Vegetation indices play an important role in monitoring variations in vegetation. The Enhanced Vegetation Index (EVI) proposed by the MODIS Land Discipline Group and the Normalized Difference Vegetation Index (NDVI) are both global-based vegetation indices aimed at providing consistent spatial and temporal information regarding global vegetation. However, many environmental factors such as atmospheric conditions and soil background may produce errors in these indices. The topographic effect is another very important factor, especially when the indices are used in areas of rough terrain. In this paper, we theoretically analyzed differences in the topographic effect on the EVI and the NDVI based on a non-Lambertian model and two airborne-based images acquired from a mountainous area covered by high-density Japanese cypress plantation were used as a case study. The results indicate that the soil adjustment factor “L” in the EVI makes it more sensitive to topographic conditions than is the NDVI. Based on these results, we strongly recommend that the topographic effect should be removed in the reflectance data before the EVI was calculated—as well as from other vegetation indices that similarly include a term without a band ratio format (e.g., the PVI and SAVI)—when these indices are used in the area of rough terrain, where the topographic effect on the vegetation indices having only a band ratio format (e.g., the NDVI) can usually be ignored.

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