Most members of our lab continue to use Slicer 2.7 to do DWI-DTI estimation since Slicer4's version is still not as efficient as Slicer 2's.

In Slicer 2:
1) We load the DWI volume
2) Navigate to the module DTMRI
3) Select the Input Volume
4) Choose which 'weight' we want to use for the automatic mask extraction (usually .5)
5) Click Convert volume

This creates an Output Baseline Volume, a labelmap estimation and an Output DTI Volume that is very clean. We are easily able to proceed to editing the mask and/or tractography

In Slicer 4, there is no way to perform automatic mask extraction, thus the Output DTI volume is very messy (contains random colors outside the brain and over the skull) and there is no easy way to proceed to the next step.