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Hi Moran - To do things like this it gets a bit more complex - you probably want to write a small bash script, using the 'bc' calculator. Something like: #!/bin/sh M=`fslstats image -M` S=`fslstats image -S` uthr=`echo $M+2*$S | bc -l` lthr=`echo $M-2*$S | bc -l` fslmaths image -thr $lthr -uthr $uthr out It would be worth having a look at the scripting lecture on the FSL 2009 course web page to learn how this works and to make the script more flexible. Eugene 2009/11/25 Moran Artzi <[log in to unmask]> > Hi Andrew, > Regarding to this issue - one more question > I need to calc the following option: > Calculate image mean + standard deviation value (fslatats -M and -S option) > and then threshold the original image with Mean value +/- 2 std > (falmath Orig_Imge -thr <-2*S-M values> -uthr <2*S-M values> > Threshold_Image) > > Any suggestions? > Thanks > Moran > > > > > > On Mon, Nov 23, 2009 at 8:18 PM, Andrew Jahn <[log in to unmask]>wrote: > >> Try using the backwards quotes (the upper left of the keyboard) to capture >> the output and use it in the command. For example, >> >> fslmaths image1 -sub `fslstats image2 -M` outputImage >> >> Is this what you wanted to do? >> >> -Andrew >> >> 2009/11/23 Moran Artzi <[log in to unmask]> >> >> Hi >>> I'm trying to read fslstats results from the command line and to use in >>> as a >>> values for fslmath. >>> For example: >>> Calculate image mean value (fslatats -M option) and then subtract from >>> each >>> voxel of the original image (falmath -sub <value> OrigImge) >>> >>> Any suggestions how its can be done? >>> Many thanks >>> Moran >>> >>> >> > -- Eugene Duff Centre for Functional MRI of the Brain (FMRIB) University of Oxford John Radcliffe Hospital, Headington OX3 9DU Oxford UK Ph: +44 (0) 1865 222 523 Fax: +44 (0) 1865 222 717 --