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Dear BettyAnn, Sorry to hear about your long-term frustration. The easiest way to achieve your goal is to use the Renderstats GUI which will output the desired overlay command. For instance, I just ran one to do the sort of thing you are saying and it produced the command: /usr/local/fsl/bin/overlay 1 0 /Users/mark/testdir/example_func 0.000000 8836.757812 /Users/mark/testdir/zstat1 2.5 15.546515 /Users/mark/testdir/zstat1 -2.5 -10 /Users/mark/testdir/outputimage This command was displayed in the terminal window, so you can then use this for subsequent scripting calls or just avoid the GUI thereafter. I suspect that your command were probably failing just due to the order of the negative thresholds (which are confusing). Once you have this image file output from overlay, slicer works straightforwardly (no need to specify any colourmap options at all). All the best, Mark On 19 Dec 2012, at 20:56, bettyann <[log in to unmask]> wrote: > Okay, no really. After years of trying (and I'm not kidding), I still cannot create an overlay/slicer .png displaying both positive voxels in red-yellow scale and negative voxels in blue-white scale. > > Searching the archives, I see replies that imply, 'Oh, this is simple,' or 'Just do [blah].' Sigh. > > I've tried a few things but below is the least frantic rendition: > > rng1=`fslstats zstat1 -l 0.0001 -R` > rng2=`fslstats zstat1 -u -0.0001 -R` > echo $rng1 # 0.000111 10.265674 > echo $rng2 # -5.066993 -0.000104 > > oVol=zstat1_render_posNeg > cmd="overlay 1 0 ../example_func -a zstat1 $rng1 zstat1 $rng2 $oVol" > echo $cmd > # overlay 1 0 ../example_func -a zstat1 0.000111 10.265674 zstat1 -5.066993 -0.000104 zstat1_render_posNeg > eval $cmd > > fslstats zstat1_render_posNeg -R > 11.559369 45.564034 > > I get it that the 'composite' volume does not have negative values. I am assuming that some range of voxel values in the composite volume represents the positive values in the original volume and another range represents the negative values. But how do I tell slicer to use Red-Yellow for some range (that I don't know) and Blue-White for some other range (that I also do not know)? > > These commands do not do it: > slicer zstat1_render_posNeg -S 2 750 zstat1_render_posNeg.png > slicer zstat1_render_posNeg -l [anyLUT] -S 2 750 zstat1_render_posNeg.png > > Do I need to construct my own color table -- half red; half blue -- to match the two ranges in the output from overlay? > > If it matters, I am running FSL v4.1.8. > > I would be very, very grateful if someone could help me. > > Hang doggedly, > - BettyAnn >