[VoxBo] align image to atlas

[jay chen]

Dear all:

           I read a paper " A template for spatial normalization of MR
images of the rat brain" Journal of Neuroscience Methods 129(2003)
105-113.  In paper, authors mention to align the MR images to the
Paxinos atlas in order to have coordinate
information for MR template.  This is where confuses me.  The MR image
is a 3D volume which has dimension like 128*128*63 and voxel size like
0.2*0.2*1 mm.  But the Paxinos atlas is a series of 2D images which
are saved in pdf format.  How can you align these images ?  Thank you
for help.

                    Best Regards,
                    Jay Chen