I want to use 3dDegreeCentrality and 3dLFCD method to analysis my data. But there are many options. It is hard for me to choose the best parameters. Does any one have some example codes to run 3dDegreeCentrality and 3dLFCD?
Thank you so much!
Some of the options depend on what type of prepreocessing has already been done to the data. Based on what is in the literature and what my own experiences, I would use 1% sparsity for degree centrality and R>0.6 for LFCD.
I would recommend that you use the same mask for all of the datasets that you compare. That way, degree centrality will have the same max value across datasets.
3dDegreeCentrality -prefix <outputname.nii.gz> -sparsity 1 -mask <maskfilename.nii.gz>
and for 3dLFCD
3dLFCD -prefix <outputname.nii.gz> -thresh 0.6 -mask <maskfilename.nii.gz>
Thank you so much for your help. My data is preprocessed using afni (-block despike tshift align tlrc volreg blur mask regress ). Do I need to smooth the input data before calculating DC and LFCD? if not I need to rerun the preprocessing without blur option.