evaluate-overlap <target> [<source>...] [options]


Computes the overlap of either two intensity images (average SI) or two segmentations (see evaluate-overlap -label). If more than one source image is given, the overlap between each of these and the target is evaluated.



Target image/segmentation.


Transformed source image/segmentation.

Command options

-images <file>

Text file with source image file paths.

-images-delim, -images-delimiter <c>

Delimiter used in -images file. (default: ‘,’ for .csv, ‘t’ for .tsv, and ‘ ‘ otherwise)

-Rx1 <int>

Region of interest lower index threshold in x dimension.

-Ry1 <int>

Region of interest lower index threshold in y dimension.

-Rz1 <int>

Region of interest lower index threshold in z dimension.

-Rx2 <int>

Region of interest upper index threshold in x dimension.

-Ry2 <int>

Region of interest upper index threshold in y dimension.

-Rz2 <int>

Region of interest upper index threshold in z dimension.

-Tp <value>

Padding value in target.

-label, -segment <value|lower..upper>...

Segmentation labels. When more than one specified, the segments are merged. This option can be given multiple times to evaluate the overlap of more than one (merged) segment at once. Use ‘-label 0’ to evaluate overlap of all labels merged into one segment (i.e., union of all labels). (default: none)


All (positive) segmentation labels individually. Can be combined with -label.

-probs [<threshold>]

Evaluate overlap of class probability maps (fuzzy membership functions). The values of the input images are rescaled to [0, 1]. When no <threshold> is specified, a value of 0.5 is used to binarize the fuzzy segmentation masks. When no <threshold> is specified and the metric is either Dice (DSC) or Jaccard (JSC), these metrics are evaluated using their respective definition based on scalar products.

-precision <int>

Number of significant digits. (default: 2)

-metric <name>

Segmentation overlap metric (see https://en.wikipedia.org/wiki/Confusion_matrix). (default: Dice / F1-score)

-delimiter, -delim <char>

Delimiter for output of multiple overlap values. (default: ,)

-table [<file>|stdout|cout]

Write table with overlap measures for all segments in a row, one row per input source image which is compared to the target segmentation. By default, the output to STDIN with verbosity 0 is the transpose table and excludes a table header. (default: off)

-header, -noheader

Whether to output a header row when -table is used. (default: on)

-id [<name>]

Print ID column with given <name> when -table is used and multiple source images are given. When only one image is given, the table is normally transposed with the label value in the first column. With this option, the table is always such that each row corresponds to one input source image, also when only one is given. (default: off)


Do not print ID column when -table is used.

-id-path, -noid-path

Use full input source image file path as ID column entry. (default: off)

Standard options

-v, -verbose [n]

Increase/Set verbosity of output messages. (default: 0)

-debug [level]

Increase/Set debug level for output of intermediate results. (default: 0)

-version [major.minor]

Print version and exit or set version to emulate.


Print revision (or version) number only and exit.

-h, -help

Print help and exit.

Terminal options

-color, -nocolor

Enable/disable colored output. (default: off)

Parallelization options

-threads <n>

Use maximal <n> threads for parallel execution. (default: automatic)