afni.nimh.nih.gov

I see what you mean. However, I don't understand what your concern might be in "prepping images for preprocessing". What follows the preprocessing? If you are going to do quantitative image segmentation (i.e., partition into WM and GM and count voxels), then the effect you see might be a concern. If you are going on to skull stripping or the like, then I don't think these small brightness patches will matter much.