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Hello, fslmaths *dr_stage3_ic0000_tfce_corrp_tstat1* *-thr 0.95* -bin ROI_2functional For TFCE explanation it would be better you go to FSL website and look the meaning of randomise and what is TFCE (is a type of correction like FDR = Family Discovery Ratio) to avoid false positives. Cheers. 2011/8/1 Leslie Engineering <[log in to unmask]> > Hello- > > Just for clarification (b/c I don't understand what tfce is and why I would > need a dual regression): Basically, I loaded my zstat1_2highres data on top > of my anatomical scan. Made a mask over a specific cluster and now would > like to threshold so all voxels with p value less than .05 go away. I > transformed the mask to functional space and let's say it is now called > ROI_2functional. Are you saying I would type the following: > > fslmaths ROI_2functional -thr 0.95 -bin NEW > > where NEW is the name I give my mask that has now lost all voxels with a p > value greater than .05 > > Is this correct? > > Thanks and sorry I don't understand! > > On Sun, Jul 31, 2011 at 6:27 PM, Rosalia Dacosta Aguayo < > [log in to unmask]> wrote: > >> Hi Helen >> >> Have you done dual_regression first? >> >> I you have it, you could see than you have a lot of data, the data of >> interest is (in red) and the threshold is (green) >> >> >> >> >> But, if you have a little sample, like me, and you have results with TFCE >> you would have to take into account that TFCE corrp is very conservative, >> so, you may do the following: >> >> fslmaths *dr_stage3_ic0000_tfce_p_tstat1* -*thr 0.99* -bin (and the name >> of your mask). >> >> I hope this helps you more. >> >> Rosalia. >> >> >> 2011/7/31 Leslie Engineering <[log in to unmask]> >> >>> I'm sorry I don't understand the values you gave me. >>> >>> Maybe writing out the command line would help me. For instants, if I want >>> to isolate voxels with a p value .05 or less within a functional ROI mask I >>> made (ex: ROI.nii.gz) I would type the following: >>> >>> fslmaths ROI.nii.gz -tfce .05 ROI_thresh05.nii.gz >>> >>> ? >>> >>> >>> On Sun, Jul 31, 2011 at 4:27 PM, Rosalia Dacosta Aguayo < >>> [log in to unmask]> wrote: >>> >>>> I think threshold with TFCE corr.p tstats is 0.95 and with uncorrected >>>> results (only TFCE p tstats) is 0.99. >>>> >>>> I understand you perfectly, I am naive too, but I am doing this for my >>>> work. >>>> >>>> I hope this help you. >>>> >>>> Rosalia. >>>> >>>> >>>> >>>> 2011/7/31 Leslie Engineering <[log in to unmask]> >>>> >>>>> Hello- >>>>> >>>>> I'm sorry to ask such basic questions, but I am still confused by the >>>>> threshold option when using fslmaths. >>>>> >>>>> For instants, if I create a mask in anatomical space then transform it >>>>> to anatomical space and want to threshold for some finite p value would I >>>>> use fslmaths -thr? >>>>> >>>>> thanks >>>>> >>>> >>>> >>> >> >