hecktor22 update for latest monai ver (#1438)

hecktor22 update for latest monai ver

Signed-off-by: myron <amyronenko@nvidia.com>

Author: myron

auto3dseg/tasks/hecktor22/hecktor22_folds.json

@@ -4,6 +4,41 @@
             "image": "imagesTr/CHUP-049__CT.nii.gz",
             "image2": "imagesTr/CHUP-049__PT.nii.gz",
             "fold": 0
+        },
+        {
+            "image": "imagesTr/CHUP-034__CT.nii.gz",
+            "image2": "imagesTr/CHUP-034__PT.nii.gz",
+            "fold": 0
+        },
+        {
+            "image": "imagesTr/CHUS-089__CT.nii.gz",
+            "image2": "imagesTr/CHUS-089__PT.nii.gz",
+            "fold": 0
+        },
+        {
+            "image": "imagesTr/CHUP-061__CT.nii.gz",
+            "image2": "imagesTr/CHUP-061__PT.nii.gz",
+            "fold": 0
+        },
+        {
+            "image": "imagesTr/CHUP-010__CT.nii.gz",
+            "image2": "imagesTr/CHUP-010__PT.nii.gz",
+            "fold": 0
+        },
+        {
+            "image": "imagesTr/HGJ-013__CT.nii.gz",
+            "image2": "imagesTr/HGJ-013__PT.nii.gz",
+            "fold": 0
+        },
+        {
+            "image": "imagesTr/CHUM-040__CT.nii.gz",
+            "image2": "imagesTr/CHUM-040__PT.nii.gz",
+            "fold": 0
+        },
+        {
+            "image": "imagesTr/HGJ-062__CT.nii.gz",
+            "image2": "imagesTr/HGJ-062__PT.nii.gz",
+            "fold": 0
         }
     ],
     "training": [

auto3dseg/tasks/hecktor22/hecktor_crop_neck_region.py

@@ -36,7 +36,7 @@ def __init__(
         super().__init__(keys=keys, source_key=source_key, allow_missing_keys=allow_missing_keys, **kwargs)
         self.box_size = box_size
 
-    def __call__(self, data):
+    def __call__(self, data, **kwargs):
         d = dict(data)
 
         im_pet = d["image2"][0]

auto3dseg/tasks/hecktor22/input.yaml

@@ -13,10 +13,11 @@ extra_modalities: {image2 : pet}    # a second modality
 custom_data_transforms:
   - key: after_resample_transforms
     path: '.'
-    transform: {_target_: hecktor_crop_neck_region.HecktorCropNeckRegion}
+    transform: {_target_: hecktor_crop_neck_region.HecktorCropNeckRegion, box_size: [200, 200, 310]}
 
 # indicate the new avg image size (to correctly determine amount of caching required)
-image_size: [200, 200, 310]
+image_size_mm_90: [200, 200, 310]
+resample_resolution: [1, 1, 1]
 
 # update the random crop size (for training) to be slightly smaller, since the automatically
 # determined size was based on the whole image