Computes a dissimilarity metric between two images


mrmetric [ options ]  image1 image2
  • image1: the first input image.

  • image2: the second input image.


Currently only the mean squared difference is fully implemented.


  • -space iteration method voxel (default): per voxel image1: scanner space of image 1 image2: scanner space of image 2 average: scanner space of the average affine transformation of image 1 and 2

  • -interp method set the interpolation method to use when reslicing (choices: nearest, linear, cubic, sinc. Default: linear).

  • -metric method define the dissimilarity metric used to calculate the cost. Choices: diff (squared differences), cc (non-normalised negative cross correlation aka negative cross covariance). Default: diff). cc is only implemented for -space average and -interp linear and cubic.

  • -mask1 image mask for image 1

  • -mask2 image mask for image 2

  • -nonormalisation do not normalise the dissimilarity metric to the number of voxels.

  • -overlap output number of voxels that were used.

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: David Raffelt ( and Max Pietsch (

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

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