ISO

ISO is the disk image format used for the PS2 versions of Persona 3 and Persona 4. Due to the games being printed on single-layer DVDs, a size limit of 4.7 GB exists for game ISOs.

UltraISO
There are many free programs that edit ISO files. However, a premium version of UltraISO is recommended for its reliablility.

PCSX2
For running the ISO, the PS2 Emulator PCSX2 is suggested. For recommended specs and settings, check this thread.