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Hi Steve, Thank you for your prompt reply! I used the same binary mask for six contrasts on one subject. The position of the max voxel for some of the contrasts is (0 0 0 ) which does not make sense. I was wondering why this is happening? Below is a sample featquery with the above problem (i.e. pe2 and pe4) 1 stats/pe1 5 0.00 0.31 0.59 0.62 0.89 0.89 23 37 7 25.32 1.38 -15.90 1 stats/pe2 5 -0.74 -0.74 -0.62 -0.70 -0.39 0.00 0 0 0 103.93 -112.31 -36.09 1 stats/pe3 5 -0.35 -0.35 -0.07 -0.17 0.32 0.32 24 36 7 22.06 -1.59 -15.59 1 stats/pe4 5 -2.54 -2.54 -1.94 -1.92 -1.46 0.00 0 0 0 103.93 -112.31 -36.09 1 stats/pe5 5 -0.13 -0.13 0.52 0.59 0.90 0.90 24 36 7 22.06 -1.59 -15.59 1 stats/pe6 5 -0.65 -0.65 -0.25 -0.45 0.64 0.64 24 37 7 22.03 1.34 -16.02 Many thanks, Heather Quoting Steve Smith <[log in to unmask]>: > Hi, > > On 12 Jul 2007, at 16:30, Heather Cogswell wrote: > >> Dear FSL users, >> >> I'm an FSL newbie, so thanks in advance for your help! >> >> How can I make a mask from a 3rd level activation? I tried avwroi but it >> just creates the mask of the specific voxels that I input . . . I want to >> create a mask of the chosen voxels overlaid on the entire brain. > > I'm not sure what you're asking - you should probably take the > appropriate thresh_zstat image from inside the appropriate > something.gfeat/cope??.feat directory and maybe binarise this with > avwmaths++ > >> For Featquery analysis I can choose "stats/pe" or "stats/cope". Which one >> should I use for ROI analysis? > > It's up to you. If this isn't clear then you should probably read the > FEAT manual carefully, including the intro to GLM etc stuff in it - > hopfully then it will be clear which is what you want. > > Cheers, Steve. > > > >> >> >> Thanks, >> Heather > > > ------------------------------------------------------------------------ --- > Stephen M. Smith, Professor of Biomedical Engineering > Associate Director, Oxford University FMRIB Centre > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > +44 (0) 1865 222726 (fax 222717) > [log in to unmask] http://www.fmrib.ox.ac.uk/~steve > ------------------------------------------------------------------------ --- >