skip anatomical metrics when running on anatomical fast track derivat…

…ives

giga_auto_qc/assessments.py

@@ -334,6 +334,12 @@ def calculate_anat_metrics(
     """
     if verbose > 0:
         print("Calculate the anatomical dice score.")
+    # check if the derivative was created with anatomical fast-track
+    check_anat = fmriprep_bids_layout.get(datatype="anat", return_type="file")
+    if not check_anat:
+        print("`anat/` not present in the derivatives. " "Skip anatomical QC.")
+        return pd.DataFrame()
+
     metrics = {}
     for sub in tqdm(subjects):
         anat_filter = {

giga_auto_qc/workflow.py

@@ -51,6 +51,12 @@ def workflow(args):
         derivatives=True,
         reset_database=args.reindex_bids,
     )
+    if fmriprep_bids_layout is None:
+        raise ValueError(
+            f"Cannot index directory in {bids_dir}. "
+            "Please ensure the path is a fMRIPrep output directory."
+        )
+
     # check output path
     output_dir.mkdir(parents=True, exist_ok=True)