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I am having difficulty in georeferencing an existing tiff (already has georeference information - but is out of alignment). Using the georeference plug-in I can create the map's GCP in the 4 corners and run the transformation (using WGS84). However, even trying other transformations I get a map that is not georeferenced to the Lat & Long. The Lat / Long of the original map shows 26.00, -25.00 (top left corner), the georeference after transformation is 974, -747.

How can I get the transformation to reflect Lat / Long as per the original georeference as all I am trying to achive is a re-aligned map?

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Please check this for reference qgis.spatialthoughts.com/2012/02/… –  Sunil Mar 3 '13 at 4:59

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If you think your Geotiff has a wrong CRS, you can Rightclick -> Set CRS for Layer to choose another CRS.

How much offset do you have? If it is about 200m, it is most probably a matter of wrong +towgs84 parametres. To make the change permanent, you have to use Raster -> Projection -> Define CRS

Georeferencing is a bit tricky, see this answer: Layer not aligning after georeferencing using BC Albers

There was a (now fixed) bug ticket for this: http://hub.qgis.org/issues/2465. Could you try QGIS Master to see if the problem is solved?

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