for release r20240628

neuropoly · Jun 28, 2024 · 8d05598 · 8d05598
1 parent f02d053
commit 8d05598
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/scripts/inference_nnunet.sh b/scripts/inference_nnunet.sh
@@ -51,7 +51,7 @@ export nnUNet_preprocessed="$TOTALSPINESEG_DATA"/nnUNet/preprocessed
 export nnUNet_results="$TOTALSPINESEG_DATA"/nnUNet/results
 export nnUNet_exports="$TOTALSPINESEG_DATA"/nnUNet/exports
 
-nnUNetTrainer=nnUNetTrainer_16000epochs
+nnUNetTrainer=nnUNetTrainer_8000epochs
 nnUNetPlans=nnUNetPlans
 configuration=3d_fullres
 
@@ -72,7 +72,7 @@ echo ""
 # ensure the custom nnUNetTrainer is defined in the nnUNet library and add it if it is not
 source "$TOTALSPINESEG"/scripts/add_nnunet_trainer.sh
 
-FOLD=0
+FOLD=all
 step1_dataset=101
 step2_dataset=102
 
@@ -111,7 +111,7 @@ 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.
-totalspineseg_generate_labels_sequential -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
+totalspineseg_generate_labels_sequential -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.
 totalspineseg_fix_csf_label -s "${OUTPUT_FOLDER}"/output -o "${OUTPUT_FOLDER}"/output --largest-cord --largest-canal