add simulation examples

README.md

@@ -23,3 +23,41 @@ docker run -i -t --network host dce-mri
 ```
 
 ## Simulation examples
+### Direct problem
+Inside the docker container:
+Create the vascularization
+
+```terminal
+mkdir /Output/no_tumor
+mkdir /Output/tumor
+cd /Output/no_tumor
+/build/Vascularization.out -x100 -y100 -z1 -V. -Irandom0 -R100 -X/Output/no_tumor/no_tumor.xml
+
+cd /Output/tumor
+/build/Vascularization.out -V/Output/no_tumor/no_tumor.xml -R10 -r7 -Tr15 -Tx25 -Ty25 -Tc10 -N -R100 -X/Output/tumor/tumor.xml
+```
+
+Compute the transport in the created vascularization
+```terminal
+cd /Output/tumor
+mkdir conc && cd conc
+/build/Vascularization.out -V../tumor.xml -Cupwind
+```
+
+### Inverse problem
+Inside the docker image
+
+```terminal
+cd /Output/tumor/
+mkdir inverse && cd inverse
+COMMAND="/build/VascularizationInverse.out"
+PREF="/Output/tumor/conc/markerMRI00"
+SUFF=".C.binary"
+
+for i in $(seq -f "%03g" 0 180)
+do
+  COMMAND="$COMMAND $PREF$i$SUFF"
+done
+
+$COMMAND
+```
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