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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April 02, 2010 02:37PM
Hello AFNIers,

Perhaps you can help me with the following question: How to do FDR so that the AFNI threshold slicer works with the following?

I have a volume of T-values (two-sided) which was not computed with AFNI and it is not marked as AFNI-statistical volume. It is a 4D volume of T-stats such that each subbrick includes different statistics. Besides, each voxel has different number of degrees of freedom which is saved in another volume.

In order to compute the p-values I did
;; Create mask of positive and negative T-values
3dcalc -a Tstats+orig -expr '1*ispositive(a)-1*isnegative(a)' -prefix signTstats
;; Absolute value of T-values
3dcalc -a Tstats+orig -expr 'abs(a)' -prefix absTvalues
;; compute p-values
3dcalc -a absTstats+orig -b df+orig -expr 'fitt_t2p(a,b)' -prefix pvaluesUNC

Now that I have the p-values I can compute FDR z-scores with 3dFDR (I want to consider the p-values=1 so I use -old option)
3dFDR -old -input pvaluesUNC+orig -mask mask+orig -force -prefix zvaluesFDRabs
and finally multiply by the mask of signed values to get the signed statistic
3dcalc -a zvaluesFDRabs+orig -b signTstats -expr 'a*b' -prefix zvaluesFDR

However, I would like to see the q-values in the AFNI GUI as I move the slicer.
This might not be possible, but in case it were possible, any suggestion will be great. Thanks very much in advance!!

Cesar

Pd. I also have F-values but i guess the reasoning will be the same...
Subject Author Posted

FDR with t-stats in non-statistical volume

cesar April 02, 2010 02:37PM

Re: FDR with t-stats in non-statistical volume

Gang Chen April 02, 2010 03:04PM

Re: FDR with t-stats in non-statistical volume

cesar April 02, 2010 03:17PM

Re: FDR with t-stats in non-statistical volume

Gang Chen April 02, 2010 03:54PM

Re: FDR with t-stats in non-statistical volume

cesar April 02, 2010 04:48PM

Re: FDR with t-stats in non-statistical volume

Gang Chen April 02, 2010 05:00PM

Re: FDR with t-stats in non-statistical volume

cesar April 02, 2010 05:04PM