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Hi, On 15 Jul 2009, at 19:46, Heather C. wrote: > Hello, > > I am running contrast masks on each subject in my lower level > analysis. For > one such mask, I am masking contrast 7 with contrast 8, which shows > up like > this in my report log: > > /usr/local/fsl/bin/fslmaths thresh_zstat7 -mas stats/zstat8 > conmask/thresh_zstat7 > > I have a few questions about this..... > > 1. Why is it masking a z stat image (stats/zstat8) onto a > thresholded image > (thresh_zstat7)? Presumably because you asked it to? If you selected the "zstat>0" option then this is what you're asking for. The "-mas" option uses wherever the following argument is >0 as the mask. > > 2. What exactly are the thresholded images (e.g. thresh_zstat7) and > how do > they differ from a regular zstat image (e.g.zstat7)? The latter is unthresholded and the former is thresholded according to whatever thresholding you selected in the FEAT GUI. > > 3. It appears that the original thresh_zstat7 is being overwritten > by the > new contrast masked thresh_zstat7...is this correct? Yes > > 4. Does this mean I want to look at thresh_zstat7 for my new contrast > masked image and that zstat7 is my old, original contrast 7 image > that is > unaffected by the contrast mask? Not quite -see above. > > 5. Is there an easy way to get the contrast masked images to be named > something new, or some way to create them without overwriting any of > the > original contrast images? The easiest thing to do would be to run FEAT twice, with and without the contrast masking. > > Thank you so much for your help! > --------------------------------------------------------------------------- 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 ---------------------------------------------------------------------------