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Hi Himanshu, Please, see below: On 08/01/2014 11:28, Himanshu Joshi wrote: > Hello Anderson, > Cluster means command "cluster" like in the below example > cluster-i dr_stage3_corrp_tstat3 -t 0.95 -o > dr_stage3_corrp_tstat3_index --osize=dr_stage3_corrp_tstat3_size > >>dr_stage3_corrp_tstat3_Cordinate_details.txt > > And then using dr_stage3_corrp_tstat3_index file for labeling the > differential connectivity maps with the help of probability maps > (Harvard cortical and subcortical atlas). > > Is this method correct? I think I have a script that automates this task, please here if it's what you need: http://brainder.org/2012/07/30/automatic-atlas-queries-in-fsl > > I had lot of confusion regarding dr_stage3_corrp_tstat$x file > generated after dual regression. > what is the default level of significance for > dr_stage3_corrp_tstat$x...nii.gz. There is no default. The image contains the corrected 1-p values, ranging between 0 and 1. It's you who apply the significance threshold after you already have the image, not before. Be careful not to confuse this significance threshold with the cluster-forming threshold, which is given to randomise with the options -c, -C, -F or -S. None of these options is used by default in the dual_regression script. As you are producing these images, I can only assume that you edited the dual_regression to include these options, which is fine (it's line 180 of the script). > Does it shows difference between two group with corrected covariates > as implemented through design.mat and design.con file. Yes, it does. Of course, as long as the design matrix and contrasts are correct for what you want. See here: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/GLM > Can we report the results of this file? Yes, sure. > more often this file looks as if it contains spurious information that > doesn't make sense always(some very scattered activation maps) Is the design correct? Was the preprocessing good? Many things can cause undesirable results. > I think this is not the desired (p<0.05) file because that doesn't > matches the output with the min (0.95) and max (1) values for same > file in fslview is seen. The image contains 1-p, so whatever you want to do with it, you need to take this into account. Threshold it at 0.05 or 0.95 is completely different, so be careful. All the best, Anderson > > Kindly assist > > Thanking you in anticipation > > > On Wed, Jan 8, 2014 at 3:19 PM, Anderson M. Winkler > <[log in to unmask] <mailto:[log in to unmask]>> wrote: > > Hi Him anshu, > > I'm not sure if I follow the question. Do you mean you use the > command "cluster", or do you mean cluster-level inference in > randomise? In any case, no, there isn't a way, nor is it > necessary, to specify the alpha (significance level) before > running the dual regression, because this is to be done after you > have produced the image with p-values, which happens only at stage 3. > > Remember that to use 0.05, you have to use 0.95, because the > outputs are always 1-p. > > Regarding a default level, no, there isn't one, although it's > common to use 0.05 for the corrected p-values. > > All the best, > > Anderson > > > > On 07/01/2014 13:34, Him anshu wrote: > > Hello Anderson, > How I was using alpha value p<0.05 is after generation of dual > regression maps (dr_stage3 maps), I use cluster to provide > significant threshold level. > Is there a phenomenon where we can provide significant > threshold before dual regression so that dr_stage3 file would > be generated according to our defined threshold level. > By the way what is the default level of significance for > dr_stage3_corrp_tstat ...nii.gz. > > > > > -- > *Himanshu Joshi* > M.Tech. Cognitive & Neuroscience. > Senior Research Fellow > Ph.D Scholar, > Department of Psychiatry > NIMHANS, Bangalore > > http://mbial.weebly.com/himanshu-joshi.html