Bettyann,
overlay is inclusive wrt the intensity ranges you specify, i.e. in your
case you ask overlay to add the red->yellow color range from 0->12 and
the dark blue -> light blue color range to 0 -> -9. Therefore, 0 values
turn green. If you use
avwstats thresh_zstat -l 0.001 -R
you'll get the correct 'positive' image range. Similarly,
avwstats thresh_zstat -u -0.001 -R
gives you the right 'negative' intensity range. Use these for the
overlay call and things should work fine
Alternatively, you can directly change the code in melreport.cc and
re-compile.
cheers
christian
On 16 Dec 2004, at 18:03, Bettyann Chodkowski wrote:
> hello all,
>
> i am trying to make a few cosmetic changes to the .png files of the ICs
> created by melodic (ie, the IC_nn_thresh.png files). by looking in
> melreport.cc, i can see that the .png files are created via the overlay
> and slicer methods. i tried to duplicate the creation of these .png
> files using the (assumed equivalent) programs in $FSLDIR/bin --
> overlay and slicer. my results are close ... except the colors are
> wrong. my off-color :) results can be viewed here:
>
> http://godzilla.kennedykrieger.org/~bettyann/oversli20b_050_500.png
>
> this is what i did:
> (1) create background image:
> % avwroi filtered_func_data ffd_49 49 1
>
> (2) get min/max values from thresholded zstat image for IC 20:
> % avwstats xyz.ica/stats/thresh_zstat20 -R
> [[ (min,max) = (-9.47,12.00) ]]
>
> (3) overlay thresholded zstat over background:
> % overlay 1 0 ffd_49 -a \
> xyz.ica/stats/thresh_zstat20 0 12.00 \
> xyz.ica/stats/thresh-zstat20 0 -9.47 over20b
>
> (for some reason, reversing the order of the numbers i thought
> would be the <s2min> <s2max> gives a better image ... but this
> is hard to determine since the colors in the final .png are
> fundamentally wrong; direction as to what these values should
> be is appreciated.)
>
> (4) create .png from overlay'd image:
> % slicer overb -s 0.5 -A 500 oversli20b_050_500.png
>
> the resulting background image is green not greyscale. also, i
> don't know how to get the color bar included in the .png. any
> guidance?
>
> thank you,
> - bettyann
> _____________________________________
> BettyAnn Chodkowski F.M. Kirby Center
> e: [log in to unmask] Kennedy Krieger Institute
> v: 443.923.9524 707 N. Broadway
> f: 443.923.9279 Baltimore, MD, USA 21205
>
>
--
Christian F. Beckmann
Oxford University Centre for Functional
Magnetic Resonance Imaging of the Brain,
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
Email: [log in to unmask] - http://www.fmrib.ox.ac.uk/~beckmann/
Phone: +44(0)1865 222782 Fax: +44(0)1865 222717
|