While the 'hide zeros' option will work in a pinch, for full control of an overlay statistical map that has both positive and negative values I would encourage loading the overlay twice. You can then adjust the range and threshold independently for each layer. You can do this with the graphical interface by adding choosing File/AddOverlay twice and then selecting each layer in the "Layers" box - set one to have darkest/brightest values that are positive and the other with ranges that are negative. 

You can also do this using a script. Below is a script for MRIcroGL 1.2.20190410. The attached image shows this. Here I have set the negative range to -1..+4 and the positive range to 1..4, but these do not need to be symmetrical.


import gl
gl.resetdefaults()
gl.loadimage('mni152')
#open overlay: show positive regions
gl.overlayload('masked_Perm_Zed_new.nii')
gl.minmax(1, 1, 4)
gl.overlayload('masked_Perm_Zed_new.nii')
gl.minmax(2, -1, -4)