Dear Lorenzo,
What you have explained is not enough to be of help. Meanwhile, I think it useful to have a look at previous discussions regarding using the conservation law to easily compute the spin conductance Ref*.
You see bello a small script that might be useful:
syst = kwant.Builder()
sym = kwant.TranslationalSymmetry(lat.vec((-1, 0)))
syst = kwant.Builder(sym, conservation_law=-sigma_z)
smatrix = kwant.smatrix(syst.finalized(), energy, args=(params,))
# the spin up conductance (up to up)
Gup.append(smatrix.transmission((1, 0), (0, 0)))
# the spin down conductance (down to down)
Gdn.append(smatrix.transmission((1, 1), (0, 0)))
# total conductance
G.append(smatrix.transmission((1, 0), (0, 0))+smatrix.transmission((1, 1), (0, 0)))
Ref*
best; Adel