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Hi, If you want to create a binary mask of overlap between two thresholded zstat maps (etc) you can use something like fslmaths thresh_zstat1 -mul thresh_zstat2 -bin overlap_mask Then you can apply this to any other thresholded zstat map and rerun "cluster" to get out the local maxima, e.g. fslmaths thresh_zstat3 -mas overlap_mask masked_thresh_zstat3 cluster -i masked_thresh_zstat3 -t 0.0001 --olmax=grot Cheers. On 6 Feb 2009, at 16:33, Lisa Evans wrote: > Hello, > > I wondered if anybody could help me with some masking issues. I > have run a > within-participants experiment with 4 tasks (1,2,3,4: each a > separate scan), > with three conditions in each task: 1A,1B,1C, 2A, 2B, 2C…. > Initially I ran a > first-level analysis for each participant computing the contrasts > that I was > interested in (e.g. 1A+1B-1C etc). I then ran a higher-level mixed > analysis > computing the grand average of these contrasts. I am therefore able > to see > areas of activation within each task. What I’d like to do now is > look at the > areas of unique and common activation between pairs of tasks, in > particular > looking at the contrast A+B-C. What’s the best way of doing this? > > I have attempted the inclusive masking. I’ve generated binary masks > of > activations for A+B-C in task 1 and 2 and then used the fslmaths > command – > mul to look at common activation. Is this correct? Using this > method I am able > to see the areas of activation using fslview, however I wondered if > there is > any way of getting a list of the clusters and some z-coordinates? > > Finally, with regard to the exclusive masking I’m not sure of the > best way to > go about doing this, both theoretically and practically. So > detailed advice on > this would be much appreciated! > > Thanks very much. > --------------------------------------------------------------------------- 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 ---------------------------------------------------------------------------