diff --git a/qsiprep/interfaces/dwi_merge.py b/qsiprep/interfaces/dwi_merge.py
index 45b6a39c..1aed654a 100644
--- a/qsiprep/interfaces/dwi_merge.py
+++ b/qsiprep/interfaces/dwi_merge.py
@@ -83,7 +83,7 @@ def _run_interface(self, runtime):
         # Create a merged metadata json file for
         if isdefined(self.inputs.scan_metadata):
             combined_metadata = combine_metadata(
-                self.inputs.dwi_files,
+                self.inputs.bids_dwi_files,
                 self.inputs.scan_metadata,
             )
             merged_metadata_file = op.join(runtime.cwd, "merged_metadata.json")
diff --git a/qsiprep/workflows/dwi/fsl.py b/qsiprep/workflows/dwi/fsl.py
index ec7752fd..4382f0fb 100644
--- a/qsiprep/workflows/dwi/fsl.py
+++ b/qsiprep/workflows/dwi/fsl.py
@@ -168,10 +168,6 @@ def init_fsl_hmc_wf(
     )
 
     workflow = Workflow(name=name)
-    gather_inputs = pe.Node(
-        GatherEddyInputs(b0_threshold=b0_threshold, raw_image_sdc=raw_image_sdc),
-        name="gather_inputs",
-    )
     if eddy_config is None:
         # load from the defaults
         eddy_cfg_file = pkgr_fn("qsiprep.data", "eddy_params.json")
@@ -180,6 +176,13 @@ def init_fsl_hmc_wf(
 
     with open(eddy_cfg_file, "r") as f:
         eddy_args = json.load(f)
+
+    gather_inputs = pe.Node(
+        GatherEddyInputs(
+            b0_threshold=b0_threshold, raw_image_sdc=raw_image_sdc, eddy_config=eddy_cfg_file
+        ),
+        name="gather_inputs",
+    )
     enhance_pre_sdc = pe.Node(EnhanceB0(), name="enhance_pre_sdc")
 
     # Run in parallel if possible