When I suggest that you not model rest, I meant that you should not model rest for either the GLM activity nor PPI/gPPI. The basic reasoning is that after your task is over, then the BOLD activity returns to baseline. There isn't usually an active response to "rest" (e.g. the BOLD response doesn't go up/down when you start to rest).

With 2 conditions, you could use the standard PPI, but you would need the following regressors:
A-B
A+B

Then the response to A would be [1/2 1/2]:    (A-B)/2+(A+B)/2   
Then the response to B would be [-1/2 1/2] :  (A+B)/2-(A-B)/2


With 3 conditions, you could use the standard PPI, but it would become more complicated. As you suggest you could have A+B, A-B, and C. This is a mixture of the two methods. Thus, I would simple go with the gPPI approach - either by using the automated toolbox OR by building 3 PPI conditions in SPM.

Best,
Donald


Best Regards, 
Donald McLaren, PhD


On Wed, Jun 22, 2016 at 9:13 AM, clara garcia gorro <[log in to unmask]> wrote:
Thank you very much for your answer. 

I have no experience with gPPI, but I will try to use it. However, I was wondering whether is it also possible to run the analysis using standard PPI.
I'm not sure if I understood it right. When you suggest not to model rest and let it be the implicit baseline, do you mean in the PPI connectivty analysis or in the first level activity GLM model?  

Thank you very much,

Clara

Date: Mon, 13 Jun 2016 14:35:00 -0400
From: [log in to unmask]
Subject: Re: [SPM] PPI analysis with 3 conditions
To: [log in to unmask]


Clara,

I would recommend using the gPPI toolbox.

I would also not model rest and let rest be the implicit baseline.

Best Regards, 
Donald McLaren, PhD


On Mon, Jun 13, 2016 at 8:54 AM, clara garcia gorro <[log in to unmask]> wrote:
Dear SPM experts,

I have a question regarding standard PPI analysis. In have a motor tapping task in which I have 3 conditions: right hand, left hand and resting.

I am interested in studying the connectivity of the putamen with the rest of the brain during the right hand condition compared to the rest condition. 

I initially ran the PPI analysis setting the right condition to 1 and the restng condition to -1. So, the PPI inteaction term looked like this:

[1 1 -1; 2 1 1]

where the first condition is rest, the second condition is right.

However, I have been recently adviced to also include the resting condition in my PPI design too, setting left as a 0, in order to exclude the part of the BOLD response corresponding to the left hand condition.

I have read is this paper:


that standard PPI analysis is "potentially limited to simple experiments with only one or two conditions, respectively, or experiments that can be collapsed into two conditions for analysis".

I was wondering if it is correct then to calculate my PPI interaction term like this:

[1 1 -1; 2 1 1; 3 1 0]

where the first condition is rest, the second condition is right and the third condition is left.

Thank you very much in advance,

Clara