We examine a method of calculating the magnetic helicity of cylindrical magnetic flux rope of arbitrary cross section from in-situ spacecraft data. First we examine the gauge invariance of the definition of relative helicity by Finn and Antonsen (1985). Two approaches based on Grad-Shafranov equation are then described. A case study is presented to illustrate the method. The results show significant discrepancies from an earlier study utilizing axially symmetric models. We briefly discuss the potential applications for Sun-Earth connection.