**Index**

Contents

# Name

**mri_compute_overlap** - Computing three label overlap measures: volume difference, Dice and Jaccard.

# Synopsis

**mri_compute_overlap** [options] <volume 1> <volume 2> [label numbers]

# Arguments

## Positional Arguments

volume 1 |

volume 2 |

[labels] list of labels to be studied, needs to be specified if -a (analyze all option) is not specified |

## Optional Flagged Arguments

-a compute overlap of all labels (if missing, labels of interest should be listed) |

-s show label name for segmentation |

-l <fname> filename to write results to |

-h print help |

# Description

**mri_compute_overlap** computes three different types of overlap measures either for all the existing labels in the input volumes or a subset of them that the users lists in the command line. The three overlap measures are the following:

**relative volume difference**= 2*(|A|-|B|)/|A|+|B|`(the volume difference normalized by the mean)`**relative volume overlap (Dice)**= 2*|A-B|/|A|+|B|`(the intersection over the mean of the segmentation volumes)`**relative volume overlap (Jaccard)**= |A-B|/|A+B|`(the intersection over the union of the segmentation volumes)`

Note, that the label files (e.g. aseg.mgz) need to be in a common space. You can use mri_convert with -rt nearest and -at to apply a transform to the segmentations.

# Examples

# References

None