Resize sometimes adds a dimension to LabelMap images about torchio HOT 5 CLOSED

Hi, @Bigsealion. Thanks for reporting and for sharing the data. How strange. I will investigate this.

from torchio.

I'm getting this warning. It might be causing the issue.

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1934
NiftiImageIO (0x38b4ad0): /tmp/img1.nii.gz has unexpected scales in sform

from torchio.

That warning is raised by ITK here.

from torchio.

Given that your images seem to be meant to share physical space, that their metadata is similar and that your img1 seems to be the problematic one, maybe you can use tio.CopyAffine('mask') before tio.Resize. I added it in your snippet and didn't get an error.

transform = tio.Compose([
    tio.CopyAffine('mask'),
    tio.Resize(target_shape=tar_shape)
])

Would that work for you?

from torchio.

Thanks! It works!

from torchio.