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Hi, On 28 May 2007, at 09:27, Benny Liberg wrote: > Dear FSLers, > > I have two questions, and I would really appreciate if anyone could > help me > out on this rather simple matter. > > I compare 5 individuals that have done two slightly different > experiments. > So far, I've done a FFX higher level, regional analysis of both > experiments. I rerun the higher level analysis with each of the eight > masks. I then extract the peak vxl from rendered_zstats (avwstats) > and then > create a mask containing peak vxl and the 26 surrounding ones > (avwmaths). I > then run featquery with that new mask to get mean BOLD % change. Fine - though it is dangerous to use rended_zstats images - they are combined greyscale/colourmap images showing activation combined with a background image. You should use thresh_zstat images > I can't help thinking that this could be solved by running avwstats > -x with > some kind of mask option and then create the 27 vxl ROI with > avwmaths. Any > suggestions? Indeed - see below > Also, is there any way of dilating a mask? Sure - use the -dil option in avwmaths. Steve. > > Best regards, > Benny Liberg > > > > > Instead of rerunning the higher analysis with new pre-thr masks > applied > masks (8) for each anatomical strucuture, I would like to: > > 1. extract the peak vxl within a mask (avwstats) and > 2. create a new mask containing 26 vxls around the peak vxl > (avwmaths) and > extract mean %BOLD change from these 27 vxls. > > I know how to do 1 and 2 but can't figure out how to avoid ------------------------------------------------------------------------ --- 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 ------------------------------------------------------------------------ ---