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Hi - you're right that it won't correctly process these "0" labels for the label atlases - though that wouldn't make sense to select anyway as they correspond to the background. Thanks for pointing this out - I've amended Featquery so that it doesn't show the "0" label option for the labels atlases. Cheers. On 3 Mar 2009, at 10:51, Feng Xue wrote: > Dear folk, > > When using Talairach Daemon Lables or JHU ICBM-DTI-81 White-Matter > Lables as atlas in Featquery, Featquery will first call fslmaths to > generate a binary mask (command as below) > $FSLDIR/bin/fslmaths $FSLDIR/data/atlases//Talairach/Talairach- > labels-2mm -thr 1058 -uthr 1058 -bin /tmp/featquery_4VE87F > Mostly, it'll run as precise as we predict. But if we chose label 0 > as our roi, there would be no valid mask, because of uthr = 0 > (command as below) > $FSLDIR/bin/fslmaths $FSLDIR/data/atlases//Talairach/Talairach- > labels-2mm -thr 0 -uthr 0 -bin /tmp/featquery_4VE87F > > So I would suggest to judge atlas id first then call fslmaths in > $FSLDIR/tcl/featquery.tcl. > > > Best Regards > > > Feng Xue > [log in to unmask] > 2009-03-03 > > National Key Laboratory of Cognitive Neuroscience and Learning > Beijing Normal University > Beijing, China. 100875 > Tel: 86-13810154455(m) > Fax: 86-10-58806154(o) > web: http://psychbrain.bnu.edu.cn > ============================================================ > Welcome to MuDuo JinSheng BBS @ Beijing Normal University > telnet://bbs.mdjs.org > http://bbs.mdjs.org --------------------------------------------------------------------------- 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] http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------