Ben,

Answer to Q1: The parameter file use structures. Structures have different fields. For example, the P structure that is the input has a number of different fields (e.g. cond, meth, Contrasts, contrast, etc.). Some of the fields contain structure array, with Contrasts being one of those fields. The way to index each element of the array is to use the number (e.g. 1, 2, etc.). The 1 and 2 refer to the first and second elements in the array for the your first and second contrast. The left and right fields within the structure represent the left and right side of the contrast you want. 

For example if the null hypothesis is: A1=A2, then 'A1' goes in the left field and 'A2' would go in the right field.

Answer to Q2: For your specific case, you probably want to do a two-sample t-test using the contrast E_re>E_nre from the first-level analyses. The null hypothesis is E_re-E_nre=0 OR E_re=E_nre.

To setup this contrast:
P.Contrasts(1).left={'E_re'}
P.Contrasts(2).right={'E_nre'}

Hope this helps. Feel free to ask more questions if anything is unclear.


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 Fri, Jan 27, 2012 at 7:19 AM, Ben Becker <[log in to unmask]> wrote:
Dear SPMers,

im using gppi (@Donald: cutting-edge tool – thanks!) to futher explore my data from a GLM Model. Briefly I used an event related design with the following four conditions:

-       E_re
-       E_nre
-       N_re
-       N_nre

The second level analysis revealed between-group differences (patients, controls) in the insula for the contrast E_re > E_nre, which I now want to test for between-group differences in connectivity.  My main issue is the design of the ppi-contrast and its implementation in gppi.
Running the gppi-script (method = cond / analysis = psy / all 4 task conditions & movement regressors included) without estimating the contrasts works fine and results in a design matrix with the conditions:

E_re / E_nre / N_re / N_nre / PPI_E_re / PPI_Enre / PPI_N_re / PPI_N_nre / constant / 6xmov_parameters

 However, setting up the contrasts results in error messages such as ‘P.Contrasts(1).left is not formatted correctly.’

My questions:
1.      P.Contrasts(1/2) Left / Right
             What does the 1 or 2 and the left or right stand for regarding the setup of the contrasts?

2.      How to implement the contrast for the PPI regarding the above mentioned question (comparing the groups regarding differences in
             insula-connectivity under the conditions of E_re>E_nre)?


Thanks in advance & best regards

Ben