Hello all,
I would like to do a repeated measures analysis comparing pre/post treatment resting state in a single subject. Is this possible using the CONN toolbox? First I preprocessed my images in SPM. Then I followed previous instructions posted here for comparing sessions that have their own SPM.mat files. I used the posted batch commands to set up my second level covariates for the repeated measures t-test:

n=1;
X=[kron(eye(2),ones(n,1)),kron(ones(2,1),eye(n))];
clear batch;
batch.Setup.subjects.effect_names=[{'Session1'},{'Session2'},arrayfun(@(n)sprintf('within%d',n),1:n,'uni',0)];
batch.Setup.subjects.effects=num2cell(X,1);
conn_batch(batch);

This successfully set up "Session1", "Session2", and "within1" in the 'Setup->Covariates->Second-level' area.

I then ran a paired t-test by entering [1 -1 0] and also [-1 1 0] in the "between subject contrasts" area in the second level results tab. Unfortunately my p-values are all NAN, the Beta's are very small, and the T values are -0.00 or 0.00.

My specific questions:
1. Is it possible to do a single-subject repeated measures resting state analysis (i.e., case study) in CONN?
2. If is it possible, are my results true null results or have I done something wrong?

Thank-you for any assistance you can provide.
Regards,
Helen