aggregate-images <mode> <image> <image>... -output <file> [options]


Aggregates multiple (co-registered) input images into a single output image or report statistics thereof within a specified region of interest. The input images have to be defined in the same discrete finite image space.



Name of function used to aggregate input values:

  • mu, mean, average, avg: Mean intensity.
  • sd, stdev, stddev, sigma: Standard deviation.
  • gini, gini-coefficient: Gini coefficient in [0, 1].
  • theil, theil-index: Theil index, equivalent to GE(1).
  • entropy-index, ge: Generalized entropy index (GE), see also -alpha.”
  • entropy: Shannon entropy, see also -bins and -parzen.
  • mode, majority: Smallest modal value, can also be used for majority voting of labels.
  • label-consistency, overlap: Mean Dice overlap of all pairs of labels.

File names of at least two input images.

-output <file>

Voxel-wise aggregate image.

Command options

-dtype char|uchar|short|ushort|int|uint|float|double

Data type of output image. (default: float)

-padding <value>

Background value of voxels to be ignored during -normalization (default: NaN).

-normalization, -normalize <mode>

Input intensity normalization:

  • none: Use input intensities unmodified. (default)
  • mean: Divide by mean foreground value.
  • median: Divide by median foreground value.
  • z-score: Subtract mean and divide by standard deviation.
  • unit: Rescale input intensities to [0, 1].
-rescale [<min>] <max>

Rescale normalized intensities to specified range. When <min> not specified, it is set to zero, i.e., the range is [0, <max>]. Intensities are only rescaled when <min> is less than <max>. (default: off)

-threshold <0-1>

Percentage in [0, 1] of input images that must have a value not equal to the specified -padding value. Otherwise, the output value is background. (default: 0)

-alpha <value>

Alpha value of the generalized entropy index, where alpha=0 is the mean log deviation, alpha=1 is the Theil coefficient, and alpha=2 is half the squared coefficient of variation. (default: 0)


No. of bins used for histogram-based aggregation functions. (default: 64)

-parzen [yes|no|on|off]

Use Parzen window based histogram estimation. (default: off)

-intersection [yes|no|on|off]

Calculate aggregation function for every voxel for which no input value is equal the specified -padding value. By default, only voxels for which all input values are equal to the -padding value are excluded. (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)