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Hi Steve, As I said in my email, I think the problem is with fslview rather than tbss_fill. Thanks for your suggestion about adjusting the intensity display range. I hadn't thought of that because of specifying the 0.95 threshold at the tbss_fill stage, It does the trick though. For some reason the intensity range was coming up as 0.2,1 but changing it to 0.05,1 fixes it. Many thanks, Clare ________________________________ From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Stephen Smith [[log in to unmask]] Sent: 23 April 2013 15:22 To: [log in to unmask] Subject: Re: [FSL] tbss_fill and fslview using fsl 5.0.2 You need to work out if the problem is tbss_fill or fslview. Have you tried adjusting the intensity display range in fslview? Steve. On 23 Apr 2013, at 08:11, "Gibbard, Clare" <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hello, I have FSL 5.0.2 installed on Ubuntu 12.04 LTS. When I run the tbss_fill command it completes without an error message, but when I load up the filled output in fslview the results haven't been filled. I have fslview version 4.0.1. I then tried running the same tbss_fill and fslview commands on a colleague's Mac, which is running FSL 4.1.2 and fslview 3.1.8, and it all worked perfectly. Loading up the correctly filled files from FSL 4.1.2 on my computer doesn't work, but I can visualize results filled on my computer on the Mac running 4.1.2. This suggests that the problem is with visualizing filled files in FSL 5.0.2, but that the actual tbss_fill stage works fine. Has anyone come across this problem? Do you know how I can work around it? Thanks, Clare --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask]<mailto:[log in to unmask]> http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------