Different dimensions of anatomical scans cause error in anatomy preproc in fmriprep?

I have run fmriprep (version 1.5.8) on a large dataset in which scans were taken on two different MRI scanners.
I have noticed that all the participants from one scanner had an error;
Node Name: fmriprep_wf.single_subject_controlPS43_wf.anat_preproc_wf.t1w_dseg
I have realised that participants in the error group have a dimensions of 512x512x392 for T1w scans, whereas the group that had fmriprep run correctly had a dimension of 288x288176.
I was wondering whether running fmriprep on a group that has different dimensions of T1w anatomical scans would be causing the error in the anat_preproc workflow?

In which case, I would assume that running fmriprep on just the datasets of the same dimensions would work, or is there another way to specify the differences in dimensions?