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Hi use fslmaths, fslstats and fsl2ascii fslstats input -S gives you the standard deviation in the image (across non-zero voxels) which you can use within fslmaths to do whatever you fancy. fsl2ascii can convert to a standard text file, though I think you're better of reading the file into matlab using read_avw (supplied by us in $FSLDIR/etc/matlab) hth Christian On 31 Jul 2009, at 09:08, Moran Artzi wrote: > Hi, > How can I threshold image by its standard deviation (to keep values > only in > the range of 1-2 std from mean)? > In addition, is it possible to save results (after using fslstats& > fslmaths > options) in a text file? > > Thanks > Moran _______________________________________________ Christian F. Beckmann, DPhil Senior Lecturer, Clinical Neuroscience Department Division of Neuroscience and Mental Health Imperial College London, Hammersmith Campus Rm 419, Burlington Danes Bldg, Du Cane Road, London W12 0NN, UK Tel.: +44 (0)20 7594 6685 --- Fax: +44 (0)20 7594 6548 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 222551 --- Fax: +44 (0)1865 222717 Email: [log in to unmask] http://www.fmrib.ox.ac.uk/~beckmann