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I layer stacked the Landsat 8 Bands (1-7) in QGIS and made a polygon shapefile. Every time I try to clip my layerstack with the Mask layer I just get a completely black output raster. I want to use the clipped raster as a input for "Exact Large-Scale Mean-Shift Segmentation" in the Orfeo Toolbox. Has anyone a solution?

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The cause can be that your polygon layer is in a different projection system. Besides that, my tip is to use the clipping tool present in Semi-automatic classification plugin, in case you have problem with a multiband raster.

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