If the labels are correct then everything is fine.
If the labels are not correct (with respect to the anatomy) then there is a problem with the nifti file.
I'm not quite sure what you mean by things swapping labels but the lateralities being correct.
Does FSLView swap just the L and R labels for the manual labels vs the anatomical images?
I've not seen that and don't really understand how it could happen.
I think we'd need some more info to be able to figure out precisely what's going on.
All the best,
> On 10 Apr 2017, at 20:43, Martin Kavec <[log in to unmask]> wrote:
> I have a series of 1600+ anatomical nifti images and lesion segmentation masks images. When I display them in fslview they are correctly oriented. However, I noticed that for some L-R labels are swapped though lesion lateralities are correct. I need to continue processing the dataset using a third-party software using nibabel-2.1.0 and I am not certain if laterality will still hold.
> I would appreciate advice how to ensure correct orientation of the lesion masks.
> Many thanks,