Conv3D size doesn't make sense with NIFTI data?


So I am writing custom dataset for medical images, with .nii (NIFTI1 format), but there is a confusion.

My dataloader returns the shape torch.Size (1,1,256,256,51) . But NIFTI volumes use anatomical axes, different coordinate system, so it doesn’t make any sense to permute the axes, which I normally would with volume made of 2D images seprately stored in local drive with 51 slice images (or depth), as Conv3D follows the convention (N,C,D,H,W).

so torch.Size (1,1,256,256,51) (ordinarily 51 would be the depth) doesn’t follow the convention (N,C,D,H,W) , but I should not permute the axes as the data uses entirely different coordinate system ?

Could you explain this statement a bit?
Does the depth dimension represent the number of slices or what do you mean by “different coordinate system”?
What wouldn’t it be possible to permute the data?