Looks like your normalization with the mesh is not great. You may want to create a custom mesh for each individual. Regardless, you will want to improve your normalization. This will depend on the tools you use (SPM, FSL, ANTS, AFNI), and are beyond the scope of this help list. You can adjust the transparency of a mesh with respect to the nodes by adjusting the overlay sliders. If you prefer Python scripts, the command gl.shaderxray will adjust this property:

import gl
gl.resetdefaults()
gl.meshload('BrainMesh_ICBM152.lh.mz3')
gl.edgeload('LPBA40.edge')
gl.clipazimuthelevation(0.3, 0, 130)
gl.nodesize(6, 1)
gl.edgesize(3,1)
gl.nodehemisphere(-1)
gl.azimuthelevation(250, 35)
gl.edgecolor('actc',1)
gl.nodecolor('blue',1)
gl.nodethresh(1.0,1.0)
gl.edgethresh(0.5,1.0)
gl.meshcurv()
gl.overlayminmax(1,-1,1)
gl.overlaycolorname(1,'surface')
gl.overlayinvert(1,1)
gl.overlaytranslucent(1, 1)
gl.meshhemisphere(-1)
gl.shaderxray(0.5, 0.5)