Dear SPMers:

Long time listener, first time caller. I am having some issues with a
repeated-measures ANOVA design in SPM5 and was hoping someone could point
out where things are going awry.

Basically, I have a 2x4 design (so, all subjects perform the same 8
conditions). In my design files the factors are called "RefRep" and "Delay"
but for the rest of this email let's just call them factor A (2 levels) and
factor B (4 levels). Right now I have 10 subjects and would like to assess
the A-by-B interaction in a repeated-measures analysis.

I am using SPM5's "Full Factorial" design option, specifying both factors to
be dependent with unequal variance in both cases. No other special stuff
going on. Each of the 8 conditions has an associated contrast file from
first-level analyses that is numbered the same for each subject (e.g.,
condition A1B1 = con 2, condition A1B2 = con 3, ..., condition A2B4 = con
9). So in the job file, the cells are specified such that cell [1 1] has
each sub's con_0002 file, cell [1 2] has each sub's con_0003 file, ..., cell
[2 4] has each sub's con_0009 file. Thus in the job file structure there are
8 cells with 10 identically numbered contrast files in each cell, one for
each subject, which as far as I can tell is how it should be.

When I run the job file, the design matrix looks mostly as it should except
for one small (read: big) problem. The matrix itself appears to be basically
OK -- 8 columns for the cells/conditions, 80 rows for the files, with the
cells labeled correctly at the top. However, the filenames along the right
appear to be in the wrong order. I believe they should go:

sub01_con2
sub02_con2
sub03_con2
...
sub10_con2
sub01_con3
sub02_con3
...etc

However, it looks like they actually go:

sub01_con2
sub01_con3
sub01_con4
...
sub01_con9
sub02_con2
sub02_con3
...etc

So it looks to me like somewhere in the bowels of SPM, there is a matrix of
filenames that looks like:

sub01_con2 sub01_con3 sub01_con4 ...
sub02_con2 sub02_con3 sub02_con4 ...
...
sub10_con2 sub10_con3 sub10_con4 ...

and when it is converted to a vector, it is getting read across-then-down
instead of down-then-across. Or vice versa. I have extracted single voxel
data and run the stats in SPSS, and it jibes with this idea (i.e., I get
similar p values to SPM's output when I reshape the matrix incorrectly by hand).

Where am I going wrong? If I were sure this is the only place, I could just
figure out the correct transformation to put in the filenames initially that
makes them come out right in the end, but I figure something else must be afoot.

My job and SPM files are located here:

http://pantheon.yale.edu/~mrj9/spm/stats_refvd_anova_job.mat
http://pantheon.yale.edu/~mrj9/spm/SPM.mat

N.b.: the job file was created with a script, but as far as I can tell the
job files generated by the script are substantively the same as when I try
to do the same thing by hand, and SPM throws no errors at any point.

Thanks so much for any help... I think this is a great feature of SPM5 (much
as I loved poring over Rik and Will's tech note to do this in SPM2), if only
I could get it to work.

Cheers,
Matt Johnson

PS: Just as I reached the end of this email, I had the bright idea to check
a simpler one-way repeated-measures design I have run (using just the four
conditions within level 1 of factor A), and it appears to be experiencing
the same problem. Forgive my not rewriting the whole thing for the simpler case.

PPS: Just updated to the latest-and-greatest SPM5 to make sure I hadn't
missed a key update... problem still there.