Hey SPM Experts,

I just ran some preprocessing and analysis on a small data set (7 patients
and 4 controls - all children) and I am stumped! After doing so, I ran some
contrasts and didn't get any significant activations whatsoever.

The study has a pre- and post- therapy scan for the patients, whereas the
controls are only scanned once. Painful stimuli is administered, followed
by nonpainful stimuli, on a symptomatic body part as well as a
nonsymptomatic body part . I was hoping to see significant activations when
performing the contrast for (SP - NSP) - (NSP - NSNP), where S =
symptomatic; NS = Nonsymptomatic; P = painful; and NP = nonpainful. And I
was hoping that after therapy, these significant activations would be
reduced (or at least resemble the activation pattern in controls).

It is a block design, with 4 sessions. Sessions 1 and 3 are on the
Symptomatic Body Part, and Sessions 2 and 4 are on the Nonsymptomatic Body
Part. Each session consists of 10 painful stimuli administration
alternating with 10 nonpainful stimuli administration for 4 repetitions (80
TRs total).

Preprocessing steps include:
1) realignment to first volume of first run - created mean image
2) segmentation
3) coregistering the grey matter with the mean epi
4) Normalization of grey matter to grey matter of CCHMC Pediatric template,
then applying the parameters to the functional (3x3x3 voxel sizes)
5) smoothing at an 8 mm kernel

When I was just looking at each individual subject, I redid the same steps
as above, but during realignment, I created all images + mean image to avoid
getting the "images do not all have same orientation & voxel size" error
message that I got before. And of course, no normalization was done.

Because of the few number of subjects, I put all the data (7 patients
pre-therapy/7 patients post-therapy/4 controls) into one big fixed effects
model. Since there were four sessions, there was a total of 72 sessions
(for anyone who had memory problems, I might be able to help - just ask!).

Design Matrix:
1) fMRI -> specify design
2) TR = 4
3) Scans per session: 80 80 80 80 ..etc for a total of 72 sessions
4) How to specify - Scans
5) Are sessions replications: No
6) Basis Set: Hrf
7) Model interactions: No
8) # of conditions: 4
11) Duration: 10

Motion parameters were included as regressors. The data was specified
using the smoothed images, and I selected "none" for remove global effects.
 A high pass filter of 128 s was chosen (the default).

For individual analyses, AR(1) serial correlations = yes. For the big fixed
effects model, I chose "no" for the AR(1) serial correlations. The
estimation took a lovely 19 hours! Isn't that grand?

The contrasts were created for (SP - NSP) - (NSP - NSNP) for patients
pre-therapy, controls, and patients post-therapy. The motion parameters
were taken into account when creating the contrasts.

For the p-value adjustments of the patient contrasts in the fixed effects
model, I saw the results under a p-value of 0.001, 0.005 and 0.05 (scattered
activations) - I figured they were noise for the most part, since when I
applied either an FWE or FDR of 0.05, there were no significant activations
pre- or post-therapy! Even when I did a contrast for the main effect of SP
and applied FDR of 0.05, there were no activations! For the controls, there
were significant activations for the difference contrast...Remember, AR(1) =
no...

Individually, in which AR(1) serial correlations = yes, there were no
significant activations under an FWE/FDR of 0.05 for any subject!

Can someone explain this?? Am I doing something wrong? Is there something
else I should try? Any help would be greatly appreciated...

Many thanks in advance,
Vy