diff --git a/ScaFFold/cli.py b/ScaFFold/cli.py
index 2caf981..82532fe 100644
--- a/ScaFFold/cli.py
+++ b/ScaFFold/cli.py
@@ -177,6 +177,24 @@ def main():
                 print(f"Overriding '{key}={combined_config[key]}' with '{key}={value}'")
                 combined_config[key] = value
 
+        # Recalculate unet_layers to capture any CLI overrides
+        combined_config["unet_layers"] = (
+            combined_config["problem_scale"]
+            - combined_config["unet_bottleneck_dim"]
+            + 1
+        )
+
+        # Resolve paths to absolute, matching Config() behavior
+        if "base_run_dir" in combined_config and combined_config["base_run_dir"]:
+            combined_config["base_run_dir"] = str(
+                Path(combined_config["base_run_dir"]).resolve()
+            )
+
+        if "dataset_dir" in combined_config and combined_config["dataset_dir"]:
+            combined_config["dataset_dir"] = str(
+                Path(combined_config["dataset_dir"]).resolve()
+            )
+
         # Calculate these variables after override
         combined_config["vol_size"] = pow(2, combined_config["problem_scale"])
         combined_config["point_num"] = int(combined_config["vol_size"] ** 3 / 256)