Dear Donald and SPM users,

I am trying to use GLM Flex to specify the scans for my 2x2 factor within model in the I.Scans part of the script. The example in GLM Flex says:

I.Scans = {...

?s01_c11_c21.nii?;

?s01_c11_c21.nii?; 

?s01_c11_c21.nii?; 

?s01_c11_c21.nii?;

?s01_c11_c21.nii?;

?s02_c11_c22.nii?;

?s02_c11_c22.nii?;

?s02_c11_c22.nii?;

?s02_c11_c22.nii?;

?s02_c11_c22.nii?;

?s03_c12_c21.nii?;

?s03_c12_c21.nii?;

?s03_c12_c21.nii?;

?s03_c12_c21.nii?;

?s03_c12_c21.nii?;

?s04_c12_c22.nii?;

?s04_c12_c22.nii?;

?s04_c12_c22.nii?;

?s04_c12_c22.nii?;

?s04_c12_c22.nii?;

};

However, as a beginner, I am very confused at this point. I have two questions:

(a) where do these nii's come from? I used SPM8 and all the results from 1st-level analysis are just .img and .hdr? Are these beta's?

(b) what are the order of these nii's? I checked out my F.name matrix and realized that I have 2 within factors and 2 levels each. I also have 8 subjects in each condition. What orders of the nii filename should I adhere to?

Many thanks in advance!

Daniel

From: <MCLAREN>, Donald <[log in to unmask]>
Date: Wednesday, May 9, 2012 3:36 PM
To: Daniel Yang <[log in to unmask]>
Cc: "[log in to unmask]" <[log in to unmask]>
Subject: Re: [SPM] Interpretation of 2x2 interaction effect

If you use GLM Flex, then OrthoView (by Aaron Schultz) will allow you to plot the 4 conditions and to show the interaction.

To statistically determine what drives the interaction, then you need post-hoc t-tests. There are 4 possible tests with a 2x2 design (1 -1 0 0, 0 0 1 -1, 1 0 -1 0, 0 1 0 -1)

If you create an F-contrast: [ones(1,N)/N 1 0 1 0 1 0 0 0;ones(1,N)/N 1 0 0 1 0 1 0 0;ones(1,N)/N 0 1 1 0 0 0 1 0;ones(1,N)/N 0 1 0 1 0 0 0 0 1 ]. Then you can plot all four conditions inside SPM. This contrast assumes: subject factor, condition1 factor, condition2 factor, interaction as the column order.

The F-contrast should not be interpreted as its a between-subject effect, but it will allow you accurately plot the condition estimates in SPM.

Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=====================
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.

On Wed, May 9, 2012 at 3:15 AM, Yang, Daniel <[log in to unmask]> wrote:

Dear SPM users,

I am new to SPM 8 and have a group dataset of within-subject 2 x 2 factorial design. With the contrast of "1 –1 –1 1" specified for the interaction effect, I found a few regions that were activated. There were main effects as well. My question is how to interpret those interaction effects? For example, is there any established toolbox or suggested procedure that I can use or follow to plot the beta values within some ROIs? Presumably I guess this will help me to make sense of the nature of the interaction effects (e.g., cross-over vs. non-cross-over)? Any suggestions for me to begin with or explore more are greatly appreciated!

Thanks so much for your help in advance.

Best,

Daniel