Hello, 

I am interested in your toolbox. I was able to successfully install, run and get some results printed. Could you please explain what "effective volume" is? What its unit is (voxels, mL etc)? Looking at the preliminary numbers I am guessing it is not normalized to intracranial volume, correct? Thank you for your help.

It is Effective Volume which is the number of hyperintense voxels weighted by their probability measure. This is why it is hard to say that it has actual units since it is more of a theoretical quantity. It should still provide very useful information about a subject such as the difference in EV between an AD subject versus a control ect..

It is better to use effective volume as opposed to a strict voxel count in this case since W2MHS is automated and may misclassify some regions.

Thank you. What would you recommend doing to account for differences in head sizes?

I'm not an expert on this but I would find some other software that gets a good volume estimate of white matter and use that to relate cross subject data. You could even use the entire cranial volume. Alternatively, since I am a MatLab programmer and W2MHS allows you to keep all of the preprocessing images, It wouldn't be too hard to write a script that quantifies cranial / white matter volume.