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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June 29, 2021 10:34AM
How much "rest" time occurs before and after the onset of the continuous stream of stimuli (that is, at the beginning and end of the imaging run)? Probably not much, I'd guess.

In this situation, IMHO you can only reasonable find the difference between the linguistic condition #1 and the foil condition #2 -- that is, you can't find "linguistic only" activation, just places where "linguistic minus foil" is significantly nonzero.

There would be two ways to analyze this in AFNI. The first, which I would try since it is simpler, would be to treat condition #2 as "rest" -- that is, don't put in stimulus timing for it. Then either excise the actual rest periods at the run starts/ends and analyze that data as normal -- with BLOCK(20,1) timing for condition #1 -- or put in BLOCKs to catch the presumably small un-excised "true" rest periods.

The second would be to put in BLOCK(20,1) timing for the 2 different stimulus classes (in separate files, of course), and then modify the default AFNI baseline generation to remove the constant term in the baseline model -- that is, keep the drift terms like t1, t2, etc., but get rid of t0=1. This removal is possible, but requires a more tricksy usage of 3dDeconvolve and afni_proc.py (I've never had a request like this before) -- which is why I would start with the first method and see if the results are reasonable.

I hope this explication is clear.
Subject Author Posted

BLOCK function

acz June 28, 2021 12:03PM

Re: BLOCK function

RWCox June 29, 2021 10:34AM