Here is a snippet of c code on how to apply the transformation once you obtained the parameters of the cameras:
sample of code with opencv

if you want to use inside the libfreenect library (you need to set the option to build the opencv wrapper), you can replace the CMakeLists.txt in the wrapper/opencv folder with this
CMakeLists.txt

For kinect calibration/registration please check here:
http://nicolas.burrus.name/index.php/Research/KinectCalibration


Assignement for Homework 2

Mapping depth pixels with color pixels

The first step is to undistort rgb and depth images using the estimated distortion coefficients. Then, using the depth camera intrinsics, each pixel (x_d,y_d) of the depth camera can be projected to metric 3D space using the following formula:

P3D.x = (x_d - cx_d) * depth(x_d,y_d) / fx_d
P3D.y = (y_d - cy_d) * depth(x_d,y_d) / fy_d
P3D.z = depth(x,y)

with fx_d, fy_d, cx_d and cy_d the intrinsics of the depth camera.

We can then reproject each 3D point on the color image and get its color:

P3D' = R.P3D + T
P2D_rgb.x = (P3D'.x * fx_rgb / P3D'.z) + cx_rgb
P2D_rgb.y = (P3D'.y * fy_rgb / P3D'.z) + cy_rgb

with R and T the rotation and translation parameters estimated during the stereo calibration.