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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March 10, 2006 10:06AM
Hi Gang,

I am using the GroupAna.m script to run my fMRI group analysis, and I noticed that the 2nd order contrast results is a little "suspicious". Then later I used AFNI 3dANOVA3 as a comparison, and I noticed the t-stat subbrik of all my 2nd order contrasts are very different from the ones generated using GroupAna.m. However, the 1st order contrasts are fine.

You may also want to verify other higher order contrasts as well.

My design is a 3-factor "balanced" design with BxC(A).
Factor A = Group with 2 levels
Factor B = task with 2 levels
Factor C = task with 3 subjects for each group. (one coworker of mine ran his data with 16 subjects per group as well and he discovered the same issue as I mentioned above, so I guess this problem is not due to the number of levels in Factor C)

For the 3dANOVA3, I am using AFNI version:
Version AFNI_2005_12_30_0934
[[Precompiled binary linux_gcc32: Jan 31 2006]]

For the GroupAna.m script, I downloaded it from the link below earlier this year:
[afni.nimh.nih.gov]

Thanks very much.

Cheers,
Ricky
Subject Author Posted

2nd order contrast for the matlab GroupAna.m script

Ricky Tong March 10, 2006 10:06AM

Re: 2nd order contrast for the matlab GroupAna.m script

rick reynolds March 10, 2006 12:16PM

Re: 2nd order contrast for the matlab GroupAna.m script

Stacia Friedman-Hill March 10, 2006 12:44PM

Re: 2nd order contrast for the matlab GroupAna.m script

Gang Chen March 10, 2006 01:40PM

Re: 2nd order contrast for the matlab GroupAna.m script

Stacia Friedman-Hill March 10, 2006 03:38PM

Re: 2nd order contrast for the matlab GroupAna.m script

Gang Chen March 10, 2006 04:20PM

Re: 2nd order contrast for the matlab GroupAna.m script

Stacia Friedman-Hill March 13, 2006 10:16AM

Re: 2nd order contrast for the matlab GroupAna.m script

Gang Chen March 13, 2006 10:55AM

Re: 2nd order contrast for the matlab GroupAna.m script

Stacia Friedman-Hill March 13, 2006 11:35AM

Re: 2nd order contrast for the matlab GroupAna.m script

Gang Chen March 13, 2006 04:33PM

Found the problem - Re: 2nd order contrast for the matlab GroupAna.m script

Gang Chen March 13, 2006 05:44PM

Re: Found the problem - Re: 2nd order contrast for the matlab GroupAna.m script

Gang Chen March 13, 2006 09:39PM

Re: Found the problem - Re: 2nd order contrast for the matlab GroupAna.m script

Stacia Friedman-Hill March 14, 2006 01:53PM

Re: Found the problem - Re: 2nd order contrast for the matlab GroupAna.m script

Stacia Friedman-Hill March 14, 2006 04:04PM

Re: 2nd order contrast for the matlab GroupAna.m script

Gang Chen March 10, 2006 01:37PM

Re: 2nd order contrast for the matlab GroupAna.m script

Ricky Tong March 13, 2006 09:56AM

Re: 2nd order contrast for the matlab GroupAna.m script

Gang Chen March 13, 2006 11:02AM

Re: 2nd order contrast for the matlab GroupAna.m script

Ricky Tong March 13, 2006 11:20AM

Re: 2nd order contrast for the matlab GroupAna.m script

Gang Chen March 13, 2006 04:35PM

Re: 2nd order contrast for the matlab GroupAna.m script

Ricky Tong March 14, 2006 10:18AM

Re: 2nd order contrast for the matlab GroupAna.m script

Gang Chen March 16, 2006 02:18PM

Re: 2nd order contrast for the matlab GroupAna.m script

ye March 16, 2006 10:57AM

Re: 2nd order contrast for the matlab GroupAna.m script

Gang Chen March 16, 2006 02:26PM

Re: 2nd order contrast for the matlab GroupAna.m script

ye March 16, 2006 03:16PM

Re: 2nd order contrast for the matlab GroupAna.m script

Gang Chen March 16, 2006 05:50PM

Better solution - Re: 2nd order contrast for the matlab GroupAna.m script

Gang Chen March 17, 2006 03:05PM

Re: Better solution - Re: 2nd order contrast for the matlab GroupAna.m script

Ricky Tong March 20, 2006 04:40PM

Re: Better solution - Re: 2nd order contrast for the matlab GroupAna.m script

Gang Chen March 20, 2006 05:10PM