Update readme.md

readme.md

@@ -9,17 +9,44 @@ https://pan.baidu.com/s/1jvJ2W4MK24JdpZLwPqMIfA
 code：7be9 
 
 ## Before Training
-install tutils
+### install tutils
 ```
 pip install trans-utils
 ```
 
-prepare datasets
+### prepare datasets
+We recommend you to convert the dataset into the nnUNet format.
+```
+00_custom_dataset
+  imagesTr
+    xxx_0000.nii.gz
+    ...
+  labelsTr
+    xxx.nii.gz
+    ...
+```
+try to use the function ```organize_in_nnunet_style``` or ```organize_by_names``` to prepare your custom datasets.
+
+Then run
 ```
 python -m  datasets.generate_txt
 ```
 
-cache 3d data into slices
+A ```[example]_train.txt``` will be generated in ```./datasets/dataset_list/```
+
+The content should be like below
+```
+01_BCV-Abdomen/Training/img/img0001.nii.gz	01_BCV-Abdomen/Training/label/label0001.nii.gz
+01_BCV-Abdomen/Training/img/img0002.nii.gz	01_BCV-Abdomen/Training/label/label0002.nii.gz
+01_BCV-Abdomen/Training/img/img0003.nii.gz	01_BCV-Abdomen/Training/label/label0003.nii.gz
+```
+
+### cache 3d data into slices
+After generating the ```[example]_train.txt``` file, check the config file ```configs/vit_b.yaml```.
+
+Update the params in ```dataset``` by yours. And the ```dataset_list``` should be the name of the generated txt file ```[example]```.
+
+Then run
 ```
 python -m datasets.cache_dataset3d
 ```