Nicholas,

I can see now that you are not getting accurate segmentation and I apologize for trivializing your issue. The screenshots helped. From first glance I would attribute the poor segmentation to the brightness of your FLAIR image, which could be due to different scanner and post processing of imaging data. It is relatively difficult to tell the difference between a hyperintense voxel and a normal one in your image. The error IS stemming form the training step and if rectified W2MHS should give you some better results; however, training your own RF-Regression model will require a large set (30 - 40) hand segmented training examples. It would be a tedious process for you to create your own training data but it is possible.

We can provide you with the code we used to extract features from our images as well as the code necessary to actually train the model. This code is currently not incredibly well documented or intuitive to use. If there is enough demand I will try and clean it up and make an easy to use interface for it. We would love to have your lab and others make good use of our code. I do have a other projects going on but if this is not time sensitive I can, in the next couple of weeks, get some good documentation of our training methodology.

In the meantime, you could try doing some different pre-processing on your images (Normalization / Darkening of your FLAIR images) and see if that gives you better results. Let me know if making your own trining set is still appealing or if your results improve, I will try and work on a training interface when I find the time.

Thank you for your interest in our paper and software.
Best,
Chris Lindner