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If you live out in western Tokyo you can jog along the Kanda River. It generally runs south of the Inokashira-line (Kichijoji-Shibuya). Like most rivers in Tokyo the Kanda River is concreted, but past the Keio Meidaimae station it runs through some very nice residential areas (including my own, Hamadayama). Many Japanese jog and bicycle here, but it was never crowded. Very safe too. There are cherry trees in the Spring, and several parks. I think you can jog all the way to Inokashira Park at Kichijoji, but I am not sure. A great running place away from major roads.