--- a
+++ b/scripts/commands/predict.py
@@ -0,0 +1,77 @@
+"""
+If you use this code, please cite one of the SynthSeg papers:
+https://github.com/BBillot/SynthSeg/blob/master/bibtex.bib
+
+Copyright 2020 Benjamin Billot
+
+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
+https://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.
+"""
+
+
+# imports
+from argparse import ArgumentParser
+from SynthSeg.predict import predict
+
+parser = ArgumentParser()
+
+# Positional arguments
+parser.add_argument("path_images", type=str, help="path single image or path of the folders with training labels")
+parser.add_argument("path_segmentations", type=str, help="segmentations folder/path")
+parser.add_argument("path_model", type=str, help="model file path")
+
+# labels parameters
+parser.add_argument("labels_segmentation", type=str, help="path label list")
+parser.add_argument("--neutral_labels", type=int, dest="n_neutral_labels", default=None)
+parser.add_argument("--names_list", type=str, dest="names_segmentation", default=None,
+                    help="path list of label names, only used if --vol is specified")
+
+# Saving paths
+parser.add_argument("--post", type=str, dest="path_posteriors", default=None, help="posteriors folder/path")
+parser.add_argument("--resampled", type=str, dest="path_resampled", default=None,
+                    help="path/folder of the images resampled at the given target resolution")
+parser.add_argument("--vol", type=str, dest="path_volumes", default=None, help="path volume file")
+
+# Processing parameters
+parser.add_argument("--min_pad", type=int, dest="min_pad", default=None,
+                    help="margin of the padding")
+parser.add_argument("--cropping", type=int, dest="cropping", default=None,
+                    help="crop volume before processing. Segmentations will have the same size as input image.")
+parser.add_argument("--target_res", type=float, dest="target_res", default=1.,
+                    help="Target resolution at which segmentations will be given.")
+parser.add_argument("--flip", action='store_true', dest="flip",
+                    help="to activate test-time augmentation (right/left flipping)")
+parser.add_argument("--topology_classes", type=str, dest="topology_classes", default=None,
+                    help="path list of classes, for topologically enhanced biggest connected component analysis")
+parser.add_argument("--smoothing", type=float, dest="sigma_smoothing", default=0.5,
+                    help="var for gaussian blurring of the posteriors")
+parser.add_argument("--biggest_component", action='store_true', dest="keep_biggest_component",
+                    help="only keep biggest component in segmentation (recommended)")
+
+# Architecture parameters
+parser.add_argument("--conv_size", type=int, dest="conv_size", default=3, help="size of unet convolution masks")
+parser.add_argument("--n_levels", type=int, dest="n_levels", default=5, help="number of levels for unet")
+parser.add_argument("--conv_per_level", type=int, dest="nb_conv_per_level", default=2, help="conv par level")
+parser.add_argument("--unet_feat", type=int, dest="unet_feat_count", default=24,
+                    help="number of features of unet first layer")
+parser.add_argument("--feat_mult", type=int, dest="feat_multiplier", default=2,
+                    help="factor of new feature maps per level")
+parser.add_argument("--activation", type=str, dest="activation", default='elu', help="activation function")
+
+# Evaluation parameters
+parser.add_argument("--gt", type=str, default=None, dest="gt_folder",
+                    help="folder containing ground truth segmentations, which triggers the evaluation.")
+parser.add_argument("--eval_label_list", type=str, dest="evaluation_labels", default=None,
+                    help="labels to evaluate Dice scores on if gt is provided. Default is the same as label_list.")
+parser.add_argument("--incorrect_labels", type=str, default=None, dest="list_incorrect_labels",
+                    help="path list labels to correct.")
+parser.add_argument("--correct_labels", type=str, default=None, dest="list_correct_labels",
+                    help="path list correct labels.")
+
+args = parser.parse_args()
+predict(**vars(args))