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
|