smooth-image <input> <output> [<sigma>] [options]


This program blurs an input image using a Gaussian filter with a standard deviation equal to the specified sigma value. The dimensions in which the filter recursively applied can be specified by the respective options below. Note that more than one of these options can be specified and that each can also be given more than once. The blurring of the respective dimensions is then performed in the order of the given blurring options.

The output image is by default saved as short integers if the input image was of integral voxel type, otherwise as float image.



Input image. Multiple channels/frames are smoothed independently.


Blurred output image.


Standard deviation of Gaussian smoothing kernel. When negative, its absolute value is multiplied by the average voxel size. (default: 1)

Command options


Blur image in all spatial directions. (default)


Blur image in all dimensions.


Blur image in x dimension.


Blur image in y dimension.


Blur image in z dimension.


Set data type of output to short integers.


Set data type of output to floating point.

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)