Tweedy has been prone to migraines throughout his entire life, forcing him to miss forty days of elementary school in one year. While he attempted to regulate his use of painkillers, he was never able to stop their use for more than five weeks. Tweedy attributes this to comorbidity with major depressive disorder and severe panic attacks. In 2004, he entered a dual diagnosis rehabilitation clinic in order to receive treatment for an addiction to prescription painkillers. Tweedy quit smoking the next year; John Stirratt claimed afterward that this significantly improved the focus of the band.  Tweedy is married to former talent agent Sue Miller. Tweedy first met Miller when he was trying to get Uncle Tupelo booked at Cubby Bear, where Miller worked. Miller opened a club in Chicago named Lounge Ax in 1989, and booked Uncle Tupelo for 16 shows over four years. Miller and Tweedy began dating in 1991 and they were married on August 9, 1995. Sue was diagnosed with cancer in 2014. In an interview with Rolling Stone, Tweedy said "she's doing great now." Tweedy also said that music is a healthy distraction in difficult times such as these. They have two sons: Spencer and Sam. Spencer was the drummer for pre-teen rock band The Blisters and a new band called Tully Monster. In 2008, Spencer joined Wilco on stage at Madison Square Garden to play drums on their song "The Late Greats," while opening for Neil Young.  Miller is Jewish, and Tweedy's oldest son had a Bar Mitzvah ceremony. During his son's ceremony, Tweedy played an acoustic version of Bob Dylan's "Forever Young."

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