the voxel size and rotation matrix of output images are different from those of input images.

[ruitians]

I tried to normalize the bunch of nii.gz files in a folder called t2w with a white matter masks under folder wmmaks. I applied:
nyul-normalize t2w -o t2_norm -mo t2 -p
I got normalized images under folder t2_norm. However, the rotation matrix is diagonal matrix and the voxel size is 1x1x1 (the input is 0.7x0.7x0.7). I also saw negative intensity in the output images (They are all positive in the input images).

[EBirnie]

I have the same problem using the nyul-normalize function. The left/right orientation of the normalized images is mirrored. In addition, the origin is no longer defined in the output images.