add sinuses

wasserth · Feb 10, 2025 · 69d9abc · 69d9abc
1 parent 34b9cfb
commit 69d9abc
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Showing 7 changed files with 29 additions and 5 deletions.
diff --git a/resources/prepare_weights_for_release.sh b/resources/prepare_weights_for_release.sh
@@ -23,7 +23,7 @@ print(get_full_task_name_v2($dataset_id))
     echo "Processing $task_name..."
 
     # Copy dataset folder
-    # cp -r "$nnUNet_results/$task_name" .
+    cp -r "$nnUNet_results/$task_name" .
 
     # Get the only folder inside task_name
     trainer_folder=$(ls "$task_name" | head -n 1)

diff --git a/totalsegmentator/bin/TotalSegmentator.py b/totalsegmentator/bin/TotalSegmentator.py
@@ -62,7 +62,7 @@ def main():
                         "head_glands_cavities", "head_muscles", "headneck_bones_vessels", "headneck_muscles",
                         "brain_structures", "liver_vessels", "oculomotor_muscles",
                         "thigh_shoulder_muscles", "thigh_shoulder_muscles_mr", "lung_nodules", "kidney_cysts", 
-                        "breasts", "ventricle_parts"],
+                        "breasts", "ventricle_parts", "aortic_sinuses"],
                         help="Select which model to use. This determines what is predicted.",
                         default="total")
 

diff --git a/totalsegmentator/bin/totalseg_download_weights.py b/totalsegmentator/bin/totalseg_download_weights.py
@@ -27,7 +27,8 @@ def main():
                                                  "head_glands_cavities", "head_muscles", "headneck_bones_vessels",
                                                  "headneck_muscles", "liver_vessels", "brain_structures",
                                                  "lung_nodules", "kidney_cysts", "breasts", "ventricle_parts",
-                                                 "thigh_shoulder_muscles", "thigh_shoulder_muscles_mr",
+                                                 "thigh_shoulder_muscles", "thigh_shoulder_muscles_mr", 
+                                                #  "aortic_sinuses", 
                                                  "all"],
                         help="Task for which to download the weights", default="total")
 
@@ -70,7 +71,8 @@ def main():
         "brain_structures": [409],
         "thigh_shoulder_muscles": [857],
         "thigh_shoulder_muscles_mr": [857],
-        "coronary_arteries": [507]
+        "coronary_arteries": [507],
+        # "aortic_sinuses": [920]
     }
 
     setup_totalseg()

diff --git a/totalsegmentator/libs.py b/totalsegmentator/libs.py
@@ -327,6 +327,8 @@ def download_pretrained_weights(task_id):
         weights_path = config_dir / "Dataset857_TotalSegMRI_thigh_shoulder_1088subj"
     elif task_id == 507:
         weights_path = config_dir / "Dataset507_coronary_arteries_cm_nativ_400subj"
+    elif task_id == 920:
+        weights_path = config_dir / "Dataset920_aortic_sinuses_cm_nativ_400subj"
 
     else:
         raise ValueError(f"For task_id {task_id} no download path was found.")

diff --git a/totalsegmentator/map_to_binary.py b/totalsegmentator/map_to_binary.py
@@ -599,6 +599,12 @@
         11: "third_ventricle",
         12: "fourth_ventricle"
     },
+    "aortic_sinuses": {
+        1: "left_ventricular_outflow_tract",
+        2: "right_coronary_cusp", 
+        3: "left_coronary_cusp",
+        4: "non_coronary_cusp"
+    },
     "test": {
         1: "carpal"
     }
@@ -618,7 +624,8 @@
     "brain_structures": 409,
     "thigh_shoulder_muscles": 857,
     "thigh_shoulder_muscles_mr": 857,
-    "coronary_arteries": 507
+    "coronary_arteries": 507,
+    "aortic_sinuses": 920
 }
 
 

diff --git a/totalsegmentator/preview.py b/totalsegmentator/preview.py
@@ -225,6 +225,9 @@
         "ventricle_occipital_horn_right", "ventricle_body_right", "ventricle_temporal_horn_right",
         "ventricle_trigone_right", "third_ventricle", "fourth_ventricle"]
     ],
+    "aortic_sinuses": [
+        ["left_ventricular_outflow_tract", "right_coronary_cusp", "left_coronary_cusp", "non_coronary_cusp"]
+    ],
     "test": [
         ["ulna"]
     ]

diff --git a/totalsegmentator/python_api.py b/totalsegmentator/python_api.py
@@ -482,6 +482,16 @@ def totalsegmentator(input: Union[str, Path, Nifti1Image], output: Union[str, Pa
         folds = [0]
         if fast: raise ValueError("task coronary_arteries does not work with option --fast")
         show_license_info()
+    elif task == "aortic_sinuses":
+        task_id = 920
+        resample = [0.7, 0.7, 0.7]
+        trainer = "nnUNetTrainer_DASegOrd0_NoMirroring"
+        crop = ["heart"]
+        crop_addon = [0, 0, 0]
+        model = "3d_fullres_high"
+        folds = [0]
+        if fast: raise ValueError("task aortic_sinuses does not work with option --fast")
+        show_license_info()
 
     elif task == "test":
         task_id = [517]