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

History of AFNI updates  

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December 14, 2018 10:17AM
1) I would not use -detrend on the errts file - this option was intended only for use on original data for a quick look at the noise smoothness, and not for use on already processed data. However, I don't know why -detrend sometime affects the results markedly and sometimes does not.

It does not make any sense to average the 3 ACF parameters, which each represent something completely different from the others. The spatial autocorrelation function (ACF) of the FMRI noise is modeled with these 3 parameters (a,b,c) using the formula
  ACF(r) = a * exp(-r*r/(2*b*b)) + (1-a) * exp(-r/c)
where 0 < a < 1 is the weight given to the Gaussian part with st.dev. of 'b', and (1-a) is the weight given to the longer tailed single exponential part with decay distance 'c'. To see the computed FWHM of the ACF given these parameters, commands like
  ccalc 'ACFWXM(0.558,3.154,10.885,0.5)'
  ccalc 'ACFWXM(0.7097,3.1102,11.343,0.5)'
can be used, giving 8.898mm and 8.198mm (in that order). We see that the first one is slightly wider, but also has more non-Gaussian longer tail than the second one.

2) The combination of slightly wider FWHM and the longer tail in the first case (non-detrended) is what makes the cluster size thresholds somewhat higher. Note that these cluster size thresholds differ more markedly at the larger p-value thresholds, which is due to the longer single exponential tail. At the smaller p thresholds (say p=0.002), the cluster thresholds aren't that different (14 and 11 voxels).

3) Generally, in a group study, we recommend taking the (a,b,c) values from each subject and averaging them to get a group set of (a,b,c) values, and THEN using those in 3dClustSim. This method is ad hoc, but works OK. I would not apply '-detrend' to errts.* datasets.

4) Do you have an updated copy of AFNI binaries? I made changes to ETAC in September/October and would now recommend the use of the default "global ETAC" method, rather than the previous "local ETAC" method. If your "afni -ver" indicates a date earlier than (say) 15 Oct 2018, please update your AFNI binaries and try running 3dttest++ -ETAC again. However, it looks like you have the global ETAC output file TT.c7xJqG0BM99.robin.ETACmask.global.1pos.5perc.nii.gz which is a binary mask of all voxels that passed the ETAC multi-testing method (1pos means a 1-sided t-test, on the positive side; 5perc means at the 5% global statistical significance level). The multi-level cluster-thresholds used are in the globalETAC.mthresh.*.niml files (XML formatted, but readable text).

4a) You can think of cluster-size as
   sum              z(v)^0
   {v in cluster}
where z(v) = z-statistic (converted from t-statistic) and z(v)^0 is z(v) raised to the 0 power -- that is, 1. Now replace the exponent '0' with 'hpow'. This is a generalization of cluster-size that gives more weight to more statistically significant voxels. Since the voxel p-value threshold is also a threshold on the voxel z-value, there is a floor value to z(v) in a cluster - so all voxels will count in this sum, but with hpow > 0, some voxels are more equal than others.
Subject Author Posted

3dttest++: Clustsim and ETAC questions

Robin December 05, 2018 08:53AM

Re: 3dttest++: Clustsim and ETAC questions

RWCox December 14, 2018 10:17AM

Re: 3dttest++: Clustsim and ETAC questions

Robin January 07, 2019 09:31AM

Re: 3dttest++: Clustsim and ETAC questions

Robin January 21, 2019 02:56PM

Re: 3dttest++: Clustsim and ETAC questions

rick reynolds January 28, 2019 01:15PM

Re: 3dttest++: Clustsim and ETAC questions

Robin February 04, 2019 09:07AM

Re: 3dttest++: Clustsim and ETAC questions

rick reynolds February 05, 2019 11:04AM

Re: 3dttest++: Clustsim and ETAC questions

Robin February 05, 2019 12:22PM

Re: 3dttest++: Clustsim and ETAC questions

rick reynolds February 05, 2019 12:42PM