I’ve been looking into this. I didn’t see the scaling issue with
--bold2t1w-dof 6, but the alignment is still not great (see report), and that seems to be due to low gray/white contrast in your BOLD series.
We try to use non-steady-state volumes, or the median of several volumes, to establish the reference BOLD image, but there really just doesn’t seem to be enough contrast here. There are a couple approaches we’ve been considering to better handle BOLD series that don’t produce good reference images (#253 and #620), but neither is ready to go.
If you threw away non-steady-state volumes from your BOLD series before passing them to FMRIPREP, you should try restoring those volumes. Otherwise, I can only suggest trying to get higher-contrast images with your future acquisitions. We don’t currently support single-band reference images, but that would be a relatively minor fix, if there’s no way to improve the contrast in the acquired BOLD series.