stack_greedy: Paul's histology stack to MRI registration implementation
Usage:
  stack_greedy recon [cmd_options] <project_dir>
Required Command Options:
  -z <offset> <k> <eps>  : Parameters for the graph-theoretic algorithm. Offset is the 
                           maximum distance in z when slices are considered neighbors.
                           The weight in the registration graph is calculated as
                             W = (1-metric)^k * hops * (1+eps)^hops
                           Suggested values are k=4 and eps=0.1 for the NCC metric
Options Shared with Greedy (see Greedy docs for more info):
  -m metric              : Metric to use for slice matching
  -n NxNxN               : Number of iterations per level of multi-res
  -threads N             : Number of allowed concurrent threads
  -gm-trim <radius>      : Generate mask for gradient computation 
  -search N s_ang s_xyz  : Random search over rigid transforms 

