Thanks for sharing an example of the dataset. This is a duplicate of 
  https://github.com/rordenlab/MRIcroGL12/issues/17
Sub-threshold voxels have been artificially set to "Not-A-Number" values, and then the image  is being interpolated onto a higher resolution image. You will always get a better result if you reslice PRIOR to thresholding. The thresholding is eliminating crucial information. The current pre-release of MRIcroGL tries to explicitly identify not-a-number data to. mitigate the consequences. However,  throwing away a lot of information prior to interpolation will always incur some penalty.