Hi David,
The TR shouldn't have an effect on the data, since it is so long.
The TE, per se, shouldn't have an effect on the FA values either: the formula for the intensity at any given voxel would be:
I(b) = I(0) e^(-bD)
and the effect of the TE (i.e., e^(-TE/T2)) goes into I0, so it shouldn't -in principle- affect your estimation for the diffusion tensor and, hence, the FA.
_However_, having a different TE means that the timing of the 180 pulse(s) is different in both groups, what means that, very likely, the diffusion timing is different. In a first approximation, if the b-values are the same, the diffusion tensor shouldn't change. But if the diffusion is non-gaussian, a longer diffusion time -even with a same b-value- would mean that in some directions the water might have found barriers that for the shorter time wouldn't have been reached. Therefore the diffusion tensor that you obtain and, hence, the FA, would be different.
As David Gutman states, the fact that both groups (patients and controls) were scanned with different parameters means that you cannot infer whether the differences were a group effect, or a experimental bias.
Sorry :-(
-Pablo
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