diff --git a/nnunetv2/dataset_conversion/Dataset224_AbdomenAtlas1.0.py b/nnunetv2/dataset_conversion/Dataset224_AbdomenAtlas1.0.py index 6a0a9ad59..e8f878088 100644 --- a/nnunetv2/dataset_conversion/Dataset224_AbdomenAtlas1.0.py +++ b/nnunetv2/dataset_conversion/Dataset224_AbdomenAtlas1.0.py @@ -4,6 +4,20 @@ if __name__ == '__main__': + """ + How to train our submission to the JHU benchmark + + 1. Execute this script here to convert the dataset into nnU-Net format. Adapt the paths to your system! + 2. Run planning and preprocessing: `nnUNetv2_plan_and_preprocess -d 224 -npfp 64 -np 64 -c 3d_fullres -pl + nnUNetPlannerResEncL_torchres`. Adapt the number of processes to your System (-np; -npfp)! Note that each process + will again spawn 4 threads for resampling. This custom planner replaces the nnU-Net default resampling scheme with + a torch-based implementation which is faster but less accurate. This is needed to satisfy the inference speed + constraints. + 3. Run training with `nnUNetv2_train 224 3d_fullres all -p nnUNetResEncUNetLPlans_torchres`. 24GB VRAM required, + training will take ~28-30h. + """ + + base = '/home/isensee/Downloads/AbdomenAtlas1.0Mini' cases = subdirs(base, join=False, prefix='BDMAP')