Cystoscopy is the best procedure for an urologist to look for everything in the urinary tract from the tip of the penis to your bladder, it is a little uncomfortable because I had it done and best bet is to ask the urologist before you get a procedure like that done is to take a pill called Pyrdium one hour before, eases the frequency and burning after the procedure because urination will burn for at least 24 hours, drink plenty of fluids and request that pill and you should be fine from the side effects I should say
Does MRI show more/better?
So you can see the urethra going from bladder to penis also? How about muscles, or nerves that could be out of place relating to sensation and pain and such? Vas deferens? Seminal Vesicles? Suspensory/Fundal ligament?
CT scan of the pelvis shows any stones in the bladder, kidney, prostate enlargement and urethra to penis and bladder functions would be a cystoscopy or retrograde urethragram to check for any abnormalities of your urinary tract.