--- a
+++ b/hd_glio/hd_glio_predict.py
@@ -0,0 +1,64 @@
+#    Copyright 2019 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
+#
+#    Licensed under the Apache License, Version 2.0 (the "License");
+#    you may not use this file except in compliance with the License.
+#    You may obtain a copy of the License at
+#
+#        http://www.apache.org/licenses/LICENSE-2.0
+#
+#    Unless required by applicable law or agreed to in writing, software
+#    distributed under the License is distributed on an "AS IS" BASIS,
+#    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#    See the License for the specific language governing permissions and
+#    limitations under the License.
+
+from hd_glio.utils import blockPrint, enablePrint
+blockPrint()
+from nnunet.inference.predict import predict_cases
+enablePrint()
+import argparse
+from hd_glio.paths import folder_with_parameter_files
+from hd_glio.setup_hd_glio import maybe_download_weights
+
+
+def main():
+    parser = argparse.ArgumentParser(description="This script will allow you to predict a single case with hd_glio. "
+                                                 "If you have multiple cases, please use hd_glio_predict_folder (this one "
+                                                 "will be substantially faster for multiple cases because we can "
+                                                 "interleave preprocessing, GPU prediction and nifti export."
+                                                 "\n"
+                                                 "IMPORTANT!\n"
+                                                 "The input files must be brain extracted with the non-brain region being "
+                                                 "0 (you can achieve that by using hd-bet "
+                                                 "(https://github.com/MIC-DKFZ/HD-BET). Furthermore, the input files "
+                                                 "must be co-registered and in the same co-ordinate system (pixels "
+                                                 "arrays must be aligned)\n"
+                                                 "All input files must be niftis (.nii.gz)")
+
+    parser.add_argument("-t1", type=str, required=True,
+                        help="T1 input file")
+    parser.add_argument("-t1c", type=str, required=True,
+                        help="T1c input file")
+    parser.add_argument("-t2", type=str, required=True,
+                        help="T2 input file")
+    parser.add_argument("-flair", type=str, required=True,
+                        help="FLAIR input file")
+
+    parser.add_argument("-o", "--output_file", type=str, required=True,
+                        help="output filename. Must end with .nii.gz")
+
+    args = parser.parse_args()
+    t1 = args.t1
+    t1c = args.t1c
+    t2 = args.t2
+    flair = args.flair
+    output_file = args.output_file
+
+    maybe_download_weights()
+
+    predict_cases(folder_with_parameter_files, [[t1, t1c, t2, flair]], [output_file], (0, ), False, 1, 1, None, True,
+                  None, True, checkpoint_name="model_final_checkpoint")
+
+
+if __name__ == "__main__":
+    main()