Update README.md

README.md

@@ -2,14 +2,47 @@
 license: apache-2.0
 ---
 
-Singularity container for abdominal tumor (liver, pancreas and kidney) prediction. The segmentation model used from [DiffTumor](https://github.com/MrGiovanni/DiffTumor).
+# DiffTumor
 
-Download the Singularity container.
+The Singularity container is designed for the prediction of abdominal tumors, specifically targeting the liver, pancreas, and kidneys. It utilizes a segmentation model sourced from DiffTumor. [DiffTumor](https://github.com/MrGiovanni/DiffTumor).
+
+# Instructions
+
+### 1-Download
+Download the singularity container.
 ```
 wget https://huggingface.co/qicq1c/DiffTumor/difftumor_final.sif
 ```
-You can directly inference on your own data. Just modify `inputs_data` into your data path, and modify 'outputs_data' as where you want output the segmentation results.
+### 2-Data preparation
+This is how `inputs_data` organizes
+```
+    $inputs_data/
+    ├── case00001.nii.gz
+    ├── case00002.nii.gz
+    ├── case00003.nii.gz
+    ├── case000xx.nii.gz
+    ├── ...
+    ├── case10000.nii.gz
+```
+
+### 3-Inference
+You can directly perform inference on your own data. Simply modify inputs_data to reflect 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 difftumor_final.sif
 ```
 
+This is how `outputs_data` organizes
+```
+    $outputs_data/
+    ├── case00001
+    ├── case00002
+    ├── case00003
+        │── ct.nii.gz
+        └── predictions
+            ├── liver.nii.gz
+            ├── pancreas.nii.gz
+            ├── kidney.nii.gz
+            ├── liver_tumor.nii.gz
+            ├── pancreas_tumor.nii.gz
+            ├── kidney_tumor.nii.gz
+```