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<!--
Tutorial for specifying simulation parameters for the tumor simulation software
 -->

<!--
We begin with a beginning element for the set of simulation parameters
-->
<tumor-simulation-parameters>

<!-- The name of the dataset, will be used as prefix in the output files -->
<dataset-name>SimTumor00T</dataset-name>

<!--
Input directory, the location of the uncompressed directory, obtained
from TumorSimInput.zip
For Windows, use something such as C:/scratch/TumorSim/TumorSimInput
-->
<input-directory>/scratch/TumorSim/TumorSimInput</input-directory>

<!--
Where to store all output files
-->
<output-directory>/scratch/TumorSim/Output00T</output-directory>

<!--
Location of the binary image containing the manually drawn tumor seed,
must be in the same space as the anatomical labels in the input directory
-->
<deformation-seed>/scratch/TumorSim/seed00T.mha</deformation-seed>

<!--
Parameters for mass effect simulation:
the number of iterations,
the initial pressure (in kPa),
and the parameter kappa for the von Mises-Fisher random distribution
  (larger kappa means smaller std dev)

We recommend initial pressure values around 2 kPa for stability
-->
<deformation-iterations>10</deformation-iterations>
<deformation-initial-pressure>2.5</deformation-initial-pressure>
<deformation-kappa>80.0</deformation-kappa>

<!--
Parameters for the infiltration:
the number of iterations,
the time step (values <= 2.0 is recommended),
and the early time that defines the starting point for edema
  (smaller means edema will form most of the infiltration)
-->
<infiltration-iterations>60</infiltration-iterations>
<infiltration-time-step>1.0</infiltration-time-step>
<infiltration-early-time>2.0</infiltration-early-time>

<!--
Parameters for the application of infiltration body forces:
the number of iterations,
and the coefficient lambda where each force is -del(infiltration)*lambda

lambda values between 5-10 generates moderate deformation
-->
<infiltration-body-force-iterations>2</infiltration-body-force-iterations>
<infiltration-body-force-coefficient>5.0</infiltration-body-force-coefficient>

<!-- Contrast enhancement type, can be: none, ring, or uniform -->
<contrast-enhancement-type>uniform</contrast-enhancement-type>

<!-- end of the simulation parameters element -->
</tumor-simulation-parameters>
