ini file can be edited using any standard text editor.
To easily create this file, run the GUI version Log2Phy_12. Log2Phy_12_Console gets all its setup information from the Log2Phy_12.ini file. Here is the help for the console version: You will need to modify the log2phy_12.ini file to determine the LOGICAL and PHYSICAL file name with full path. That way your MATLAB can just make an external call. You can, however, use Log2Phy_12_Console.exe so that you can run it in commandline. We cannot distribute the source for this utility.
