I re-sliced my left thalamus so that the size and number of slices correspond with the original MRI, but when I open it in freeview, it shows an extra part( like a cube) on the bottom of the image ( I have attached the  mask). do you have any idea how to solve that? 

Also how can I make sure that the position and size of the thalamus makes sense since the thalamus mask has a different slice size and number than the original mri?

Thank you

Dorsa