Suppose you have a sub-pipeline:

$ recon-all -s $SUBJ -i $T1 -all

$ bbregister --s $SUBJ --mov $EPI --init-fsl --t2 --reg bbreg.dat --fslmat fsl.mat

Now `bbreg.dat`/`fsl.mat` is registered to `$SUBJECTS_DIR/$SUBJ/mri/T1.mgz`; what's the best way to register to $T1?

I've tried:

$ tkregister2 --no-edit --mov $EPI --reg bbreg.dat --targ $T1 --fslregout adjusted.mat

And that's clearly wrong, but I'm kind of stuck on where to go from here. Anybody see where I'm going wrong?

Thanks,

Chris