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I now live at the outskirts of Tokyo (still part of Tokyo) along the Tama river. You can run for miles on either side of the river, and for most part you do not hit any road. Try Futako Tamagawa station (Denen Toshi line) or Tamagawa station (Toyoko line, from Shibuya/Nakameguro), Meguro line (from Meguro, which is connected to the Namboku line and Mita line).