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stereo reconstruction of point cloud based on rectified images

I have a pair of matched 2D features extracted from rectified stereo image. Using cvPerspectiveTransform function in OpenCV, I attempted to reconstruct those features in 3D. The result is not consistent with the actual object dimension in real world. I realize there is a function in Matlab calibration toolbox that converts 2D stereo features into 3D point cloud. Nevertheless, the features are lifted from original images.

If I want to work with rectified images, is it possible to reconstruct the 3D locations based on 2D feature locations and disparity information.