Please see inline response below.
Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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On Thu, Nov 22, 2012 at 5:01 AM, Angela Ciaramidaro
<[log in to unmask]> wrote:
> Dear experts,
>
> I am trying to use the gPPI toolbox following the instruction from
>
> http://brainmap.wisc.edu/PPI, but it's not obvious to me the steps I should
> follow.
>
> For this reason I have very simple questions:
>
> - When I install the toolbox, is it possible to open the gPPI from the SPM
> interface like the traditional PPI? Or the only way is to adapt the
> ppi_wrapper and the templatemaster from the Matlab interface?
>>> There is no graphical interface. The only way to use it is from the command line and the easiest way to set it up for multiple subjects and ROI is to use the wrapper and create a master template.
>
> - When I edit the ppi_wrapper and the templatemaster, what I have to do
> next? How I can run my data?
>>> Once you edit the ppi_wrapper and template, then you can run the wrapper at the MATLAB command line: ppi_wrapper(region,firstsubject,lastsubject)
For example, to run the ppi_wrapper on the first region in the first
10 subjects, you'd use:
ppi_wrapper(1,1,10)
>
> - Do it exit a manual described exactly what we have to do?
>>>> There is a beta version that I will email to you off the list due to its size. If anyone else wants a copy, please contact me directly.
>
> - Can I do a gPPI if I have a single ROI but different contrasts? Or is it
> more appropriate to do different PPI analysis for each contrast?
>>> I am not sure what you mean by different contrasts. The idea of gPPI is to compute the connectivity of every condition separately. Then you can compare any two conditions later to see if their connectivity differs. The single PPI will be more accurate and robust if by different contrasts you mean different pairs of regions. This is described through simulations in McLaren et al. 2012 in NeuroImage.
>
> Thanks in advance for any help.
>
> Angela
>
> --
> Angela Ciaramidaro, Ph.D. Cognitive Science
> Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und
> Jugendalters
> Deutschordenstr. 50
> 60528 Frankfurt
> Tel.: 069-6301-84057
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