started new simulation

bootstrap/demo1/blend_lvcav.fit

+FIT1        fit_sinf 0.6.19 (c) 2018 by Turku PET Centre
+Date:	2018-02-12 09:00:05
+Data file:	popinp\blend_lvcav.tac
+Data unit:	g/mL
+Time unit:	sec
+Nr of VOIs:	1
+Region Plane	Start	End	dataNr	WSS	parNr	Type	Parameters
+LV cav .	-2.092	290.000	1336	1.80E+004	8	0331	7.856170E+000	1.154150E+001	5.697422E+000	1.384451E-003	3.790469E+001	8.092264E-002	4.240644E+000	9.999998E+001

bootstrap/demo1/sim1.sh

+#!/bin/bash
+#: Title      : Very simple demonstration of bootstrapping radiowater PET data
+#: Date       : 2019-09-13
+#: Author     : "Vesa Oikonen" <vesa.oikonen@utu.fi>
+#: Options    : None
+
+
+printf "\n=====================================================================\n"
+printf "  Making or emptying result folder\n"
+if [ ! -d sim ]; then
+  mkdir sim
+else
+  rm -f sim/*
+fi
+
+
+printf "\n=====================================================================\n"
+printf "  Compute BTAC at 0.5 s sampling times \n"
+printf "=====================================================================\n\n"
+fit2dat -c=0,480,0.5 blend_lvcav.fit sim/blood.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+tacren --silent sim/blood.tac 1 blood_artery
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+tacstudy --force sim/blood.tac sim1
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
+printf "\n=====================================================================\n"
+printf "  Simulate GM TTAC \n"
+printf "=====================================================================\n\n"
+
+b2t_h2o -nosub -fpt -voiname="GM" sim/blood.tac 50 1.00 1.0 0 0 sim/gm.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+tacstudy --force sim/gm.tac sim1
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
+tac2svg -mt="" -x2=300 -legend=y sim/cbf_gm_tac.svg -l sim/gm.tac sim/blood.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
+printf "\n=====================================================================\n"
+printf "  Simulate noise \n"
+printf "=====================================================================\n\n"
+
+# Remove decay correction
+tacdecay -decay=off -i=O-15 sim/gm.tac sim/gm_nondecaycorrected.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
+# Make noise realizations
+svar4tac -minsd=0.2 -x=10 sim/gm_nondecaycorrected.tac 20 sim/gm_nondecaycorrected_noisy.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
+tac2svg -mt="Noisy simulated TTACs" -legend=n sim/gm_nondecaycorrected_noisy.svg -l sim/gm_nondecaycorrected_noisy.tac 
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
+printf "\n=====================================================================\n"
+printf "  Simulate frames \n"
+printf "=====================================================================\n\n"
+
+printf "9/13/2019 14:15:12 22 2 1 sim1 O-15\n" > sim/frames.sif
+printf "0 5\n" >> sim/frames.sif
+printf "5 10\n" >> sim/frames.sif
+printf "10 15\n" >> sim/frames.sif
+printf "15 20\n" >> sim/frames.sif
+printf "20 25\n" >> sim/frames.sif
+printf "25 30\n" >> sim/frames.sif
+printf "30 40\n" >> sim/frames.sif
+printf "40 50\n" >> sim/frames.sif
+printf "50 60\n" >> sim/frames.sif
+printf "60 80\n" >> sim/frames.sif
+printf "80 100\n" >> sim/frames.sif
+printf "100 120\n" >> sim/frames.sif
+printf "120 140\n" >> sim/frames.sif
+printf "140 160\n" >> sim/frames.sif
+printf "160 180\n" >> sim/frames.sif
+printf "180 210\n" >> sim/frames.sif
+printf "210 240\n" >> sim/frames.sif
+printf "240 270\n" >> sim/frames.sif
+printf "270 300\n" >> sim/frames.sif
+printf "300 330\n" >> sim/frames.sif
+printf "330 360\n" >> sim/frames.sif
+printf "360 420\n" >> sim/frames.sif
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
+simframe sim/gm_nondecaycorrected_noisy.tac sim/frames.sif sim/ttacs_nondecaycorrected.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
+# Correct for decay
+tacdecay -decay=on -i=O-15 sim/ttacs_nondecaycorrected.tac sim/ttacs.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
+tac2svg -mt="Noisy framed TTACs" -legend=n sim/ttacs.svg -l sim/ttacs.tac 
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
+
+printf "\n=====================================================================\n"
+printf "  Calculate perfusion using CM fit \n"
+printf "=====================================================================\n\n"
+
+fit_h2o -fpt -Vb=0 -delay=0 -k2 -fit=sim/cbf_sim1_fit_h2o.tac sim/blood.tac sim/ttacs.tac 999 sim/fit_h2o.par
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+tac2svg -mt="" -legend=y sim/cbf_sim1_fit_h2o.svg -s sim/ttacs.tac -l sim/cbf_sim1_fit_h2o.tac 
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
+
+
+printf "\n===================================================================\n"
+printf "   All done! \n"
+printf "===================================================================\n"
+exit 0
+