diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
index 22fb0b72..8710e694 100644
--- a/fmriprep/workflows/base.py
+++ b/fmriprep/workflows/base.py
@@ -580,9 +580,18 @@ def init_single_subject_wf(subject_id: str):
             suffices = [s.suffix for s in estimator.sources]
 
             if estimator.method == fm.EstimatorType.PEPOLAR:
+                # "Sophisticated" PEPOLAR schemes should be run "manually" with SDCFlows
+                # The following two cases are not considered sophisticated:
+                # 1. All PEPOLAR entities are the same modality
+                #    (typically, more than two EPI PE directions), or
+                # 2. Two modalities are involved, with at most two images to pass
+                #    into FSL TOPUP.
                 if (
                     len(set(suffices)) == 1
-                    or (len(suffices) == 2 and all(suf in ('epi', 'bold', 'sbref') for suf in suffices))
+                    or (
+                        len(suffices) == 2
+                        and all(suf in ('epi', 'bold', 'sbref') for suf in suffices)
+                    )
                 ):
                     wf_inputs = getattr(fmap_wf.inputs, f'in_{estimator.bids_id}')
                     wf_inputs.in_data = [str(s.path) for s in estimator.sources]