Megan,

I would first try setting the clean threshold to zero. Then this may fix your issue but may also cause some noise around the edges of the white matter. If that helps you can try slowly increasing Clean-Th (in steps of .1 or so) until the noise is gone. If you are still not detecting all WMHs then training your own model might be helpful.

And Nicholas,

Another member of our lab is still selecting which examples we are going to upload for users to test and compare.  If just comparing the images isn't enough to help we can give you our acquisition parameters as well. Also, we have done no preprocessing on W2MHS inputs.

Chris