Dear Paul,

I realize it's confusing, but the -g group option is *ONLY* for repeated measures data.  If you have 62 different subjects, there should be *no* group file.

The other minor problem, though, is that you're asking randomise to make inference on whether mean FA is positive (the last four contrasts).  I think I can save you some CPU cycles and tell you, Yup! FA is positive everywhere in the brain! :)

-Tom

On Thu, Jul 31, 2008 at 6:45 PM, Paul Robinson <[log in to unmask]> wrote:
Dear Randomise Experts,

I'm trying to run Randomise on four groups, but am having little luck. I was wondering if someone wouldn't mind just looking over my .mat and .con files to see if I've missed something. Thanks!

more glm_setup.mat
/NumWaves       4
/NumPoints      62
/PPheights              1.000000e+00    1.000000e+00    1.000000e+00    1.000000e+00

/Matrix
1.000000e+00    0.000000e+00    0.000000e+00    0.000000e+00
1.000000e+00    0.000000e+00    0.000000e+00    0.000000e+00
1.000000e+00    0.000000e+00    0.000000e+00    0.000000e+00
1.000000e+00    0.000000e+00    0.000000e+00    0.000000e+00
1.000000e+00    0.000000e+00    0.000000e+00    0.000000e+00
1.000000e+00    0.000000e+00    0.000000e+00    0.000000e+00
1.000000e+00    0.000000e+00    0.000000e+00    0.000000e+00
1.000000e+00    0.000000e+00    0.000000e+00    0.000000e+00
1.000000e+00    0.000000e+00    0.000000e+00    0.000000e+00
1.000000e+00    0.000000e+00    0.000000e+00    0.000000e+00
1.000000e+00    0.000000e+00    0.000000e+00    0.000000e+00
0.000000e+00    1.000000e+00    0.000000e+00    0.000000e+00
0.000000e+00    1.000000e+00    0.000000e+00    0.000000e+00
0.000000e+00    1.000000e+00    0.000000e+00    0.000000e+00
0.000000e+00    1.000000e+00    0.000000e+00    0.000000e+00
0.000000e+00    1.000000e+00    0.000000e+00    0.000000e+00
0.000000e+00    1.000000e+00    0.000000e+00    0.000000e+00
0.000000e+00    1.000000e+00    0.000000e+00    0.000000e+00
0.000000e+00    1.000000e+00    0.000000e+00    0.000000e+00
0.000000e+00    1.000000e+00    0.000000e+00    0.000000e+00
0.000000e+00    1.000000e+00    0.000000e+00    0.000000e+00
0.000000e+00    1.000000e+00    0.000000e+00    0.000000e+00
0.000000e+00    1.000000e+00    0.000000e+00    0.000000e+00
0.000000e+00    1.000000e+00    0.000000e+00    0.000000e+00
0.000000e+00    1.000000e+00    0.000000e+00    0.000000e+00
0.000000e+00    1.000000e+00    0.000000e+00    0.000000e+00
0.000000e+00    1.000000e+00    0.000000e+00    0.000000e+00
0.000000e+00    1.000000e+00    0.000000e+00    0.000000e+00
0.000000e+00    0.000000e+00    1.000000e+00    0.000000e+00
0.000000e+00    0.000000e+00    1.000000e+00    0.000000e+00
0.000000e+00    0.000000e+00    1.000000e+00    0.000000e+00
0.000000e+00    0.000000e+00    1.000000e+00    0.000000e+00
0.000000e+00    0.000000e+00    1.000000e+00    0.000000e+00
0.000000e+00    0.000000e+00    1.000000e+00    0.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00
0.000000e+00    0.000000e+00    0.000000e+00    1.000000e+00


more glm_setup.con
/ContrastName1  Control>Scz
/ContrastName2  Control>THC
/ContrastName3  Control>Scz+THC
/ContrastName4  Scz>THC
/ContrastName5  Scz>Scz+THC
/ContrastName6  Scz>Control
/ContrastName7  THC>Scz
/ContrastName8  THC>Scz+THC
/ContrastName9  THC>Control
/ContrastName10 Scz+THC>Scz
/ContrastName11 Scz+THC>THC
/ContrastName12 Scz+THC>Control
/ContrastName13 Control_mean
/ContrastName14 Scz_mean
/ContrastName15 THC_mean
/ContrastName16 Scz+THC_mean
/NumWaves       4
/NumContrasts   16
/PPheights              1.000000e+00    1.000000e+00    1.000000e+00    1.000000e+00    1.000000e
+00     1.000000e+00    1.000000e+00    1.000000e+00    1.000000e+00    1.000000e+00    1.000000e
+00     1.000000e+00    1.000000e+00    1.000000e+00    1.000000e+00    1.000000e+00
/RequiredEffect         1.419   1.226   1.794   1.543   2.024   1.419   1.543   1.894   1.226   2
.024    1.894   1.794   0.754   1.203   0.967   1.628

/Matrix
-1.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
0.000000e+00 -1.000000e+00 0.000000e+00 1.000000e+00
0.000000e+00 0.000000e+00 -1.000000e+00 1.000000e+00
1.000000e+00 -1.000000e+00 0.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00 -1.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00 0.000000e+00 -1.000000e+00
-1.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
0.000000e+00 1.000000e+00 -1.000000e+00 0.000000e+00
0.000000e+00 1.000000e+00 0.000000e+00 -1.000000e+00
-1.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
0.000000e+00 -1.000000e+00 1.000000e+00 0.000000e+00
0.000000e+00 0.000000e+00 1.000000e+00 -1.000000e+00
0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00


And here's the command I run, as well as it's error:

randomise -i all_FA_skeletonised.nii.gz -o all_groups.nii.gz -d glm_setup.mat -t glm_setup.con -f glm_setup.fts -g glm_setup.grp -n 5000 -c 3
terminate called after throwing an instance of 'NEWMAT::ProgramException'
Abort

I'm just not sure where I'm going wrong here. Any advice would be greatly appreciated.
Thanks!

Cheers,
Paul





--
____________________________________________
Thomas Nichols, PhD
Director, Modelling & Genetics
GlaxoSmithKline Clinical Imaging Centre

Senior Research Fellow
Oxford University FMRIB Centre