Hi J, 

I did this for my own hand traced lesions using a bash script and FSL tools. This runs through all the lesions e.g. on the right side and flips them to the left side. I hope this helps!

Lucy

for subj in [list of participant codes which need flipping, e.g. all right lesions]
do
fslswapdim ${subj} -x y z ${subj}_flipped
done