Update README.md

README.md

@@ -24,9 +24,28 @@ source venv/bin/activate
 
 2. Install requirements:
 ```
-pip install -r requirements.txt
+pip install /path/to/clone/.
 ```
 
+## 🤖 How to use
+Use the following CLI command to register images
+```
+ddmr --fixed path/to/fixed_image.nii.gz --moving path/to/moving_image.nii.gz --outputdir path/to/output/dir -a <anatomy> --model <model> --gpu <gpu-number> --original-resolution
+```
+where:
+* anatomy: is the type of anatomy you want to register: B (brain) or L (liver)
+* model: is the model you want to use:
+    + BL-N (baseline with NCC)
+    + BL-NS (baseline with NCC and SSIM)
+    + SG-ND (segmentation guided with NCC and DSC)
+    + SG-NSD (segmentation guided with NCC, SSIM, and DSC)
+    + UW-NSD (uncertainty weighted with NCC, SSIM, and DSC)
+    + UW-NSDH (uncertainty weighted with NCC, SSIM, DSC, and HD).
+* gpu: is the GPU number you want to the model to run on, if you have multiple and want to use only one GPU
+* original-resolution: (flag) whether to upsample the registered image to the fixed image resolution (disabled if the flag is not present)
+
+Use ```ddmr --help``` to see additional options like using precomputed segmentations to crop the images to the desired ROI, or debugging.
+
 ## 🏋️‍♂️ Training
 
 Use the "MultiTrain" scripts to launch the trainings, providing the neccesary parameters. Those in the COMET folder accepts a .ini configuration file (see COMET/train_config_files for example configurations).