"Ignore Orientation" troubles

Hi team,
Sorry for a silly question. A collaborator segmented some brain lesions from an MRI in nii format, to create some label map files in nrrd format. When I now load them into one scene, the labelmap is not aligned well with the original nii file. If I load it into the scene and tick “ignore orientation”, then it aligns perfectly.
I would like to fix them in that space and export the label map file to nii format so I can do further analysis in matlab.
How do I fix this orientation problem?