DV or DVR can be calculated pixel-by-pixel, but better quality would

be achieved by calculating from sinogram and reconstructing after that

zelda{vesa}234: ctilogan rp1057dy1.mrp.img rp1057cer.kbq 0 15 0 logan.img

plane 01

plane 02

plane 03

plane 04

plane 05

plane 06

plane 07

...