AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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ptaylor
October 04, 2016 01:12PM
Word has come down that the best way to go is likely to first use '3dttest++ -Clustsim' option; and yes, I have capitalized the letter on purpose-- see the help output from 3dttest++: 
 -clustsim   = With this option, after the commanded t-tests are done, then:
                (a) the residuals from '-resid' are used with '-randomsign' to
                    simulate about 10000 null 3D results, and then
                (b) 3dClustSim is run with those to generate cluster-threshold
                    tables, and then
                (c) 3drefit is used to pack those tables into the main output
                    dataset, and then
                (d) the temporary files created in this process are deleted.
               The goal is to provide a method for cluster-level statistical
               inference in the output dataset, to be used with the AFNI GUI
               Clusterize controls.
              ++ If you want to keep the 3dClustSim table .1D files, use this
                 option in the form '-Clustsim'.  If you want to keep ALL the
                 temporary files, use '-CLUSTSIM'.
              ++ Since the simulations are done with '-toz' active, the program
                 also turns on the '-toz' option for your output dataset. This
                 means that the output statistics will be z-scores, not t-values.
              ++ '-clustsim' will not work with less than 7 datasets in each
                 input set -- in particular, it doesn't work with '-singletonA'.
          -->>++ '-clustsim' runs step (a) in multiple jobs, for speed.  By
                 default, it tries to auto-detect the number of CPUs on the system
                 and uses that many separate jobs.  If you put a positive integer
                 immediately following the option, as in '-clustsim 12', it will
                 instead use that many jobs (e.g., 12).  This capability is to
                 be used when the CPU count is not auto-detected correctly.
          -->>++ It is important to use the proper '-mask' option with '-clustsim'.
                 Otherwise, the statistics of the clustering will be skewed (badly).

        ---==>>> PLEASE NOTE: This option has been tested for 1- and 2-sample
        ---==>>> unpaired and paired tests vs. resting state data -- to see if the
        ---==>>> false alarm rate (FAR) was near the nominal 5% level (it was).
        ---==>>> The FAR for the covariate effects (as opposed to the main effect)
        ---==>>> is still somewhat biased away from the 5% level :(
on the set of FA maps (or any other scalar map).

This is following the method described in "The Present-​ A Non­Parametric Approach to Cluster­Size Thresholding" on page 8 here:
[biorxiv.org]
The FPR prettiness of the output results is also described there, in Fig. 4.

You will want to run this on a computing cluster, if at all possible.

--pt (under advisement from G Chen)
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Subject Author Posted

3Dclustsim for analysis of DTI measures

cibuthomas August 26, 2016 12:07PM

Re: 3Dclustsim for analysis of DTI measures

ptaylor October 04, 2016 01:12PM

Re: 3Dclustsim for analysis of DTI measures

ptaylor October 04, 2016 01:13PM