First:

cd grouping/source
mkdir build && cd build && cmake ../ && make && mv *.so ../../lib
cd ../..
export LD_LIBRARY_PATH=$(pwd)/lib:/usr/lib

To run, go to the grouping folder and open up octave (or Matlab, but I have not tried on matlab yet). The run:

addpath(genpath('./'))
compile
example

As of the mail of June 2012, I am allowed to relicense gPb as BSD and integrate it in OpenCV

gPb licensing / OpenCV integration
From:	Michael Maire <mmaire@caltech.edu>
To:	Vincent Rabaud <vrabaud@willowgarage.com>
CC:	Jitendra Malik <malik@eecs.berkeley.edu>, Charless Fowlkes <fowlkes@ics.uci.edu>, Pablo Arbelaez <arbelaez@eecs.berkeley.edu>, David Martin <david.r.martin@gmail.com>
Date:	Monday 12:54:37 PM
Hi Vincent,

The current gPb-UCM code consists of some components distributed under
the GPL and some components distributed under the AGPL:
http://www.gnu.org/copyleft/gpl.html
http://www.gnu.org/licenses/agpl.html

We would like to make the following licensing arrangements to allow
integration into OpenCV:

(1) We give you, the OpenCV team, and Willow Garage permission to take 
    our current gPb-UCM code, use whatever parts of it (or all of it) 
    that you like, and distribute the result as part of OpenCV under
    the BSD license ( http://opensource.org/licenses/bsd-license.php ).

(2) OpenCV (and the gPb-UCM implementation within it) are distributed 
    under the BSD license.

(3) We will continue to distribute our own gPb-UCM code under the 
    current GPL/AGPL.

Essentially, we are taking a snapshot of the code and releasing it to
you under the BSD license.

Point (3) above is made to indicate that we intend to release our own
future enhancements under the GPL/AGPL and not under the BSD license.
You would need to negotiate separately for permission to include such
work in OpenCV.

Also note that we are not changing the license on any of our own code
which uses gPb in a larger project.  For example, I have written code
that combines gPb with object detection and released the result under
the AGPL.  At this time, I am NOT releasing this additional code with a
BSD license.

What we are granting you permission to distribute under the BSD license
is our code for the implementation of gPb-UCM corresponding to the work
described in this paper:

Contour Detection and Hierarchical Image Segmentation
P. Arbelaez, M. Maire, C. Fowlkes and J. Malik.
IEEE TPAMI, Vol. 33, No. 5, pp. 898-916, May 2011
http://www.eecs.berkeley.edu/Research/Projects/CS/vision/grouping/papers/amfm_pami2010.pdf

The code will be that found here, with a few pending improvements by
Pablo:
http://www.eecs.berkeley.edu/Research/Projects/CS/vision/grouping/BSR/BSR_source.tgz

All contributors to this code are cc'd to this email and all have agreed
to the licensing arrangement outlined above.  If anyone has additional
questions, please email me.

Turning to practical matters, Pablo and I will coordinate with Vincent
on the technical details of integrating gPb into OpenCV.  If anyone else
would also like to be a part of this process, please let me know.
Otherwise, we will leave you out of the technical discussion unless your
advice is specifically required.

Best,
Michael