new simulation

pve/heart/fdg/fdg.par

+# model := 2TCM
+Parameters	K1[mL/(mL*min)]	K1/k2	k3[1/min]	Vb[%]
+myocardium	0.2	1.0	0.02	0

pve/heart/fdg/fdg_arterial_plasma.fit

+FIT1        fit_sinf 0.8.9  (c) 2005-2013 by Turku PET Centre
+Date:	2014-02-18 10:06:45
+Data file:	fdg_arterial_plasma.dat
+Data unit:	kBq/mL
+Time unit:	min
+Nr of VOIs:	1
+Region Plane	Start	End	dataNr	WSS	parNr	Type	Parameters
+Plasma . .	0.0	60	22	0	10	0331	1.0E-01	3.461569E-01	1.111569E+02	7.805481	5.699555	3.386341E-001	4.181790	7.961674E-002	5.705464	1.393305E-002

pve/heart/fdg/frames.sif

+14/11/2019 09:09:10 18 2 1 SIMUL F-18
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+2400 3000
+3000 3600

pve/heart/fdg/myocardial_fdg.sh

+#!/bin/bash
+#: Title      : myocardial_fdg
+#: Date       : 2019-11-14
+#: Author     : "Vesa Oikonen" <vesa.oikonen@utu.fi>
+#: Options    : None
+#: Description: Simplistic simulation of partial volume errors in FDG heart studies,
+#:              and testing proposed correction methods.
+
+printf "\n=====================================================================\n"
+printf "  Making or emptying result folder\n"
+if [ ! -d sim1 ]; then
+  mkdir sim1
+else
+  rm -f sim1/*
+fi
+
+
+printf "=====================================================================\n"
+printf "Making 60 min FDG PTAC with 0.05 min (3 s) sample intervals. \n"
+printf "PTAC is based on population mean from human FDG studies.\n"
+printf "We will assume that plasma and blood TACs are equal.\n"
+printf "=====================================================================\n"
+
+fit2dat -c=0,61,0.1 fdg_arterial_plasma.fit sim1/plasma.bld
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
+printf "=====================================================================\n"
+printf "Simulating FDG TTACs with K1=0.2, K1/k2=1.0, k3=0.02, Vb=0 \n"
+printf "Ki=K1*k3/(k2+k3)= 0.004/0.22 = 0.018181818 \n"
+printf "Parameters are based on rat FDG study by Mabrouk et al, 2014 \n"
+printf "=====================================================================\n"
+
+sim_3tcm fdg.par sim1/plasma.bld none sim1/tissue.bld
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
+printf "=====================================================================\n"
+printf "Simulating time frames \n"
+printf "=====================================================================\n"
+
+simframe sim1/plasma.bld frames.sif sim1/plasma.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+simframe sim1/tissue.bld frames.sif sim1/tissue.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+tacren sim1/plasma.tac 0 blood true
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+tacren sim1/tissue.tac 0 myocardium true
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
+printf "=====================================================================\n"
+printf "Simulating dynamic FDG PET image of mouse heart \n"
+printf "=====================================================================\n"
+
+tacadd -ovr sim1/pet.tac sim1/tissue.tac sim1/plasma.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+simimyoc -3D -FWHM=2 -diameter=3 -diamin=1 -thickness=2 -pxlsize=0.25 -dim=64 sim1/pet.tac sim1/pet.v
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
+imgki -v=sim1/patlak_ic.v -thr=1 sim1/plasma.tac sim1/pet.v 10 sim1/patlak_ki.v
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
+
+printf "=====================================================================\n"
+printf "Make mask ROIs \n"
+printf "=====================================================================\n"
+
+imgthrs -mask=sim1/mask_heart.v sim1/pet.v 50 100
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+imgthrs -mask=sim1/mask_cavity.v -start=0 -end=5 sim1/pet.v 80 100
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+imgthrs -mask=sim1/mask_myocardium.v -start=50 -end=60 sim1/pet.v 90 100
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+img2tif sim1/mask_heart.v
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+img2tif sim1/mask_cavity.v
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+img2tif sim1/mask_myocardium.v
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
+printf "=====================================================================\n"
+printf "Calculate ROI TACs and plot with correct TACs \n"
+printf "=====================================================================\n"
+
+img2dft sim1/pet.v sim1/mask_myocardium.v sim1/mask_myocardium.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+img2dft sim1/pet.v sim1/mask_heart.v sim1/mask_heart.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+img2dft sim1/pet.v sim1/mask_cavity.v sim1/mask_cavity.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+tacren sim1/mask_myocardium.tac 0 myocardium from image
+tacren sim1/mask_heart.tac 0 heart from image
+tacren sim1/mask_cavity.tac 0 cavity from image
+tac2svg -legend=y -mt="" sim1/tacs.svg sim1/plasma.tac sim1/tissue.tac sim1/mask_cavity.tac sim1/mask_myocardium.tac sim1/mask_heart.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
+printf "=====================================================================\n"
+printf "Do not use simulated image but just mix blood and tissue \n"
+printf "=====================================================================\n"
+
+taccalc sim1/tissue.tac x 0.9 sim1/temp1.tac
+taccalc sim1/plasma.tac x 0.1 sim1/temp2.tac
+taccalc sim1/temp1.tac + sim1/temp2.tac sim1/mix09.tac
+tacren sim1/mix09.tac 0 m90b10
+
+taccalc sim1/tissue.tac x 0.8 sim1/temp1.tac
+taccalc sim1/plasma.tac x 0.2 sim1/temp2.tac
+taccalc sim1/temp1.tac + sim1/temp2.tac sim1/mix08.tac
+tacren sim1/mix08.tac 0 m80b20
+
+taccalc sim1/tissue.tac x 0.7 sim1/temp1.tac
+taccalc sim1/plasma.tac x 0.3 sim1/temp2.tac
+taccalc sim1/temp1.tac + sim1/temp2.tac sim1/mix07.tac
+tacren sim1/mix07.tac 0 m70b30
+
+taccalc sim1/tissue.tac x 0.6 sim1/temp1.tac
+taccalc sim1/plasma.tac x 0.4 sim1/temp2.tac
+taccalc sim1/temp1.tac + sim1/temp2.tac sim1/mix06.tac
+tacren sim1/mix06.tac 0 m60b40
+
+taccalc sim1/tissue.tac x 0.5 sim1/temp1.tac
+taccalc sim1/plasma.tac x 0.5 sim1/temp2.tac
+taccalc sim1/temp1.tac + sim1/temp2.tac sim1/mix05.tac
+tacren sim1/mix05.tac 0 m50b50
+
+taccalc sim1/tissue.tac x 0.4 sim1/temp1.tac
+taccalc sim1/plasma.tac x 0.6 sim1/temp2.tac
+taccalc sim1/temp1.tac + sim1/temp2.tac sim1/mix04.tac
+tacren sim1/mix04.tac 0 m40b60
+
+taccalc sim1/tissue.tac x 0.3 sim1/temp1.tac
+taccalc sim1/plasma.tac x 0.7 sim1/temp2.tac
+taccalc sim1/temp1.tac + sim1/temp2.tac sim1/mix03.tac
+tacren sim1/mix03.tac 0 m30b70
+
+taccalc sim1/tissue.tac x 0.2 sim1/temp1.tac
+taccalc sim1/plasma.tac x 0.8 sim1/temp2.tac
+taccalc sim1/temp1.tac + sim1/temp2.tac sim1/mix02.tac
+tacren sim1/mix02.tac 0 m20b80
+
+taccalc sim1/tissue.tac x 0.1 sim1/temp1.tac
+taccalc sim1/plasma.tac x 0.9 sim1/temp2.tac
+taccalc sim1/temp1.tac + sim1/temp2.tac sim1/mix01.tac
+tacren sim1/mix01.tac 0 m10b90
+
+tacadd sim1/mixed.tac sim1/mix0?.tac sim1/tissue.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+tacren sim1/mixed.tac 10 m100
+
+tac2svg -legend=y -mt="" sim1/mixed.svg sim1/mixed.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
+patlak -svg=sim1/mixed_patlak.svg -sd=no sim1/mixed.tac sim1/plasma.tac 10 60 sim1/mixed_patlak.res
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
+
+printf "\n===================================================================\n"
+printf "   All passed! \n"
+printf "===================================================================\n"
+exit 0
+