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On 16 Dec 2010, at 03:25, Joanne Lin wrote: > I am using tractography in FDT, working through the FSL course data at the moment. I have tracked from a single voxel seed in the internal capsule and come up with a connectivity distribution and overlaid on FA map. The next instructions from the practical are ‘adjust the min and max display thresholds to look at the relative probabilities of paths’ – the min/max values when I first open the image at 0 and 5000 respectively. With a tractography result selected in the overlay list, changing bricon settings allows you to explore the extents of tracts based on the number of particles recorded as having passed through each voxel. The bricon values simply set the range of image intensities over which the selected look up table is applied - anything less than the lower bound being rendered transparent. > If the intensity doesn’t change when I adjust values in the Bricon toolbar, how would I get it to display relative intensities? Or am I missing something in the interpretation of these figures? Not sure I know what you mean by "relative intensities"? The result image is equivalent to connectivity probabilities when normalised by total number of seed particles, i.e., 50% of the seed particles passing through a given voxel indicates a 50% confidence in the seed region(s) being connected to that voxel. I'm afraid fslview doesn't compute this value it just displays the image. Of course you could use fslmaths to form a normalised probability map and load that instead... Hope that helps, Dave -- Dave Flitney, IT Manager Oxford Centre for Functional MRI of the Brain E:[log in to unmask] W:+44-1865-222713 F:+44-1865-222717 URL: http://www.fmrib.ox.ac.uk/~flitney