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To study the atomic, molecular and ionized emission of Giant Molecular Clouds(GMCs), we have initiated a Large Program with the VLA: 'THOR - The HI, OH,Recombination Line survey of the Milky Way'. We map the 21cm HI line, 4 OHlines, 19 H_alpha recombination lines and the continuum from 1 to 2 GHz of asignificant fraction of the Milky Way (l=15-67deg, |b|<1deg) at ~20"resolution. In this paper, we focus on the HI emission from the W43star-formation complex. Classically, the HI 21cm line is treated as opticallythin with column densities calculated under this assumption. This might givereasonable results for regions of low-mass star-formation, however, it is notsufficient to describe GMCs. We analyzed strong continuum sources to measurethe optical depth, and thus correct the HI 21cm emission for optical deptheffects and weak diffuse continuum emission. Hence, we are able to measure theHI mass of W43 more accurately and our analysis reveals a lower limit ofM=6.6x10^6 M_sun, which is a factor of 2.4 larger than the mass estimated withthe assumption of optically thin emission. The HI column densities are as highas N(HI)~150 M_sun/pc^2 ~ 1.9x10^22 cm^-2, which is an order of magnitudehigher than for low mass star formation regions. This result challengestheoretical models that predict a threshold for the HI column density of ~10M_sun/pc^2, at which the formation of molecular hydrogen should set in. Byassuming an elliptical layered structure for W43, we estimate the particledensity profiles. While at the cloud edge atomic and molecular hydrogen arewell mixed, the center of the cloud is strongly dominated by molecularhydrogen. We do not identify a sharp transition between hydrogen in atomic andmolecular form. Our results are an important characterization of the atomic tomolecular hydrogen transition in an extreme environment and challenges currenttheoretical models.

THOR - The HI, OH, Recombination Line Survey of the Milky Way - The pilot study: HI observations of the giant molecular cloud W43