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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 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.
Does it shows difference between two group with corrected covariates as implemented through design.mat and design.con file.
Can we report the results of this file? more often this file looks as if it contains spurious information that doesn't make sense always(some very scattered activation maps)
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.

Kindly assist

Thanking you in anticipation 


On Wed, Jan 8, 2014 at 3:19 PM, Anderson M. Winkler <[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