I suffer from migraines and see a neurologist about it regularly. I take topomax for them and maxalt (rizatriptan) if needed. My MRI showed lesions on the brain?

What lesions? What does your neurologist say re the mri, the changes may be incidental or unimportant otherwise he would have advised you about them and take action.
Did the lesions. Enhance. I assume not. Then they are typical demyelinating lesions -ask your doctor. These are seen in many patients and are non specific. The differential is very long but the common ones in 95% of cases are non specific and ischemic demyelination. So only 5% of these lesions are important. You doctor follows you clinically to decide if they are important.