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I have applied the flow accumulation tool in arcgis 10.5.

The results map has zero values in places that it should not, which makes the further processing of my images wrong.

Any idea why this happens?

If I set a threshold values before calculating, the streams will become smaller and I dont want that either.

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This issue occurs when the DEM has not undergone proper terrain pre-proccessing. Check to see if you have the following values and ONLY these values in your flow-direction grid: 1,2,4,8,16,32,64, & 128

If you have more than the listed values, this is your issue. In the ArcHydro toolbox, the flow direction tool uses a D8 method and as such, requires that all sinks are filled. The fact that you have more than 8 directions indicates that the flow direction tool is not working. Under the terrain pre-processing menu -> DEM Reconditioning, use the Fill Sinks tool. With the filled DEM, re-run the flow-direction tool, and then the flow-accumulation tool. This should eliminate all zeros.

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