From 24c84966bf50e8d50d9c69834ccb1729ae080796 Mon Sep 17 00:00:00 2001 From: yw7 <36595323+yw7@users.noreply.github.com> Date: Sat, 1 Jun 2024 13:47:49 +0300 Subject: [PATCH] for release --- scripts/inference_nnunet.sh | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/scripts/inference_nnunet.sh b/scripts/inference_nnunet.sh index 52b27ec..e5f4d2f 100644 --- a/scripts/inference_nnunet.sh +++ b/scripts/inference_nnunet.sh @@ -48,7 +48,7 @@ export nnUNet_preprocessed=data/nnUNet/preprocessed export nnUNet_results=data/nnUNet/results export nnUNet_exports=data/nnUNet/exports -nnUNetTrainer=nnUNetTrainer_16000epochs +nnUNetTrainer=nnUNetTrainer_8000epochs nnUNetPlans=nnUNetPlans configuration=3d_fullres @@ -66,7 +66,7 @@ echo "configuration=${configuration}" echo "JOBS=${JOBS}" echo "" -FOLD=0 +FOLD=all step1_dataset=101 step2_dataset=102 @@ -105,7 +105,7 @@ done nnUNetv2_predict -d $step2_dataset -i ${OUTPUT_FOLDER}/step2_input -o ${OUTPUT_FOLDER}/step2 -f $FOLD -c $configuration -p $nnUNetPlans -tr $nnUNetTrainer -npp $JOBS -nps $JOBS # Use an iterative algorithm to to assign an individual label value to each vertebrae and IVD in the final segmentation mask. -python $utils/generate_labels_sequential.py -s ${OUTPUT_FOLDER}/step2 -o ${OUTPUT_FOLDER}/output --sacrum-labels 14 --csf-labels 16 --sc-labels 17 --disc-labels 2 3 4 5 6 7 --vertebrea-labels 9 10 11 12 13 14 --init-disc 4:224 7:202 5:219 6:207 --init-vertebrae 11:40 14:17 12:34 13:23 --step-diff-label --step-diff-disc +python $utils/generate_labels_sequential.py -s ${OUTPUT_FOLDER}/step2 -o ${OUTPUT_FOLDER}/output --sacrum-labels 14 --csf-labels 16 --sc-labels 17 --disc-labels 2 3 4 5 6 7 --vertebrea-labels 9 10 11 12 13 14 --init-disc 4:224 7:202 5:219 6:207 --init-vertebrae 11:41 14:17 12:34 13:23 --step-diff-label --step-diff-disc # Fix csf label to include all non cord spinal canal, this will put the spinal canal label in all the voxels (labeled as a backgroupn) between the spinal canal and the spinal cord. python $utils/fix_csf_label.py -s ${OUTPUT_FOLDER}/output -o ${OUTPUT_FOLDER}/output --largest-cord --largest-canal