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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January 21, 2016 10:01PM
Hi Christine,

Your command looks okay, where the timing files should
contain the starting times of the 16 s events (and the
AM.txt file should also contain modulators). Check the
terminal output from 3dDeconvolve to verify that it seems
to be censoring the right number of TRs.

Regarding whether to put "Facts" in the baseline (i.e.
whether to add -stim_base 7), it is almost irrelevant.
The only effect of that (particularly since you use
-bout) is to the Full-F, which you probably do not care
about. The individual stats should not be affected.
The Full-F result would change from showing the effect
of both classes 7 and 8 to the effect of only class 8
(it would become the same a t-stat^2 for Detail).

Note that without -bout, putting "Facts" in the baseline
would mean that there would be no beta or stats output
for that class.

But to put it another way, unless you care about the
betas or stats for polort and/or motion, I would be
inclined to skip -bout and leave "Facts" in the main
model (in order to at least see the results, even if
they are not going to be reported).

- rick
Subject Author Posted

AM analysis with a parameter that is not modulated

Christine Smith January 21, 2016 07:45PM

Re: AM analysis with a parameter that is not modulated

rick reynolds January 21, 2016 10:01PM