afni.nimh.nih.gov

Thanks! That gave similar results. But I had to use the -cm option in the @AlignCenters functions, otherwise the brain stays where it was in space (e.g. low in y-dim). Perhaps due to the native images having its center at the matrix center? Anyways, this worked:

for i in * ; do

@Align_Centers -cm -base $template -dset $i -prefix ../$out_dir/temp_$i

3dresample -master $template -inset ../$out_dir/temp_$i -prefix ../$out_dir/$i

rm ../$out_dir/temp_$i

done

Thanks =)