Update README.md

README.md

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 # dice-score-3d
-Utility for calculating the Dice Similarity Coefficient (DSC) for 3D segmentation masks. 
+Utility for calculating the Dice Similarity Coefficient (DSC) for 3D segmentation masks. Writes the results in a csv or json file and can be used both from the terminal or from a Python script.
+
+## Installation
+
+```
+pip install --upgrade dice-score-3d
+```
+
+## Usage
+
+Simple usage (Python):
+```py
+from dice_score_3d import dice_metrics
+
+
+dice_metrics(gt_dir, pred_dir, output_path='results.csv',  indices={'lung': 1, 'heart': 2}, suffix='.nii.gz', num_workers=8)
+```
+
+Simple usage (terminal):
+```
+dice_score_3d GT.nii.gz PRED.nii.gz -output results.json -indices "{'lung': 1, 'heart': 2}" --console
+```
+
+Complete documentation:
+```
+usage: dice_score_3d [-h] -output OUTPUT -indices INDICES [--reorient] [-dtype {uint8,uint16}] [-prefix PREFIX] [-suffix SUFFIX] [-num_workers NUM_WORKERS] [--console]
+                     ground_truths predictions
+
+DICE Score 3D
+
+positional arguments:
+  ground_truths         Path to Ground Truth. Can be a single file or a folder with all the GT volumes. The number of GT files must match the number of predictions. When passing a     
+                        folder of GT files, the name of the GT files must match the name of the predictions. This is not applicable when passing a single file. Supported file
+                        formats: .nii, .nii.gz, .nrrd, .mha, .gipl.
+  predictions           Path to Ground Truth. Can be a single file or a folder with all the predicted volumes. The number of prediction files must match the number of GT files. When   
+                        passing a folder of prediction files, the name of the prediction files must match the name of the GT files. This is not applicable when passing a single file.  
+                        Supported file formats: .nii, .nii.gz, .nrrd, .mha, .gipl.
+
+options:
+  -h, --help            show this help message and exit
+  -output OUTPUT        The output path to write the computed metrics. Can be a csv or json file, depending on extension. Example: "results.csv", "results.json".
+  -indices INDICES      Path to the json file describing the indices used for calculating the Dice Similarity Coefficient. Can also be a json string. Only the indices present in the   
+                        json are considered when evaluating the Dice Score. Example: "{"lung_left": 1, "lung_right": 2}".
+  --reorient            Reorients both the GT and the prediction to the default "LPS" orientation before calculating the Dice Score.
+  -dtype {uint8,uint16}
+                        Must be either "uint8" when having less than 255 classes, or "uint16" otherwise. Default: uint8.
+  -prefix PREFIX        This parameter is used when the ground truth path is a folder. It filters all the files in the folder and selects only the files with this prefix.
+  -suffix SUFFIX        This parameter is used when the ground truth path is a folder. It filters all the files in the folder and selects only the files with this suffix. Default: .nii.gz.
+  -num_workers NUM_WORKERS
+                        Number of parallel processes to be used to calculate the Dice Score in parallel. Default: 0.
+  --console             Also prints the Dice metrics to console.
+```