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Dear David, > SpMat::SolveForx: Warning requested tolerence not obtained. > Requested tolerance was 0.001, and achieved tolerance was nan > This may or may not be a problem in your application, but you should > look into it > > I'm not really sure what to make of this. I'm an undergraduate > student and have only been playing with scripts for FSL for a few > weeks now so if this is a common problem or an easy fix I apologize > for posting this question. this comes when running fnirt, right? This is a warning one gets when the solution to a linear system of equations inside fnirt is poorly conditioned. Mostly it says something like > Requested tolerance was 0.001, and achieved tolerance was 0.whatever in which case one can safely ignore it since fnirt will adjust the system to be better conditioned for the next iteration. In your case you get nan (not a number), which makes it less likely that fnirt can recover from it. My two first guesses would be 1. You forgot to specify a valid affine starting guess for the --aff parameter. 2. You have some strange values in your data Check this, and if you still have a problem get back to us with more details. Good Luck Jesper