No it isn't.
Some people argue that disc two qualifies as a concept album, but it's only one half of the album.
The first five songs (that is, disc one) are not connected in any way to each other or to disc two. The sections of "Six Degrees of Inner Turbulence" (the song) do have a connection to the other sections within that song, but it doesn't qualify it as a concept album.
Bill W. ("The Glass Prison" is dedicated to him in the liner notes) was one of the founding members of Alcoholics Anonymous. TGP is about steps 1-3 of the AA 12-step program. His 'friends' are the people who have beaten their addiction with the help of the program.
While some of the lyrics do seem to apply to JP himself, he has said that he wrote it about a religious figurehead.
It wasn't written to project a particular point of view, but rather present both sides from which the listener can make their own decision.
The title track from Six Degrees of Inner Turbulence is the story of six people who have a mental problem of some kind. JP and MP split up the lyrics and wrote for three people each.
It is not known if any of the characters are based on real people.
"I was a bit torn over whether or not we should give the song different IDís on the CD, because I wanted it to be perceived as 1 song. Ultimately I decided to index it because after a few listens, the novelty of seeing the CD timer reach 42:00 would wear off and it would become very annoying to have to scroll through the whole song to find a particular section."
- Mike Portnoy