Hi Andreas,

the only difference between rest.nii.gz and rest_res.nii.gz orientation-wise, might be that rest.nii.gz is in RAI or ASL (or some other scanner-specific orientation), while rest_res.nii.gz has been oriented to RPI.

We apply the (re)orientation to RPI to both the anatomical and functional scan to make sure we are operating in the same (subject-) orientation. However, this should not be a problem for subject space calculations (in fact we try to use subject space calculations whenever possible). I would suggest to just reorient your grey-matter masks to RPI (or derive it from head.nii.gz which is the mprage.nii.gz reoriented to RPI).

Let me know if this is not working for you!
Maarten