Your coronal image has the resolution 208x11x320 voxels (in L/RxP/AxI/S dimensions), in contrast your sagittal scan is 9x224x324 voxels. Many tools require drawing masks to have a perfect one-to-one correspondence with the image they belong to. In contrast, my tools interpolate an image if it does match perfectly. Therefore, this is a limitation of the other tools you are using. 

If you use SPM, you can use the "coreg" function to warp estimate the transform from the coronal image to your sagittal image, and then apply this function to your segmented mask. 

If you use FSL's FLIRT, choose your segmented mask as the "Secondary image"