Hi Russ,
The colormap chosen for the images is selected by slicer, the program
which creates the PNGs, based on the aux info in the header. overlay
simply takes a background image as well as one or two stats images and
creates a new image where all the 2/3 intensity informations get
scaled into new intensity ranges (either integer or float, see cmdline
usage). Overlay then sets the aux field with what it thinks should be
used as a colormap and writes saves this into a new NIFTI file. slicer
reads all this info and maps the intensity values to colors.
In order to achieve what you want you'll either have to mess about
with the inputs to overlay, e.g. set voxels which are >0 for both
images to 0 in one of the two or you'll need to create your
custom .lut file, see $FSLDIR/etc/*lut for examples. These are simple
text files containing RGB triplets, though sorting out the #entries
will be a pain.
cheers
Christian
_______________________________________________
Christian F. Beckmann, DPhil
Senior Lecturer, Clinical Neuroscience Department
Division of Neuroscience and Mental Health
Imperial College London
Hammersmith Hospital - London W12 0NN
Tel.: +44 (0) 208 383 3722 --- Fax: +44 (0) 208 383 2029
Email: [log in to unmask]
http://www.imperial.ac.uk/medicine/people/c.beckmann/
Senior Research Fellow, FMRIB Centre
University of Oxford
JR Hospital - Oxford OX3 9DU
Tel.: +44 (0) 1865 222552 --- Fax: +44 (0) 1865 222717
Email: [log in to unmask]
http://www.fmrib.ox.ac.uk/~beckmann
On 4 Mar 2008, at 18:18, Russell Poldrack wrote:
> is there a way to change the color maps that are used in overlay? I
> want to show two maps superimposed together on an anatomical image,
> but with the standard maps, the green that reflects overlap between
> my two activation maps is difficult to see on top of the orange for
> one of the maps. I could obviously do it by hand in fslview but
> would like to automate it if possible
>
> thanks
> russ
>
> ---
> Russell A. Poldrack, Ph.d.
> Associate Professor
> Wendell Jeffrey and Bernice Wenzel Term Chair in Behavioral
> Neuroscience
> UCLA Department of Psychology
> Franz Hall, Box 951563
> Los Angeles, CA 90095-1563
>
> phone: 310-794-1224
> fax: 310-206-5895
> email: [log in to unmask]
> web: www.poldracklab.org
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