  Measurements of intrinsic alignments of galaxy shapes with the large-scale
density field, and the inferred intrinsic alignments model parameters, are
sensitive to the shape measurement methods used. In this paper we measure the
intrinsic alignments of the Sloan Digital Sky Survey-III (SDSS-III) Baryon
Oscillation Spectroscopic Survey (BOSS) LOWZ galaxies using three different
shape measurement methods (re-Gaussianization, isophotal, and de Vaucouleurs),
identifying a variation in the inferred intrinsic alignments amplitude at the
40% level between these methods, independent of the galaxy luminosity or other
properties. We also carry out a suite of systematics tests on the shapes and
their two-point correlation functions, identifying a pronounced contribution
from additive PSF systematics in the de Vaucouleurs shapes. Since different
methods measure galaxy shapes at different effective radii, the trends we
identify in the intrinsic alignments amplitude are consistent with the
interpretation that the outer regions of galaxy shapes are more responsive to
tidal fields, resulting in isophote twisting and stronger alignments for
isophotal shapes. We observe environment dependence of ellipticity, with
brightest galaxies in groups being rounder on average compared to satellite and
field galaxies. We also study the anisotropy in intrinsic alignments
measurements introduced by projected shapes, finding effects consistent with
predictions of the nonlinear alignment model and hydrodynamic simulations. The
large variations seen using the different shape measurement methods have
important implications for intrinsic alignments forecasting and mitigation with
future surveys.
