diff --git a/readme.md b/readme.md index b8b6a1c..455e1e5 100644 --- a/readme.md +++ b/readme.md @@ -9,17 +9,44 @@ https://pan.baidu.com/s/1jvJ2W4MK24JdpZLwPqMIfA codeļ¼š7be9 ## 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 ```