I think in the latest versions (since 1.4(?)) it is possible to specify the native EPI as the desired output space. The option is:
“–output-spaces func”.
However, I previously ran into a bug doing this, and I needed to specify an additional template to get around it (see my previous issue Error in "native" EPI space processing (--output-spaces func))
Perhaps try the “–output-spaces func” option and see how you go…
Dror