Update app.py

app.py

@@ -165,6 +165,21 @@ def run_nnunet_predict(nifti_file):
     input_path = os.path.join(INPUT_DIR, "image_0000.nii.gz")
     os.rename(nifti_file.name, input_path)  # Move the uploaded file to the expected input location
     
+    # Apply skull-stripping with HD-BET
+    hd_bet_output_path = os.path.join(INPUT_DIR, "image_0000_stripped.nii.gz")
+    try:
+       subprocess.run([
+        "hd-bet",
+        "-i", input_path,
+        "-o", hd_bet_output_path,
+        "-device", "cpu",  # or "cuda" if available
+        "-mode", "fast"
+        ], check=True)
+        print("Skull-stripping completed.")
+        input_path = hd_bet_output_path
+    except subprocess.CalledProcessError as e:
+        return f"HD-BET Error: {e}"
+    
     # Debugging: List files in the /tmp/input directory
     print("Files in /tmp/input:")
     print(os.listdir(INPUT_DIR))