Dear Rebecca,

> I am trying to run a paired group analysis using an additional  
> covariate and
> would like some advice. I apologise if it seems basic, but I am  
> still trying to
> get a grip on the analysis.
>
> I have a group who were scanned twice and I want to compare their
> performance pre and post, as well as adding a RT covariate.
> However, I am using contrasts e.g. happy-neutral (pre) > happy-neutral
> (post).
> For my additional RT covariate do I have to calculate my mean RT as  
> happy-
> neutral for each group?

There is really no "have to" here. What you need to do is to think  
about what question you want to ask of your data. Let as say e.g. you  
were to put in the pre RT values as a covariate (mean corrected with  
the mean pre RT value). You would then ask a question like

"Where in the brain is the "change" (post vs pre) in processing of  
happy faces (controlled for faces) correlated to pre (pre training?)  
reaction time"?

Only you can know if this is a reasonable question, that might  
potentially have an interesting answer.

Similarly, if you were to put in the delta RT values you would be  
asking a question like

"Where in the brain is the "change" (post vs pre) in processing of  
happy faces (controlled for faces) correlated to changes (pre vs post)  
in reaction time"?

Again, is this a reasonable question? Only you can say.

As for mean correction, the point of the mean correction is to make  
sure that the estimates you get for your correlation are not  
contaminated by an overall mean effect in the data (such as the  
average activation across all subjects). Therefore the mean-correction  
should give you a regressor with zero mean. So whatever you put in  
there, it is the mean of those values that should be subtracted.

> Also I am a bit confused about how to set up the contrasts to look at
> pre>post with covariate. I have read a couple of previous posts and  
> remain
> confused.
> EV1 =group
> EV2-3 = partciapnts (obviously I have more this is merely for example)
> EV4= RT covariate
>
>              EV1     EV2       EV3     EV4
> con1         1         0          0        0
> con2         -1        0          0        0
>
> The above should give Pre>post and the post>pre activation. I  
> initailly though
> that this will show activation which already includes the additional  
> contrast as
> it is defined as EV4, but after reading previous posts I am not  
> sure. Is this not
> the case?

This would only look at pre>post (or vice versa) since the contrast  
does not include the RT covariate. What the covariate will do here is  
to remove any variance that could be explained by reaction time, prior  
to looking at the pre-post effect. So, let us e,g, say there is an  
effect pre>post, but let us also say that there is a consistent  
difference in RT (they are all faster post). Then by including the RT  
covariate you will effectively explain the difference with that, so  
that nothing is left for the group to explain and you will not find  
anything e.g. in your pre>post contrast. This may sound paradoxical  
(and maybe even unwanted), but it actually makes sense (sometimes). If  
an effect that can be explained by pre vs post can EQUALLY WELL be  
explained by a difference in reaction time, then you cannot really say  
which of these things that caused the change in response. It may be  
the pre vs post (whatever that was) but it may also be that if the  
subjects had somehow managed to improve their reaction times in some  
other fashion you would have obtained the same effect. And if there is  
any ambiguity, GLM will always be conservative (i.e. leave the effects  
out of the contrast).


> If not how would I define the contrast? I thought it would be con3  
> and con4
>             EV1     EV2       EV3     EV4
> con3        1         0          0         1
> con4        -1        0          0         1
> con5         0         0         0          1
>
> But reading previous posts contrast 5 was recommeded. I am unclear  
> how this
> tells me where my differences are between my groups adding in the  
> additonal
> covariate.
> I would really appreciate it if someone could explain this to me.

Again, I think you need to be much more clear about what question you  
are actually trying to ask of your data. I cannot see how con3 or con4  
could ever be valid questions (basically adding a group effect and a  
correlation with some continous variable together). Contrast 5 MAY be  
the question you want to ask. It asks

"Where in the brain is the response correlated to the reaction time,  
after I have explained away anything that could be explained by group  
(which I can only assume corresponds to pre vs post in this case).

Designs can get rather complicated when there are several levels of  
subtraction, especially when adding in also continous covariates. But  
at the end of the day it is all a matter of common sense (no maths  
training needed) to make sure that for each level of subtraction you  
put into simple words what that subtraction means, and then at the  
next level of subtraction you simply add another layer of simple words.

For example (happy_faces vs neutral_faces) gives you
"where in the brain are happy faces processed when controlling for  
faces?".

If you then add another layer (pre_happy_faces - pre_neutral_faces) -  
(post_happy_faces - post_neutral_faces) it turns into

"Where in the brain does training change the processing of happy faces  
when controlled for faces?"

Here I have pretended that pre vs post pertains to training, but just  
replace it by whatever is appropriate.

And in this way you build up your contrasts and questions gradually  
until you have the question you really want to ask.

I hope this was helpful.

Good luck Jesper