Hello.

Firstly, sorry about the late reply.

Does the final bin maps have NaNs or the intermediate ones have them ?

For the former one, just removing/neglecting these NaNs might do the job.
For later case, If I understand the issue correctly, the NaNs might be the result of bad pre-processing outputs (i.e., the GM, WM maps). These will be the intermediate files on which the detection tool works. To that end, the first thing to check would be NaNs in these maps.
Further, it seems that the images you have are unsusally bright, and hence changing around the hyper-parameters of the preprocessing might also help. Note that these parameters are different from the quantification ones.
Also, if there are atleast one/more cases with 'good' WMH images, and thereby reasonable effective volume measures, the corresponding imtermediate files of these good set of images can be compared to the bad ones for adjusting the parameters better.

If all the intermediate files look good to you, then there might be some other issue. And I may be able to help you out via command line debugging (where each step needs to be checked for errors!).