I recently needed to convert some Apple Lossless music files to FLAC. Here’s how to do it:

If you don’t already have ffmpeg or libav-tools installed, do this:

$ sudo apt-get install libav-tools

Then run this to do the conversion, in the folder with music in:

$ for f in *.m4a; do avconv -i "$f" "${f%.m4a}.flac"; done

And that’s it - it will convert all the .m4a files in that folder to .flac files, preserving the metadata. You can now delete the .m4a files if you want:

$ rm ./*.m4a