"The number of rows correspond to the number of contrasts." would be more clearly understood as  "The number of rows correspond to the number of input images, which tend to be con images in fMRI."

If you have 4 conditions and 25 subjects and the order of scans is condition 1 (e.g. Factor 2 Level 1, Factor 2 Level 1), subjects1-25; condition 2 (e.g. Factor 2 Level 1, Factor 2 Level 2), subjects 1-25; etc. and the first factor was subject, the second factor was F1 and the third factor was F2 (based on the order specified of factors (not order selected in design matrix), then the factor matrix would be:
1 1 1 1
1 2 1 1
...
1 25 1 1
1 1 1 2
1 2 1 2
...
1 25 2 2

Note: You might have the conditions in a different order such that condition 2 is Level 2 of factor 1 instead of level 2 of factor 2.

Using Flexible Factorial Module:
Under Specify Subjects or all Scans and Factors, Choose Specify All
Select all the scans
Set the factor matrix as described above. 

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
Office: (773) 406-2464
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On Thu, Dec 1, 2011 at 5:57 PM, MCLAREN, Donald <[log in to unmask]> wrote:
Carly,

For within-subject designs you should be using the flexible factorial models that include a subject term.

In the flexible factorial, you can specify all the contrast images at once and then create a factor matrix that lists what each scan corresponds to.
In the factor matrix,
column 1 should be 1
column 2 is the level of factor 1 (or 1)
column 3 is the level of factor 2 (or 1)
column 4 is the level of factor 3 (or 1)

The number of rows correspond to the number of contrasts.

With multiple within-subject factors, if you don't properly correct for violations of spherecity (either because you didn't correctly set the dependence and variance options OR the variance-covariance is not the same across all voxels) , then you could end up with inflated statistics. Ongoing work is evaluating the effects of violations of spherecity.

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
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
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responsible for delivering it to the intended recipient, you are hereby
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prohibited and may be unlawful. If you have received this e-mail
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On Thu, Dec 1, 2011 at 5:38 PM, carly sweegers <[log in to unmask]> wrote:

Good evening,

 

I have a 2x2 within subjects experiment and would like to do a full factorial on the data (to compare different sessions). I know that using the batch function you can make new factors and specify the images per cell. However, I can't imagina that for 25 subjects, and 4 conditions, I would have to individually specify 100 contrast images, would I? I could use some help on this matter.

 

Thanks in advance,

 

Carly Sweegers