feat: Discover pre-computed fieldmaps

Author: effigies

fmriprep/utils/bids.py

@@ -95,6 +95,31 @@ def collect_derivatives(
     return derivs_cache
 
 
+def collect_fieldmaps(
+    derivatives_dir: Path,
+    entities: dict,
+    spec: dict | None = None,
+):
+    """Gather existing derivatives and compose a cache."""
+    if spec is None:
+        spec = json.loads(load_data.readable('fmap_spec.json').read_text())['queries']
+
+    fmap_cache = defaultdict(dict, {})
+    layout = _get_layout(derivatives_dir)
+
+    fmapids = layout.get_fmapids(**entities)
+
+    for fmapid in fmapids:
+        for k, q in spec['fieldmaps'].items():
+            query = {**entities, **q}
+            item = layout.get(return_type='filename', fmapid=fmapid, **query)
+            if not item:
+                continue
+            fmap_cache[fmapid][k] = item[0] if len(item) == 1 else item
+
+    return fmap_cache
+
+
 def write_bidsignore(deriv_dir):
     bids_ignore = (
         '*.html',

fmriprep/workflows/base.py

@@ -533,6 +533,18 @@ def init_single_subject_wf(subject_id: str):
     if config.workflow.anat_only:
         return clean_datasinks(workflow)
 
+    fmap_cache = {}
+    if config.execution.derivatives:
+        from fmriprep.utils.bids import collect_fieldmaps
+
+        for deriv_dir in config.execution.derivatives.values():
+            fmap_cache.update(
+                collect_fieldmaps(
+                    derivatives_dir=deriv_dir,
+                    entities={'subject': subject_id},
+                )
+            )
+
     fmap_estimators, estimator_map = map_fieldmap_estimation(
         layout=config.execution.layout,
         subject_id=subject_id,