Dear Francis,


Out of interest where are you based?


I've tried to get you moving forward by quick answers below - come back to
me if needs be. I also include the spm list because many on there are much
better at answering these questions than I am - I recommend you join it.


Best regards




From: francis8 [mailto:[log in to unmask]] 
Sent: 12 May 2010 19:08
To: [log in to unmask]
Subject: Dear Dr. Carmichael, without con*.img, how to do 2nd level
Importance: High


Dear Dr. Carmichael,
Could you help me with the following questions about group analysis, which I
cannot solve even after spending two days in searching and reading relevant
webpages (including SPM emaillist archives and some ppts on it.)
I did 1st level F-test with informed basis functions on each subject's
multi-sessions (each session has the same design matrix columns). My
interested variables are two parametric ones. So, in each sesssion, the
contrast has only one 1 like 1 0 0...; for informed bf, the contrast is like
[1 0 0...; 0 1 0...; 0 0 1...] (RIGHT?). Now I move to 2nd level analysis
and encounter the following questions. My SPM edition is SPM8.
> normally you'd have a matrix with ones in the columns relating to your
regressors of interest I think as you've given above - I'm assuming you've
put each session in the same analysis using the 'replicate across sessions'
to put in your F-test.
> basically I think you've done this right according to what I have to go on
i) The first level analysis produced image files prefixing with beta, ess
and spmF (but not con as in the example in the manual.) So, which kind of
image files should I select for the 2nd level analysis? (A related question:
for a contrast 1 -1, the con*.image is just a beta*.image - another one? or
it also takes variance for each beta into account?)
> A con is a combination of betas but you should get a con for every
contrast as above you've run (as above) provided the contrast manager part
has run properly - check for messages in the matlab window.
ii) If the beta should be used, then a further question:
I have several sessions, and so have several beta images for each regressor
per subject. Since the relationship of beta images within one subject
(between sessions) should be different from that of between subjects, it
seems unreasonable to simply pool these sessions as subjects. So, what is
the reasonable solution? 
> no don't use the beta
> as above use 'replicate over sessions'when specifying the contrast in the
contrast manager (>tasks >stats >contrast manager)
a) firstly average the corresponding images across sessions within each
subject and then only input the average images for the group analysis? Is
this reasonable if not best? (note: session effect is not what I care
b) take sessions as an independent varibale? In this case, how should I
define the contrast (for the 2nd level analysis) for informed basis
functions? As I know, the original form should be eye (n); but now what
should it be? 
c) any other better solutions?
Looking forward to your help. 
Many thanks and best wishes,
Donna Francis