added simulations on the effect of Vb and integration time

renal_perfusion/perfrat/sim.sh

 #!/bin/bash
 #: Title      : Basic error simulation for perfusion ratio
-#: Date       : 2019-03-09
+#: Date       : 2019-03-13
 #: Author     : "Vesa Oikonen" <vesa.oikonen@utu.fi>
 #: Options    : None
 
@@ -80,6 +80,32 @@ tac2svg -mt="" -x2=120 -legend=y sim/rbf_ttacs200.svg -l sim/renal200.tac
 if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
 
 
+printf "  Simulate also without vascular contribution \n"
+
+b2t_h2o -nosub -fpt -voiname=f400 sim/blood.tac 400 0.94 1.0 0 20 sim/renal400vb0.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+b2t_h2o -add -nosub -fpt -voiname=f380 sim/blood.tac 380 0.94 1.0 0 20 sim/renal400vb0.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+b2t_h2o -add -nosub -fpt -voiname=f360 sim/blood.tac 360 0.94 1.0 0 20 sim/renal400vb0.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+b2t_h2o -add -nosub -fpt -voiname=f320 sim/blood.tac 320 0.94 1.0 0 20 sim/renal400vb0.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+b2t_h2o -add -nosub -fpt -voiname=f280 sim/blood.tac 280 0.94 1.0 0 20 sim/renal400vb0.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+b2t_h2o -add -nosub -fpt -voiname=f240 sim/blood.tac 240 0.94 1.0 0 20 sim/renal400vb0.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+b2t_h2o -add -nosub -fpt -voiname=f200 sim/blood.tac 200 0.94 1.0 0 20 sim/renal400vb0.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+b2t_h2o -add -nosub -fpt -voiname=f160 sim/blood.tac 160 0.94 1.0 0 20 sim/renal400vb0.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+b2t_h2o -add -nosub -fpt -voiname=f120 sim/blood.tac 120 0.94 1.0 0 20 sim/renal400vb0.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+b2t_h2o -add -nosub -fpt -voiname=f80  sim/blood.tac  80 0.94 1.0 0 20 sim/renal400vb0.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+b2t_h2o -add -nosub -fpt -voiname=f40  sim/blood.tac  40 0.94 1.0 0 20 sim/renal400vb0.tac
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
+
 printf "\n=====================================================================\n"
 printf "  Make plot of TTACs with very wide range of renal perfusion values \n"
 printf "=====================================================================\n"
@@ -125,6 +151,18 @@ if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
 perfrat sim/renal200.tac f200 sim/renal200.par
 if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
 
+printf "\n  Calculate perfusion ratios with Vb 0 \n"
+
+perfrat sim/renal400vb0.tac f400 sim/renal400vb0.par
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
+printf "\n  Calculate perfusion ratios with extended (p) or shortened (n) time \n"
+
+perfrat -etime=5 sim/renal400.tac f400 sim/renal400etp5.par
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+perfrat -etime=-5 sim/renal400.tac f400 sim/renal400etn5.par
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
 
 printf "\n=====================================================================\n"
 printf "  Plot the results \n"
@@ -148,6 +186,31 @@ if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
 tac2svg -legend=n -mt="" -xt="Perfusion" -yt="Perfusion ratio" sim/rbf_pr200.svg -l sim/c200.dat -b sim/res200.dat
 if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
 
+printf "\n  Compare the PR with and without Vb \n"
+
+tacformat -f=tsv sim/renal400vb0.par sim/res400vb0.dat
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+tacsetx sim/res400vb0.dat sim/x400.dat 1
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+tac2svg -legend=n -mt="" -xt="Perfusion" -yt="Perfusion ratio" sim/rbf_pr400vb.svg -l sim/c400.dat -b sim/res400.dat sim/res400vb0.dat
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
+
+printf "\n  Compare with extended (p) or shortened (n) time \n"
+
+tacformat -f=tsv sim/renal400etp5.par sim/res400etp5.dat
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+tacsetx sim/res400etp5.dat sim/x400.dat 1
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
+tacformat -f=tsv sim/renal400etn5.par sim/res400etn5.dat
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+tacsetx sim/res400etn5.dat sim/x400.dat 1
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
+tac2svg -legend=n -mt="" -xt="Perfusion" -yt="Perfusion ratio" sim/rbf_pr400et.svg -l sim/c400.dat -b sim/res400.dat sim/res400etp5.dat sim/res400etn5.dat
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+
 
 
 printf "\n===================================================================\n"