SIMIND Simulation Scripts

The scripts contained in this repository are used to run SIMIND simulation on XCAT phantom data. The files are as follows:

• simind.smc controls the simulation parameters of the SIMIND Monte Carlo program. This file, however, is not to be editted by the user. Rather, once SIMIND is installed, one should use the change command to edit this file, which will automatically detect the simind.smc file in the current directory. It's important to understand every flag in this file by reading the SIMIND manual.

• run_one.sh is a bash script that runs a SIMIND simulation for a given organ of the XCAT phantom.

• run_all_organs.sh is a bash script that runs run_one.sh for a specified list of organs.

• run_all_lesions.sh is similar to the above.

• run_calibration.sh is similar to run_one.sh, but it doesn't save any data. It's primary purpose is to determine a calibration factor which allows one to convert from counts per second (cps) to MBq per mL (MBq/mL). This information is contained in line 128 of the output .res file. This can be done for any organ/lesion, though it is typically done with a small volume near the center of the object space.

• scattwin.win specifies the different energy windows of the Monte Carlo simulation. See the SIMIND user's manual.

• add_together.py is a python script that is used to add together the results of the many parallel simulation jobs. It is called during the run_one.sh script.