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Best. Christmas. Present. Ever. Thank you! > Hi BettyAnn, > > I wrote me a little tool to create some overlay png files in a simple > way, wrapping around the frustrating slicer part. So maybe this could > help you (hope it does not cause further problems and frustration though). > > See the help information to see, how it works. In your case, the -neg > option might be the desire one. Let me know, if you have further > questions or come accross bugs... > > good luck, > wolf > > >On 12/20/2012 10:09 AM, Mark Jenkinson wrote: >> 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 >>>