Thanks, I think it works. At first I thought that the results are far away from significance, but then I realized that it matters what color map I am using when loading P-values.spvcm. Over which color map I should load it? I guess it is rawP or rawP original.

Also I would like to ask again how can I get such a color map as in http://www.ncbi.nlm.nih.gov/pmc/articles... where difference in mm is showed. I have looked at the MeshMath Absolute Distance feature at http://www.nitrc.org/plugins/mwiki/index... but I am not sure what are the inputs. Can I use meanA and meanB?

Btw: what does the numbers in DiffMagnitude_original stand for? And why is the colormap different from rawP?


Thanks for all you help,
A.