If you have a ipod you know it can’t play FLAC files. If you still want lossless quality music you’ll have to convert it to ALAC. This can be done very easily with ffmpeg. Here is how to do it:

ffmpeg -i input_flac_file -acodec alac outputfile.m4a

Here is a script to convert all flac files in a directory to alac.

#!/bin/bash
#get all flac files in a directory
#loop over all files
#get file name without extention
#run it through ffmpeg with the output file as the filename.m4a

for file in *flac
do 
  basename=`basename "$file" .flac`
  ffmpeg -i "$file" -acodec alac "$basename".m4a;
done