Segmentation from Landmark Registration images not aligned

I am trying to do segmentation on fusion of 2 image sets(PET-CT and mpMRI). PET-CT is full body and MRI is pelvic. With the help of Landmark Registration module I am able to overlap the two images. I prefer mpMRI is fixed and CT is moving. As mp MRI show great anatomical detail, I need it to be the fixed one. But when I try to segment my ROI on the fusion image, the result of the segmentation in 3d is far off from where I expect it to be. Is there any suggestion on how to overlap the segmentations also.

Best Regards

You can apply the same transform to the segmentation as you applied to the underlying image. See instructions here.