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Dear Hannah, > I have yet another question about FNIRT, this time about the cnf file. I would like to use one of the configuration files you provide. However, since I need a 1mm instead of 2 mm template brain, I was wondering, if I could just change that part in the configure file, or if then, all the other set parameters would not work anymore? why do you need a 1mm template? That is a quite high resolution to perform your 2nd level analysis in given that the resolution of your fMRI data is typically ~3mm or so. The, slightly sad, truth is that changing to a 1mm template does change some other things. Luckily the changes are quite subtle and you would get away with just changing the line --subsamp=4,4,2,2,1,1 to --subsamp=8,8,4,4,2,2 You will then also need to specify your own mask in the space of your template by including --refmask=your_mask_goes_here where the mask should be in the space of your template and have one everywhere where there is brain and zero elsewhere. Good Luck Jesper