Project-MONAI / Project-MONAI/MONAILabel

Spacingd makes label and image shape mismatch

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Description

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load_transforms = monai.transforms.Compose([
monai.transforms.LoadImaged(keys=["image", "label_path"]),
monai.transforms.AddChanneld(keys=["image", "label_path"]),
monai.transforms.Orientationd(keys=["image", "label_path"], axcodes="RAS"),

    ])

and out put is untransformed is (1, 512, 512, 254),(1, 512, 512, 254)

while:
spacing_transforms = monai.transforms.Compose([
monai.transforms.LoadImaged(keys=["image", "label_path"]),
monai.transforms.AddChanneld(keys=["image", "label_path"]),
monai.transforms.Orientationd(keys=["image", "label_path"], axcodes="RAS"),
monai.transforms.Spacingd(keys=["image", "label_path"],
pixdim=(args.space_x, args.space_y, args.space_z),
mode=("bilinear", "nearest")),

    ])

and output is transformed is (1, 326, 326, 423),(1, 342, 342, 170)
and my version is monai 1.1.0,there is a warning——pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to

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Research direction

No repository files or tests are identified. Start by reproducing the LoadImaged, AddChanneld, Orientationd, and Spacingd pipeline shown with MONAI 1.1.0, then inspect the image and label metadata and resulting shapes; done requires a clarified expected shape relationship or a reproducible defect with a proposed test case.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
machine-learning
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
20/100

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