Add training script

nnunet_scripts/run_5fold_cross_validation.sh

@@ -0,0 +1,47 @@
+#!/bin/bash
+#
+# Training nnUNetv2 on multiple folds
+#
+# NOTE: This is a template script, modify it as needed
+#
+# Authors: Naga Karthik, Jan Valosek
+#
+
+# !!! MODIFY THE FOLLOWING VARIABLES ACCORDING TO YOUR NEEDS !!!
+config=2d                     # e.g. 3d_fullres or 2d
+dataset_id=002             # e.g. 301
+dataset_name=Dataset002_TEM         # e.g Dataset301_XXX
+nnunet_trainer="nnUNetTrainer"
+
+# Select number of folds here
+folds=(0 1 2)
+# folds=(0)
+
+echo "-------------------------------------------------------"
+echo "Running preprocessing and verifying dataset integrity"
+echo "-------------------------------------------------------"
+
+nnUNetv2_plan_and_preprocess -d ${dataset_id} --verify_dataset_integrity
+
+for fold in ${folds[@]}; do
+    echo "-------------------------------------------"
+    echo "Training on Fold $fold"
+    echo "-------------------------------------------"
+
+    # training
+    CUDA_VISIBLE_DEVICES=2 nnUNetv2_train ${dataset_id} ${config} ${fold} -tr ${nnunet_trainer}
+
+    echo ""
+    echo "-------------------------------------------"
+    echo "Training completed, Testing on Fold $fold"
+    echo "-------------------------------------------"
+
+    # inference
+    CUDA_VISIBLE_DEVICES=2 nnUNetv2_predict -i ${nnUNet_raw}/${dataset_name}/imagesTs -tr ${nnunet_trainer} -o ${nnUNet_results}/${nnunet_trainer}__nnUNetPlans__${config}/fold_${fold}/test -d ${dataset_id} -f ${fold} -c ${config}
+
+    echo ""
+    echo "-------------------------------------------"
+    echo " Inference completed on Fold $fold"
+    echo "-------------------------------------------"
+
+done