What kind of visualization are you "envisioning"?
If you are working with volumetric data, then you will need to make either NIFTI or AFNI datasets. Our matlab library or others could be used for that, but you will have to be careful about the header parameters like orientation.
For specific xyz locations, you can place spheres. Again, you have to be careful about the various conventions of coordinates and orientation that we use, which may be different from the one you use in matlab. Connection strength between pairs of spheres are possible too (in the last example).
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/rois_corr_vis/suma_spheres.html