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I have some sets of MODIS MOD13Q1 data sets during March and December for year 2000 to 2015. I need to extract the NDVI and EVI for those two months from the entire 15 years.

How do I apply the Pixel reliability and VI Quality to mask out pixel that are unreliable using ArcGIS 10?

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You don't need to extract NDVI or EVI from MOD13Q1 data sets as they are two separate bands in your data set like the pixel reliability and VI Quality bands. There is a scale factor of 0.0001. You can multiply your NDVI and EVI data to be in the expected data value range.

In order to analyse time-series you can use TIMESAT application which allows the usage of quality data as an optional input.

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