Update README.md

README.md

@@ -1,3 +1,47 @@
 ---
 license: apache-2.0
 ---
+# Instructions
+
+### 1-Download
+Download the singularity container.
+```
+wget https://huggingface.co/qicq1c/SuPreM/resolve/main/suprem_final.sif
+```
+### 2-Data preparation
+This is how `inputs_data` organizes
+```
+    $inputs_data/
+    ├── casename00001
+    │   └── ct.nii.gz
+    ├── casename00002
+    │   └── ct.nii.gz
+    ├── casename00003
+    │   └── ct.nii.gz
+    ...
+```
+
+### 3-Inference
+You can directly perform inference on your own data. Simply modify `inputs_data` into your data path and adjust `outputs_data` to specify the desired output location for the segmentation results.
+```
+SINGULARITYENV_CUDA_VISIBLE_DEVICES=0 singularity run --nv -B $inputs_data:/workspace/inputs -B $outputs_data:/workspace/outputs suprem_final.sif
+```
+
+This is how `outputs_data` organizes
+```
+    $outputs_data/
+    ├── case00001
+    ├── case00002
+    ├── case00003
+        │── combined_labels.nii.gz
+        └── segmentations
+            ├── aorta.nii.gz
+            ├── gall_bladder.nii.gz
+            ├── kidney_left.nii.gz
+            ├── kidney_right.nii.gz
+            ├── liver.nii.gz
+            ├── pancreas.nii.gz
+            ├── postcava.nii.gz
+            ├── spleen.nii.gz
+            ├── stomach.nii.gz
+```