Merge pull request #2692 from effigies/fix/multi_syn_atlases

FIX: Create single fmap_select_std node for use with all ANAT estimators
nipreps · Jan 20, 2022 · 32dac40 · 32dac40
2 parents 2530ea8 + f68ece8
commit 32dac40
Showing 1 changed file with 19 additions and 12 deletions.
diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
@@ -429,7 +429,25 @@ def init_single_subject_wf(subject_id):
         if node.split(".")[-1].startswith("ds_"):
             fmap_wf.get_node(node).interface.out_path_base = ""
 
-    # Step 3: Manually connect PEPOLAR
+    # Step 3: Manually connect PEPOLAR and ANAT workflows
+
+    # Select "MNI152NLin2009cAsym" from standard references.
+    # This node may be used by multiple ANAT estimators, so define outside loop.
+    from niworkflows.interfaces.utility import KeySelect
+    fmap_select_std = pe.Node(
+        KeySelect(fields=["std2anat_xfm"], key="MNI152NLin2009cAsym"),
+        name="fmap_select_std",
+        run_without_submitting=True,
+    )
+    if any(estimator.method == fm.EstimatorType.ANAT for estimator in fmap_estimators):
+        # fmt:off
+        workflow.connect([
+            (anat_preproc_wf, fmap_select_std, [
+                ("outputnode.std2anat_xfm", "std2anat_xfm"),
+                ("outputnode.template", "keys")]),
+        ])
+        # fmt:on
+
     for estimator in fmap_estimators:
         config.loggers.workflow.info(f"""\
 Setting-up fieldmap "{estimator.bids_id}" ({estimator.method}) with \
@@ -455,7 +473,6 @@ def init_single_subject_wf(subject_id):
                 )
 
         elif estimator.method == fm.EstimatorType.ANAT:
-            from niworkflows.interfaces.utility import KeySelect
             from sdcflows.workflows.fit.syn import init_syn_preprocessing_wf
 
             sources = [str(s.path) for s in estimator.sources if s.suffix == "bold"]
@@ -470,18 +487,8 @@ def init_single_subject_wf(subject_id):
             syn_preprocessing_wf.inputs.inputnode.in_epis = sources
             syn_preprocessing_wf.inputs.inputnode.in_meta = source_meta
 
-            # Select "MNI152NLin2009cAsym" from standard references.
-            fmap_select_std = pe.Node(
-                KeySelect(fields=["std2anat_xfm"], key="MNI152NLin2009cAsym"),
-                name="fmap_select_std",
-                run_without_submitting=True,
-            )
-
             # fmt:off
             workflow.connect([
-                (anat_preproc_wf, fmap_select_std, [
-                    ("outputnode.std2anat_xfm", "std2anat_xfm"),
-                    ("outputnode.template", "keys")]),
                 (anat_preproc_wf, syn_preprocessing_wf, [
                     ("outputnode.t1w_preproc", "inputnode.in_anat"),
                     ("outputnode.t1w_mask", "inputnode.mask_anat"),