Hello. Firstly, I apologize for this very late reply.
Note that REFEG_out is the file containing the final hyperintense regions, and RFREG_pmap is the output of the learning algorithm (before applying the WhyD_quant script that quantifies hyperintense regions). Please check if the RFREG_out is also not making sense ?!
Also, it looks like the image has lot of hyperintense regions, and in general the tissue map itself looks bright.
There are a few things you can try -- changing the default parameters of preprocessing (SPM) steps, changing around the quantification parameters (pmap_cut and clean_th). Please refer to the documentation for what/how these parameters can be changed.
Lemme know if things dont seem to work out. Thanks for your interest!