Accurate corrections of atmospheric effects on thermal infrared remote sensing data are an essential pre-requisite for the development of thermal infrared airborne-derived crop water stress indices. These corrections can be performed using ground surface temperature measurements, which are time consuming and expensive. Atmospheric effects can also be corrected using radiative transfer models that require knowledge of atmospheric status. The latter can be accurately characterized from radiosoundings, but these are usually unavailable. It can also be derived from meteorological model simulations, but spatial and temporal resolution are often too coarse. This study proposes performing atmospheric corrections by using temperature and relative humidity profiles acquired in flight from on-board sensors during data collection. Such measurements are used to document the atmospheric radiative transfer model MATISSE. First results from an experimentation over a tropical cropped area show that corrections are made with a 1.46°K accuracy.