A bash shell script using ffmpeg to encode all the .mov files in the current directory to Motion-Jpeg, to use in MaxMSP/Jitter.

vj.sh

#!/bin/bash
# Script using ffmpeg to convert all the .mov files in the current
# directory to "Motion Jpeg".mov codec

# Remember to $chmod 
                      
for ff in *.mov; 
do
    filename=$(basename $ff)
    extension=${filename##*.}
    filename=${filename%.*}
    mkdir converted
  #echo "ffmpeg -i ${ff} -an -pix_fmt yuvj420p -vcodec mjpeg -f mov -y ${filename}vj.mov" # test
	ffmpeg -i ${ff} -an -pix_fmt yuvj420p -vcodec mjpeg -f mov -y converted/${filename}vj.mov
done