Exporting segmentations for analysis in SPM/FSL

I have been segmenting lesions on brain MRIs. My brain MRIs are in .nii format. I have saved my manually drawn segmentation labels as nrrd files. When I open my subject’s MRI in 3dslicer, and then add the segmentation label files to the scene, as long as I click “Centered” for both the MRI and the label files in the “add data into the scene” options, I am able to see the labels correctly aligned to the MRI. If I do not click “centered” the label files are slightly displaced from where the lesions are on the MRI.
I am now interested in exporting them to be using in FSL and SPM. I have tried to save them as nifti files, but when I open the nifti file on top of the MRI, the labels are not in the same space as the MRI, and are instead misaligned somewhere else.
How do I make sure that my lesion masks remain spatially registered to my MRI when I save them? It does not seem to be an exclusively nifti problem as I have similar problems with nrrd too.

I would not recommend clicking “Centered”, as it discards the image origin information.

You may find SlicerFreeSurfer extension useful for importing images, segmentations, and overlays from FreeSurfer.

Thanks for the suggestion.
It sound like they are in the wrong space, so I am assuming that I will have to manually realign them using a linear transformation and then save them in the correct space.
Is this what others would do?
The problem is that this is very cumbersome and clearly slicer is able to have them perfectly aligned if I do the centering. Surely there is a better way?