Awesome, thanks Doug!

For clarity, I got it working with:

bbregister --s <day1subjID> --mov <day1funcvol> --reg day1func-to-day1anat.lta --init-fsl --bold

bbregister --s <day2subjID> --mov <day2funcvol> --reg day2func-to-day2anat.lta --init-fsl --bold

bbregister --s <day2subjID> --mov $SUBJECTS_DIR/<day1subjID>/mri/brain.mgz --reg day1anat-to-day2anat.lta --init-fsl --t1

mri_concatenate_lta day1func-to-day1anat.lta day1anat-to-day2anat.lta test/day1func-to-day2anat.lta

mri_concatenate_lta -invert2 day1func-to-day2anat.lta day2func-to-day2anat.lta day1func-to-day2func.lta

mri_vol2vol --mov <day1funcvol> --targ <day2funcvol> --reg day1func-to-day2func.lta --o day1func-in-day2func.nii.gz

Cheers,

DB