First of all, what would you like to segment? Simple thresholding works well in cases when structures of interest have highly distinctive intensity value on the image (bone on CT, contrasted vessels, etc.). If you want to segment bone on MRI then you need to use more sophisticated tools than thresholding.
Another problem is that, quite often 3 anisotropic MRI images are acquired (high resolution along two axes, very low resolution along a third axis) to reduce time spent in the MRI scanner. However, these images are not well suited for 3D model generation. See more information here: Combining volumes - what am I missing?. To reduce artifacts caused by low-resolution third axis you can follow the technique explained here: Segmenting Issue: I Can't Remove "ridges" in 3-D model