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On 10 Nov 2008, at 04:27, SUBSCRIBE FSL Susan wrote: > Hi - > > I am a new FSL user, converting over from using SPM99 many years > ago. I was > wondering if there's a way to 3D render the thresh_zstat from one of > my > higher level analyses to a structural image (e.g., bg_image). > > I tried opening bg_image in FSLview, then adding the zstat file, and > using > 3D Viewer. But that gave me a solid brain with no gyral/sulcal > anatomy, and Use the threshold control (next to the "Clipping" check box) to adjust the level until you see a nice pial surface representation. > no activation blobs. I tried changing the opacity of the structural > brain, > to find that showed me the opposite side of the brain, rather than > internal > anatomy (and still no functional activation). To see the activations you will need to cut away part of the brain to reveal them. Turn on clipping then press "b" to toggle on the control that allows you to adjust the position and extent of the clipping box. Using the control points you should be able to carve away a section revealing the activations. Look at the online help for the description of the 3D controls: http://www.fmrib.ox.ac.uk/fsl/fslview/3D-vtkkbd.html > I am trying to create an image similar to SPM, with activation > rendered on > the surface of the brain. I'm afraid we don't have an equivalent view. It has been at the back of my mind to add a function to project the nearby activation intensities onto the surface but we haven't tried to implement that yet. > I would appreciate any help I can get. Thank you! > Cheers, 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