Fmriprep issue: bbregister rejected & brain upside down

[amhaun01]

Hi, I’ve been looking for help on a similar issue I think:

Fmriprep output badly misaligned?

Some more info: The affine matrices in the (input) niftis all are the same. These are relatively narrow-angle scans (back of the head). So I guess that makes the alignment harder. Here are means of the raw (pre-fmriprep) images: [rawbids] Here they are after: [preprocd] To my eye 3 of those are perfect, two are poor and one (the top left) is very bad. How do I track down the problem?

I am getting some badly misaligned EPIs. Headers look identical between the goods and the bads. Not sure where to start to figure it out..