Reorientation of Accelerometer axes to car's axes in matlab mobile application

I am trying to acquire data from matlab mobile sensors (accelerometer, gyroscope, GPS, etc.) while driving a car. 
The phone is set in an arbitrary position inside the car,
that’s why I need to reorient the accelerometer axis to align with the car axis. 

I found an article mentioning a virtual reorientation algorithm for this matter. 
But I don’t know how they used the GPS to calculate the post-rotation and how they monitored the pre-rotation angles.

Any advice or even an alternate way of doing this using matlab would be greatly appreciated.