Monte Carlo Command Line (MCCL) application

Getting the MCCL application

Download the application from GitHub:

• Download latest version for your operating system from Releases
• Once the zip file has been downloaded, extract or unzip contents
• The downloaded files include:
  • mc.exe - the MCCL executable on windows
  • mc - the MCCL executble on linux or OSX
  • infile_* - several sample input files
  • *.m, jsonlab folder - MATLAB scripts to enable viewing the results using MATLAB

Running a sample input file

The sample input files are named infile_*, where * indicates the source, tissue and detector definitions designated within the file. Note that the default source definition is a point source perpendicular to the tissue surface and when the infile has this source definition, it is not part of the name. For example, the infile "infile_one_layer_all_detectors.txt" designates a point source, one layer tissue and all detectors currently available.

To run on windows:

• Requirements: .NET Core 2.1 - download here
• Open a command window and set the current directory to the folder of the unzipped files
• Type: "mc.exe infile=infile_one_layer_all_detectors.txt"
• This sample infile only specifies 100 photons to be launched so should execute quickly
• Progress of the simulation should be seen on the screen (percentage complete)

To run on linux:

• Requirements: dotnet runtime 2.1 - instructions here
• Make a folder to put the download zip file "mkdir foldername"
• Download zip file and move to folder "mv MC_vx.x.xBeta.zip foldername"
• Set current directory to folder "cd foldername" and unzip files "unzip MC_vx.x.xBeta.zip"
• Make the MCCL an executable file "chmod 755 mc"
• To run sample infile "./mc infile=infile_one_layer_all_detectors.txt"
• Output to the screen will be similar to that shown in figure above will be displayed
• Output will be in folder named by infile "OutputName"
• To view plots of results using Matlab, see next section

Viewing the results using MATLAB

For both windows and linux:

• Requirements: MATLAB R2011b and higher
• After running a sample infile, a folder will be created in the current directory. For the infile described above, "infile_one_layer_all_detectors.txt", the folder will be named "one_layer_all_detectors"
• Bring up MATLAB and edit the script file load_results_script.m. Set "datanames = { ' one_layer_all_detectors' };" (see figure below) and save changes
• Execute this script by typing "load_results_script" at the MATLAB prompt
• Plots of the all detector results specified in the infile will come to the screen