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Hi slicer only adds red outlines if the base lookup table is standard greyscale. In order to achieve what you want using fsl tools only one would need to modify the code (nightmare). The alternative is to use the imagemagick tools, i.e. run your call to slicer twice (with and without the -l option), then use imagemagick to extract only the red component from the greyscale image. These two images you can then combine, again using imagemagick... I don;t quite know the commands but check out http://www.imagemagick.org/Usage/ hth Christian On 18 May 2011, at 18:39, bettyann wrote: > yes, thank you, 'overlay' does a better job of creating the basic image i wish to display. > > but what i am trying to accomplish in the 'slicer' command is to display the basic image (just created by 'overlay') with the outline of a the hippocampus stamped on top. the 'slicer' command allows for a 2nd input volume whose edges are stamped on top of the first volume. this is exactly what i wish to do. > > unfortunately, i do not see this edge. can you recommend how i might achieve this? the commands i am using are: > > overlay 1 0 MNI152_T1_2mm_brain -a cope1 0.241417 3.307448 /tmp/overlay_cope_over_mni > slicer overlay_cope_over_mni hippocampus_left -s 2 -L -e 0.5 -x -50 sliceX_050.png -x -51 sliceX_051.png -x > > thanks, > - bettyann