Dear SPM users,

I have an unusual question and hope that one of you can help me. I have
conducted a preliminary study investigating the brain changes associated
with a course of treatment in 4 patients. The patients were therefore
scanned before therapy (preT) and after therapy (postT) in a simple Task
vs Rest fMRI block design. To control for the effect of "time elapsed
between preT and postT", I have also scanned matched controls twice at
about the same time, but the controls did not undergo any treatment. In
theory this enables me to explore the brain regions that are under- and
overactive in the patients relative to the controls before and after
therapy, as well as the difference.

HOWEVER, my problem is that, due to unforeseen circumstances, the
treatemnt did not start at the time originally planned, and our scanner
was REPLACED in the middle of the study.
This means that my preT data were acquired on Scanner#1 and my postT data
on Scanner#2. The TRs and TEs are different.

Had this not happened, I would have put all the data in a fixed effect
model and tested the interaction:
(preT Patients vs. PreT controls) vs (postT Patients vs. postT controls)
1 -1 -1 1 and -1 1 1 -1
Unfortunately I cannot do that because the scanning parameters are different.

I am wondering whether there is any way I can still compare my preT and
post T data within SPM2, using a method that would be acceptable to a
reviewer.

For instance, would it be acceptable/legal to bring my Patients vs
Controls contrasts (con1_preT and con2_postT) to a second level analysis
to explore the interaction I am intested in?
If so, is that considered a one-sample t-test, a two-sample t-test, or a
paired t-test? These are the same subjects (so repeated measures) but as
they were not scanned on the same machine I am not sure about which one to
use to be as conservative as possible.

Should I instead/additionally compare (Patient preT vs Patient postT) and
(controls preT vs control postT) in a second-level analysis (two-sample t
test), and bring those two contrasts to a third-level?

Is there another way I can process my data that would enable me control
for the effect of scanner change?

Any help would be greatly appreciated as these treatment studies are very
time-consuming and I really hope I can still use my data.

Many thanks in advance for your help,

Frederique

--
Frederique Liegeois, PhD
UCL Institute of Child Health