Dear Experts, 

I have a few questions regarding a longitudinal study using TBSS.  I have a group of patients who have been scanned at 3 time points pre/pr - before intervention and at 2 times points after intervention (post1/po1 and post2/po2 after intervention) - the time from intervention to po1 and po2 scans varies from subject to subject.

1) With regard to data analysis I have registered all images to the first time point and then proceeded with registration to a target template (using combined warps to ensure images are only written out once).  Is this ok ?

2) With regard to model design I have opted for the "tripled t-test" to compare diffusion parameters on a pair wise basis between time points.  Is this ok ? The model and contrasts are similar to those on the FEAT web page.  That is (example shown for 2 subjects only):

                                  Group       Ev 1     Ev 2     Ev 3     Ev 4

Subj1-pr                       1                 1           1          1        0 
Subj1-po1                    1                 1           1          0        1 
Subj1-po2                    1                -1           0          1        0
Subj2-pr                       1                -1           0          0        1
Subj2-po1                    1                 0          -1          1        0 
Subj1-po2                    1                 0          -1          0        1

eg Contrast pr-po2 = 1 2 0 0 
 

 My questions are:

a) Does one have to correct in some way if one decides to use all 6 possible pairwise contrasts between the 3 time points ?  Or does the model take care of that.

b) If one wants to then see how the magnitude of difference in a diffusion contrast (g FA) between time points (eg the contrast shown above) correlates with other co-variates how would one do this ?  For example using the contrast above if one also wanted to see if there was a correlation between the difference between pr and po2 scans and the time from intervention to po2 scan how would this best be done ?

3) I have seen some posters from HBM using the mode of anisotropy to distinguish between where changes in FA are due to changes in voxels containing 2 fibre bundles to 1 fibre bundle (causing an increase in the mode to more positive values)  - is this interpretation only valid in areas where there are crossing fibres - how does one interpret such changes in the mode in areas where crossing fibres are less likely ?

Thanks.

Mahinda