Hi Hassna,
By applying SIFT2 the values of the mean FA in each edges would very small and not interpretable anymore.
I think that perhaps this is a misunderstanding regarding how this calculation is performed.
By using the -scale_file option in tck2connectome, the contribution of each streamline is multiplied by the corresponding factor in this file; if you then additionally use -stat_edge mean, then it will be the mean of these values from across those streamlines corresponding to a particular edge that is stored in the connectome matrix.
By additionally providing per-streamline weights via the -tck_weights_in option, then yes, the contribution of each streamline is multiplied by both the streamline weight and the factor provided via -scale_file; however, in the calculation of the per-edge mean, this sum is divided by the sum of streamline weights within that edge.
So in this way, the combination of SIFT2 weights and -stat_edge mean act as a weighted mean: those values ascribed to streamlines with large weights contribute more to the final result than those ascribed to streamlines with small weights, but the magnitude of that weighted mean is still faithful to the magnitudes of those values within the file provided via -scale_file.
Rob