You can you imagemagick to do this. Here are some examples from product manual:
convert rose: rose.gif convert rose: -crop 40x30+10+10 crop.gif convert rose: -crop 40x30+40+30 crop_br.gif convert rose: -crop 40x30-10-10 crop_tl.gif convert rose: -crop 90x60-10-10 crop_all.gif convert rose: -crop 40x30+90+60 crop_miss.gif
And one sample loop can exec it for all the images. Something like:
for i in `ls in\` do convert $i -crop 40x30+10+10 out/`basename $i` done
Above i assume in files are in directory in/ and out files will be stored in directory out/