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Thanks Anderson for your response You mean i should first analyze it with uncorrected threshold without any masking and after that use these codes? ttologp -logpout logp1 varcope1 cope1 `cat dof` - fslmaths logp1 -exp p1 - fdr -i p1 -m ../mask -q 0.05 fslmaths p1 -mul -1 -add 1 -thr .99660181 -mas ../mask thresh_1_minus_p1 i should use my mask in the line 3 and 4 ? or only in 3 ? On Thu, Nov 27, 2014 at 12:59 PM, Anderson M. Winkler < [log in to unmask]> wrote: > Hi John, > > Yes, it is possible. See the option -m in the command "fdr". > > All the best, > > Anderson > > > On 26 November 2014 at 19:40, John adler <[log in to unmask]> wrote: > >> Dear all >> I am new to FSL and i don't know if FSL have small volume correction >> (recalculating corrected p-value for a ROI ) like SPM? >> >> if it is available, can i use it with FDR? >> >> thanks in advance >> >> >> cheers >> john >> > >