 |
 |
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