Dear Y.P.,
> Does anybody know how to make sure the FNIRT warpfield / FNIRT registration is carried on to higher-level analyses? I.e. if I've FNIRTed my first-level FEAT output, how do I specify that the FNIRT registration be used at higher levels? We normally don't rerun the registration at higher levels, and I'm concerned it's preset to use the FLIRT output (which has to be run before FNIRT can be run). I.e. in my reg folder, there are both: 1) .mat files produced by the linear flirt registration, and 2) a nonlinear warpfield produced by FNIRT. How can I make sure only the FNIRT output is used?
if the files that are produced by fnirt (there should be a *_warp* file) are present in the reg directory then it will be used for resampling the copes and varcopes when taking them to a higher level. No need to worry.
Good Luck Jesper
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