Fixes #6840

According to the issue, this PR addresses on the meta dictionary `data['pixdim']` of NIfTI images does not update after applying the `spacing` or `spacingd`.
To align with `affine`, we update `data['pixdim']` and keep the original metainfo in `data['original_pixdim']`.
Additionally, this PR also update the metainfo `key_{meta_key_postfix}['pixdim']` in NIfTI images, consistent with `spaced_data_dict['image_meta_dict']['pixdim']` in issue #6832.

Signed-off-by: Wei_Chuan, Chiang <[email protected]>
Co-authored-by: einsyang723 <[email protected]>
Co-authored-by: IamTingTing <[email protected]>

Author: 3 people

monai/data/image_reader.py

@@ -989,6 +989,8 @@ def get_data(self, img) -> tuple[np.ndarray, dict]:
 
         for i, filename in zip(ensure_tuple(img), self.filenames):
             header = self._get_meta_dict(i)
+            if MetaKeys.PIXDIM in header:
+                header[MetaKeys.ORIGINAL_PIXDIM] = np.array(header[MetaKeys.PIXDIM], copy=True)
             header[MetaKeys.AFFINE] = self._get_affine(i)
             header[MetaKeys.ORIGINAL_AFFINE] = self._get_affine(i)
             header["as_closest_canonical"] = self.as_closest_canonical

monai/data/meta_tensor.py

@@ -477,6 +477,10 @@ def pixdim(self):
             return [affine_to_spacing(a) for a in self.affine]
         return affine_to_spacing(self.affine)
 
+    def set_pixdim(self) -> None:
+        """Update pixdim based on current affine."""
+        self.meta[MetaKeys.PIXDIM][1 : 1 + len(self.pixdim)] = affine_to_spacing(self.affine)
+
     def peek_pending_shape(self):
         """
         Get the currently expected spatial shape as if all the pending operations are executed.

monai/transforms/spatial/array.py

@@ -535,6 +535,9 @@ def __call__(
             dtype=dtype,
             lazy=lazy_,
         )
+        if isinstance(data_array, MetaTensor) and "pixdim" in data_array.meta:
+            data_array = data_array.clone()
+            data_array.set_pixdim()
         if self.recompute_affine and isinstance(data_array, MetaTensor):
             if lazy_:
                 raise NotImplementedError("recompute_affine is not supported with lazy evaluation.")

monai/transforms/spatial/dictionary.py

@@ -24,11 +24,13 @@
 import numpy as np
 import torch
 
+import monai.transforms as transforms
 from monai.config import DtypeLike, KeysCollection, SequenceStr
 from monai.config.type_definitions import NdarrayOrTensor
 from monai.data.box_utils import BoxMode, StandardMode
 from monai.data.meta_obj import get_track_meta
 from monai.data.meta_tensor import MetaTensor
+from monai.data.utils import is_supported_format
 from monai.networks.layers.simplelayers import GaussianFilter
 from monai.transforms.croppad.array import CenterSpatialCrop
 from monai.transforms.inverse import InvertibleTransform
@@ -520,6 +522,9 @@ def __call__(self, data: Mapping[Hashable, torch.Tensor], lazy: bool | None = No
                 output_spatial_shape=output_shape_k if should_match else None,
                 lazy=lazy_,
             )
+            if isinstance(d[key], MetaTensor) and "filename_or_obj" in d[key].meta:
+                if is_supported_format(d[key].meta["filename_or_obj"], ["nii", "nii.gz"]):
+                    d = transforms.sync_meta_info(key, d)
             if output_shape_k is None:
                 output_shape_k = d[key].peek_pending_shape() if isinstance(d[key], MetaTensor) else d[key].shape[1:]
         return d

monai/utils/enums.py

@@ -528,6 +528,8 @@ class MetaKeys(StrEnum):
     Typical keys for MetaObj.meta
     """
 
+    PIXDIM = "pixdim"  # MetaTensor.pixdim
+    ORIGINAL_PIXDIM = "original_pixdim"  # the pixdim after image loading before any data processing
     AFFINE = "affine"  # MetaTensor.affine
     ORIGINAL_AFFINE = "original_affine"  # the affine after image loading before any data processing
     SPATIAL_SHAPE = "spatial_shape"  # optional key for the length in each spatial dimension