Chris,

I wanted to chime in on this conversation and post a picture depicting the issues that we are having as well.
The image is of the T2 registered to the T1 and overlayed with the pmap displayed at a .5 to 1 threshold. This test subject was pre-processed through the W2MHS program and had the default, 2.5 cleaning threshold as well. You can see from the attached image that the program is identifying major hyperintensities (although not some of the smaller ones in this particular slice), but more importantly, is missing the center of the hyperintensities. The probability for the voxels along the edge of that hyperintensity are slightly above .5, while the voxels in the center are around .2.
Therefore, we would be interested in the features and training codes as well. Any thoughts on this issue are greatly appreciated.

Megan