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Hello Freesurfer Developers,
I'm attempting to use Univariate LME analysis to compare the symptomatic and asymptomatic hemispheres of early stage Parkinson's disease patients.
I re-organized the data so that the symptomatic hemisphere is the left hemisphere and the Asymptomatic is the right (by flipping the orig.mgz before recon-all).
I followed the LME model tutorial for univariate on the freesurfer wiki and created my qdec.tabel.dat to have the same layout as in the example with group 1 as left hemisphere and group 2 as right hemisphere.
I have a design matrix to do a simple linear model containing a group by time interaction with the contrast of [0 0 0 1 0 0]
After running the F-test however, I noticed that the p-value was really inconsistent across atlases. I used multiple atlases and noticed that the p-value can be as low as 1.00E-30 for many structures. This is too good to be true especially since after sending the thickness value to a statistician she came back with values greatly different from mine. However, the Bhat values were similar.
Can someone give me a hint as to what is going on?
Xiaoyu