NIfTI to RTStruct - no registration with CT (rotation problem?)

Hello, I am having problems with this code: I have many structures in NIfTI format that, once I create the RTStruct file, do not correctly overlap with the original CT. Even applying rotations as suggested by other users, I cannot achieve a good overlap with the CT. However, if I open these structures directly with 3D Slicer, they overlap perfectly, so it is not a segmentation issue. I am leaving the code here hoping for some help. Thank you, Emanuele.

from rt_utils import RTStructBuilder
import nibabel as nib
import numpy as np
import os
import colorsys

def generate_unique_colors(n):
    colors = []
    for i in range(n):
        hue = i / n
        saturation = 0.7  # Scegli un valore di saturazione medio-alto
        value = 0.9  # Scegli un valore di luminosità medio-alto
        rgb = colorsys.hsv_to_rgb(hue, saturation, value)
        colors.append([int(x * 255 + 0.5) for x in rgb])
    return colors

folder_path = r"\path_folder_with_nifti_segmentation"
dicom_series_path = r"\path_CT_reference"

rtstruct = RTStructBuilder.create_new(dicom_series_path)

nii_files = [f for f in os.listdir(folder_path) if f.endswith('.nii.gz')]
unique_colors = generate_unique_colors(len(nii_files))

for file, color in zip(nii_files, unique_colors):
    nii_path = os.path.join(folder_path, file)
    nii_image = nib.load(nii_path)
    data = nii_image.get_fdata() > 0

    mask_dataflip = np.flipud(data)
    mask_dataflip2 = np.flip(mask_dataflip)
    mask_rtdata = np.rot90(mask_dataflip2)

    roi_name = os.path.splitext(file)[0]

    rtstruct.add_roi(mask=mask_rtdata, color=color, name=roi_name)

rtstruct.save(r'\path_RTStruct_output\new-rt-struct.dcm')

Start with the example using RTStructBuilder.create_new, add_roi, and save, then inspect how the NIfTI data loaded by nibabel is transformed before being passed as a mask. Compare the NIfTI orientation and CT reference geometry, using the 3D Slicer overlap as the expected result. Done means the generated RTStruct aligns with the original CT without ad hoc rotations.