stack_greedy: Paul's histology stack to MRI registration implementation
Usage:
  stack_greedy init [cmd_options] <project_dir>
Required Command Options:
  -M <manifest>      : Manifest of slices to be reconstructed in 3D. Each line of
                       the manifest file contains the following fields:
                         unique_id         : a unique identifier, for output dirs
                         z_position        : a float indicating slice z-position
                         leader            : a flag (1/0) indicating whether this slide
                                             is a leader or a follower in registration
                         image_filename    : path to image filename
                         [mask_filename]   : path to an image mask filename
Additional Command Options:
  -ext <extension>   : Extension to use for output image files (without trailing period).)
                       Default extension is nii.gz.
  -gm                : Indicates that the manifest includes mask images in the fifth column.
