Dear Ling,

The essential change with randomise v2.1 is a change in the way that confounds were handled.  When there are no confounds, and model is a simple one-sample, two-sample test or a correlation, an exact permutation test is available.  When you have confounds, there is no one 'right' permutation test, and there are many possible methods.  Randomise v2.0 and before used a method due to Kennedy (1995; see randomise help page for references), and randomise v2.1 uses a method due to Freedman & Lane (1983).  The reason for the change is that, while both the Kennedy & Freedman-Lane method are accurate for large n, for small n the Kennedy method is actually not so good and tends to falsely inflate significances.  Hence, we changed to the more accurate method; unfortunately, you might see some decrease in significance, but this was only because the Kennedy method was too generous :)  Sorry for any trouble!

If you have have *no* confounds, then I can think of any reason why it would change.

Please  let me know if don't have any confounds.

-Tom

PS: The documentation for randomise is behind... it still references Kennedy... I'll update it asap.

On Sun, Sep 14, 2008 at 8:36 AM, Wang, Ling <[log in to unmask]> wrote:
Dear All,
 
Previously I ran a TBSS analysis with v1.1, and used randomise v2.0 to do the statistical analysis. Now, I just wanted to try the new version of randomise, v2.1, but on the identical data, design martix and contrasts, I got different results, e.g., much less significant results in voxel level in v2.1 than in v2.0. The command I used in randomise v2.1 was "randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d design.mat -t design.con -n 5000 --T2 -x -V".
 
I read the "what's new" about TBSS v1.2, which suggests re-run the TBSS analysis from the first step. Should I re-run the analysis on my data and then do the statitical analysis with randomise v2.1, or any other suggestions? Many thanks.
 
Best wishes,
Ling

--
Ling Wang
Cognitive Neurology
Institute of Neuroscience and Biophysics - Medicine
Research Centre Juelich
52425 Juelich, Germany
phone: +49-2461-612481
Fax: +49-2461-612820

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

Senior Research Fellow
Oxford University FMRIB Centre