This proposes a new program, called mri_overlap, that will replace the redundant (and buggy) mri_compute_seg_overlap and mri_compute_overlap. A detailed report of the overlap results can be output to a json file.

USAGE:

    mri_overlap <vol1> <vol2> [options]

OPTIONAL ARGUMENTS:

    -o, --out
        Save detailed overlap report to a json file.

    -m, --measures        
        List of measures to compute. By default, only dice scores
        are computed. Options include:
          dice    - ... 
          jaccard - ...
          voldiff - ...

    -l, --labels
        Space-separated list of labels to use. By default, the overlap
        will be computed between all labels available in both input volumes.

    -f, --labelfile
        File with space-separated list of labels to use.

    -s, --seg
        Compute overlap between the major segmentation structures listed above.

    -q, --quiet
        Quiet mode - do not print computed results to stdout