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Hi, Right, when you run the 3rd level you'll most likely enter the 2nd level copes, which are in a .gfeat/cope#.feat/stats/cope# directory (the #'s depend on your study). The lower level feat option allows you to enter gfeat/cope#.feat and it applies your model to all the copes in the .gfeat/cope#.feat/stats/ directory. Not sure what you mean by the variance and the degrees of freedom. Perhaps you were wondering how the higher level analysis runs if you only feed in a cope? Feat will automatically find the varcope files in order to run the Flame analysis. Cheers, Jeanette On Fri, Sep 28, 2012 at 1:46 PM, Joyce Yu Guo <[log in to unmask]>wrote: > Dear Jeanette, > > Thanks for the confirmation. I had other question about high level > analysis input. According to the FSL website, the input for high level > analysis could be 3D cope imaging or low level FEAT directory. What is the > difference between these two? Does it has something to do with variance and > degree of freedom which would be used in the high level or not? Thank you > in advance. > > BW, > Joyce >