cd <directory with 6000 files>
md new
for %i in (*.jpg) do convert <switches> %i new\%i
That's for DOS (Windows command line). Linux would be similar in idea.
I don't know what switches specifically to use, but check help on "convert". I bet -size would do it.
**EDIT**
Just saw your gentoo comment
cd <directory with 6000 files>
mkdir new
for i in *.jpg; do convert <switches> $i new/$i; done;
Same disclaimer about the switches.