Calculate the average (unbiased) coordinate space of all input images


mraverageheader [ options ]  input [ input ... ] output
  • input: the input image(s).

  • output: the output image


The voxel spacings of the calculated average header can be determined from the set of input images in one of four different ways, which may be more or less appropriate in different use cases. These options vary in two key ways: 1. Projected voxel spacing of the input image in the direction of the average header axes versus the voxel spacing of the input image axis that is closest to the average header axis; 2. Selecting the minimum of these spacings across input images to maintain maximal spatial resolution versus the mean across images to produce an unbiased average.


  • -padding value boundary box padding in voxels. Default: 0

  • -spacing type Method for determination of voxel spacings based on the set of input images and the average header axes (see Description). Valid options are: min_projection,mean_projection,min_nearest,mean_nearest; default = mean_projection

  • -fill set the intensity in the first volume of the average space to 1

Data type options

  • -datatype spec specify output image data type. Valid choices are: float16, float16le, float16be, float32, float32le, float32be, float64, float64le, float64be, int64, uint64, int64le, uint64le, int64be, uint64be, int32, uint32, int32le, uint32le, int32be, uint32be, int16, uint16, int16le, uint16le, int16be, uint16be, cfloat16, cfloat16le, cfloat16be, cfloat32, cfloat32le, cfloat32be, cfloat64, cfloat64le, cfloat64be, int8, uint8, bit.

Standard options

  • -info display information messages.

  • -quiet do not display information messages or progress status; alternatively, this can be achieved by setting the MRTRIX_QUIET environment variable to a non-empty string.

  • -debug display debugging messages.

  • -force force overwrite of output files (caution: using the same file as input and output might cause unexpected behaviour).

  • -nthreads number use this number of threads in multi-threaded applications (set to 0 to disable multi-threading).

  • -config key value (multiple uses permitted) temporarily set the value of an MRtrix config file entry.

  • -help display this information page and exit.

  • -version display version information and exit.


Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch, M.; Christiaens, D.; Jeurissen, B.; Yeh, C.-H. & Connelly, A. MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 2019, 202, 116137

Author: Maximilian Pietsch (

Copyright: Copyright (c) 2008-2024 the MRtrix3 contributors.

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