WholeBody CT Segmentation (104 classes) | SegResNet | TotalSegmentator

models/swin_unetr_btcv_segmentation/configs/metadata.json

@@ -1,7 +1,8 @@
 {
     "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
-    "version": "0.4.1",
+    "version": "0.4.2",
     "changelog": {
+        "0.4.2": "fix train params of use_checkpoint",
         "0.4.1": "update params to supprot torch.jit.trace torchscript conversion",
         "0.4.0": "add name tag",
         "0.3.9": "use ITKreader to avoid mass logs at image loading",

models/swin_unetr_btcv_segmentation/configs/train.json

@@ -19,7 +19,7 @@
         "in_channels": 1,
         "out_channels": 14,
         "feature_size": 48,
-        "use_checkpoint": false
+        "use_checkpoint": true
     },
     "network": "$@network_def.to(@device)",
     "loss": {

models/wholeBody_ct_segmentation/LICENSE

@@ -0,0 +1,201 @@
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models/wholeBody_ct_segmentation/configs/evaluate.json

@@ -0,0 +1,78 @@
+{
+    "validate#postprocessing": {
+        "_target_": "Compose",
+        "transforms": [
+            {
+                "_target_": "Activationsd",
+                "keys": "pred",
+                "softmax": true
+            },
+            {
+                "_target_": "AsDiscreted",
+                "keys": [
+                    "pred",
+                    "label"
+                ],
+                "argmax": [
+                    true,
+                    false
+                ],
+                "to_onehot": 105
+            },
+            {
+                "_target_": "Invertd",
+                "keys": [
+                    "pred",
+                    "label"
+                ],
+                "transform": "@validate#preprocessing",
+                "orig_keys": "image",
+                "meta_key_postfix": "meta_dict",
+                "nearest_interp": [
+                    true,
+                    true
+                ],
+                "to_tensor": true
+            },
+            {
+                "_target_": "SaveImaged",
+                "_disabled_": true,
+                "keys": "pred",
+                "meta_keys": "pred_meta_dict",
+                "output_dir": "@output_dir",
+                "resample": false,
+                "squeeze_end_dims": true
+            }
+        ]
+    },
+    "validate#handlers": [
+        {
+            "_target_": "CheckpointLoader",
+            "load_path": "$@ckpt_dir + '/model.pt'",
+            "load_dict": {
+                "model": "@network"
+            }
+        },
+        {
+            "_target_": "StatsHandler",
+            "iteration_log": false
+        },
+        {
+            "_target_": "MetricsSaver",
+            "save_dir": "@output_dir",
+            "metrics": [
+                "val_mean_dice",
+                "val_acc"
+            ],
+            "metric_details": [
+                "val_mean_dice"
+            ],
+            "batch_transform": "$monai.handlers.from_engine(['image_meta_dict'])",
+            "summary_ops": "*"
+        }
+    ],
+    "evaluating": [
+        "$setattr(torch.backends.cudnn, 'benchmark', True)",
+        "$@validate#evaluator.run()"
+    ]
+}