diff --git a/xcp_d/cli/run.py b/xcp_d/cli/run.py
index 424db9da0..a4aacb2c4 100644
--- a/xcp_d/cli/run.py
+++ b/xcp_d/cli/run.py
@@ -309,7 +309,7 @@ def main():
             packagename="xcp_d",
         )
         write_derivative_description(
-            config.execution.bids_dir,
+            config.execution.fmri_dir,
             config.execution.output_dir / "xcp_d",
         )
 
diff --git a/xcp_d/cli/workflow.py b/xcp_d/cli/workflow.py
index 433aeb885..83ede94b1 100644
--- a/xcp_d/cli/workflow.py
+++ b/xcp_d/cli/workflow.py
@@ -36,7 +36,7 @@ def build_workflow(config_file, retval):
         build_log.warning(msg)
 
     # Please note this is the input folder's dataset_description.json
-    dset_desc_path = config.execution.bids_dir / "dataset_description.json"
+    dset_desc_path = config.execution.fmri_dir / "dataset_description.json"
     if dset_desc_path.exists():
         from hashlib import sha256
 
@@ -95,7 +95,7 @@ def build_workflow(config_file, retval):
     # Build main workflow
     init_msg = f"""
     Running XCP-D version {config.environment.version}:
-      * BIDS dataset path: {config.execution.bids_dir}.
+      * BIDS dataset path: {config.execution.fmri_dir}.
       * Participant list: {subject_list}.
       * Run identifier: {config.execution.run_uuid}.
       * Output spaces: {config.execution.output_spaces}."""
diff --git a/xcp_d/config.py b/xcp_d/config.py
index 9ef3a57c0..1ef84ce40 100644
--- a/xcp_d/config.py
+++ b/xcp_d/config.py
@@ -445,7 +445,7 @@ def init(cls):
                 ),
             )
             cls._layout = BIDSLayout(
-                str(cls.bids_dir),
+                str(cls.fmri_dir),
                 database_path=_db_path,
                 reset_database=True,
                 indexer=_indexer,