I did have an MRI several years ago because I was experiencing symptoms of MS, which is classified as an AI disease. fortunately, the MRI showed nothing. My symptoms were most likely related to other AI things (e.g., RA, and/or sjogren's). I don't know that I've ever experienced brain fog like you're referring to, however. My symptoms concerned paresthesias (tingling) in my feet and hands. I do know that lupus is related to MS, among other things, and with some of these drugs we're all taking (e.g., the biologics), drug-induced lupus and drug-induced MS is a real threat.
I'm certainly no expert, but I wouldn't think an MRI would show any obvious brain abnormalities related to brain fog, would it? An MRI/brain scan would only show physical abnormalities (e.g., lesions associated with MS). I don't know how they would track a decline in cognitive functioning (e.g., memory, etc...) without using a cognitive test battery (paper/pencil tests). Just my opinion, though--perhaps others will have more information on this.
Current dx: Rheumatoid Arthritis
Suspected dx: UCTD/Early Lupus
Current Meds: Enbrel, Plaquenil, Methotrexate, nexium, tramadol, nasonex,Tylenol PM
Past Meds: Relafen, Vioxx, Mobic, Voltaren, Sulfasalazine, Entocort, Prednisone, Humira, Reglan, zyrtec, zegerid, aciphex