fmriprep anat placement is unintuitive with multiple sessions #1068
fmriprep places T1w files in different places depending on the number of T1w images across sessions. If there are multiple T1w images, fmriprep averages them and creates a top level "anat" folder to store the average. When only one session has a T1w image, no top-level folder is created.
(folder structure if ses-1 and ses-2 had a T1w image):
(folder structure if only ses-1 had a T1w image):
Considering that both sessions are referencing the same T1w image regardless, I think it'd make sense to move the T1w image to a top level anat folder in the second case.