MATLAB: Why my Pixel Indices are so different from that in Spatial Coordinates The question is revised to make it more specific and constructive. 

I am doing imtransform, yet the xdata and ydata are very much different from that of size(output).

[ output, xdata, ydata ] = imtransform( imgDouble{1}, tform );

Real data test: 

K&gt;&gt; size(output)

ans =

         854        1230

K&gt;&gt; xdata(2) - xdata(1)

ans =

   1.6635e+03

K&gt;&gt; ydata(2) - ydata(1)

ans =

  876.1373
It is about Expressing Image Locations.

There are two kinds of image location expression, 

One and the most common one is the 

pixel indices: 

in row and column

The other one is Intrinsic Coordinate System: 

express in x and y: