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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July 10, 2012 03:13PM
Hey Rick,

One of my labmates is also using dmBlock with trials of different durations and is under the impression that AM2 is better to use than AM1. I've been using AM1 based on an earlier comment you made in this thread that AM1 was more likely a better fit for my design. Now I'm not sure which is better to use, especially based on this commentary in the 3dDeconvolve help page thta suggests that AM2 is the option one should probably use and that AM1 is for special cases and not really for fMRI tasks.

[-stim_times_AM2 k tname Rmodel]
Similar, but generates 2 response models: one with the mean
amplitude and one with the differences from the mean.
*** Please note that 'AM2' is the option you should probably use!
*** 'AM1' is for special cases, and normally should not be used
for FMRI task activation analyses!!
*** 'AM2' will give you the ability to detect voxels that activate
but do not change proportional to the amplitude factor, as well
as provide a direct measure of the proportionality of the
activation to changes in the input amplitude factors. 'AM1'
will do neither of these things.
*** Normally, 3dDeconvolve removes the mean of the auxiliary
parameter(s) from the modulated regressor(s). However, if you
set environment variable AFNI_3dDeconvolve_rawAM2 to YES, then
the mean will NOT be removed from the auxiliary parameter(s).
This ability is provided for users who want to center their
parameters using their own method.

Can you clarify when it's better to use AM1 and when it's better to use AM2??

Thanks!
Subject Author Posted

3dToutcoun​t and censoring volumes

Tim Souza May 16, 2012 11:18AM

Re: 3dToutcoun​t and censoring volumes

rick reynolds May 16, 2012 11:24AM

Re: 3dToutcoun​t and censoring volumes

lianablair June 21, 2012 04:20PM

Re: 3dToutcoun​t and censoring volumes

Peter Molfese June 21, 2012 08:23PM

Re: 3dToutcoun​t and censoring volumes

rick reynolds June 21, 2012 09:07PM

Re: 3dToutcoun​t and censoring volumes

lianablair June 27, 2012 04:04PM

Re: 3dToutcoun​t and censoring volumes

rick reynolds June 27, 2012 04:13PM

Re: 3dToutcoun​t and censoring volumes

lianablair June 28, 2012 12:18PM

Re: 3dToutcoun​t and censoring volumes

rick reynolds June 28, 2012 12:32PM

Re: 3dToutcoun​t and censoring volumes

lianablair June 28, 2012 04:55PM

Re: 3dToutcoun​t and censoring volumes

rick reynolds June 28, 2012 09:12PM

Re: 3dToutcoun​t and censoring volumes

lianablair June 29, 2012 11:47AM

Re: 3dToutcoun​t and censoring volumes

lianablair July 10, 2012 03:13PM

Re: 3dToutcoun​t and censoring volumes

rick reynolds July 10, 2012 09:28PM