FRAGSTATS accepts raster images in a variety of formats, including ArcGrid, ASCII, BINARY, ERDAS, and IDRISI image files.Also it indicates it will accept 16 bit rasters, and will convert the data to 32 bit when exported to avoid losing data. Further down, it appears that FragStats will also accept .img files. Per their help,
FRAGSTATS accepts .gis, .lan, and .img files used by current versions of ERDAS IMAGINE, including signed 8-, 16-, and 32-bit integer grids.