Hey Donald,

Thanks for the clarification regarding our study design. I have been trying to set up the flexible factorial, and have been reading the SPM8 manual. I am still a little confused about a few things, and was wondering if you would be able to answer a few more questions.

If I understand the manual correctly, under “Factors” I create one factor named “Subject” (we have 10) which will automatically generate my subjects factor. I select Independence “No” and Variance “Unequal”.

I create another factor named “Time” (we have 3 levels) and select Independence “No” and Variance “Unequal”.

Under “Subjects” I enter all three contrast images (one for each time) under “Scans” and repeat for each subject.  (From reading the thread entitled "adding images to cells in within subjects full factorial" from 12/1/2011 and 12/2/2011, I'm led to believe that I could enter the contrast images for all of the subjects (30 images) at once as long as I specify the "factor matrix" appropriately, is this correct?)

Where my confusion begins is “Subject -> Conditions”. It says I must enter an X-by-X array. I am unsure what values to enter. (if I enter all 30 images, is this the 30x5 matrix described in the post referenced above?)

Then I assume I would Select “Main Effect and Interactions -> Main Effect” and enter “2” if I was interested in the main effect of time, which was entered as the second factor under “Factors”.

Any help you would be able to provide would be appreciated. I apologize for the lengthy emails, but I am having trouble implementing the information from the manual. Thanks again.

Annchen

On Mar 13, 2012, at 6:25 PM, MCLAREN, Donald wrote:

On Mon, Mar 12, 2012 at 11:07 PM, Annchen Knodt <[log in to unmask]> wrote:

Hello Everyone,

I am analyzing repeated measures data for the first time in SPM8, and I just wanted to verify that I am doing so properly. We are scanning subjects 3 times using the same task, and are interested in what areas show differential responses as a function of time (e.g. Are responses greater at time 1 than at time 2 and 3?). 

In order to test this question, I am using the Second Level: Full Factorial option.

You should use the flexible factorial design and specify a subject factor in addition to the time factor.
 

I specify one factor with three levels (time, at visit one, two, and three). Under “Independence” I select “No” because it is a within-subject design. I then specify three cells, and enter the contrast images from my first level analyses for time 1 into the Level 1 cell, the con images from time 2 into the Level 2 cell, and the con images from time 3 into the Level 3 cell.

After design specification, and estimation, I create the following contrasts:

In order to test what areas show a main effect of task across all 3 times, I create an F contrast:

1 0 0

0 1 0

0 0 1

Once you add subjects, you will need to add zeros over the subject columns and the contrast would be:
1 -1 0
0 1 -1

Your contrast tests whether any time is significant, not if there are differences across time. The main effect of task/time is the difference across tasks/times.

 

In order to test which areas show a significantly different response at different times, I create an F contrast:

2 -1 -1

-1 2 -1

-1 -1 2

This is redundant to the main effect.

 

Am I analyzing the data correctly in order to test my question? Also, are the F contrasts I am creating appropriate for those questions? Any feedback you would be able to provide would be appreciated. Thanks in advance.

Annchen Knodt

~~~~~~~~~~~~

Annchen Knodt

Graduate Student

Computational Biology & Bioinformatics Program

Laboratory of Neurogenetics

Duke University