Perform calculations on linear transformation matrices


transformcalc [ options ]  inputs [ inputs ... ] operation output
  • inputs: the inputs for the specified operation
  • operation: the operation to perform, one of: invert, half, rigid, header, average, interpolate, decompose, align_vertices_rigid (see description section for details).
  • output: the output transformation matrix.


invert: invert the input transformation:

matrix_in invert output

half: calculate the matrix square root of the input transformation:

matrix_in half output

rigid: calculate the rigid transformation of the affine input transformation:

matrix_in rigid output

header: calculate the transformation matrix from an original image and an image with modified header:

mov mapmovhdr header output

average: calculate the average affine matrix of all input matrices:

input … average output

interpolate: create interpolated transformation matrix between input (t=0) and input2 (t=1). Based on matrix decomposition with linear interpolation of translation, rotation and stretch described in Shoemake, K., Hill, M., & Duff, T. (1992). Matrix Animation and Polar Decomposition. Matrix, 92, 258-264. doi:

input input2 interpolate output

decompose: decompose transformation matrix M into translation, rotation and stretch and shear (M = T * R * S). The output is a key-value text file containing: scaling: vector of 3 scaling factors in x, y, z direction; shear: list of shear factors for xy, xz, yz axes; angles: list of Euler angles about static x, y, z axes in radians in the range [0:pi]x[-pi:pi]x[-pi:pi]; angle_axis: angle in radians and rotation axis; translation : translation vector along x, y, z axes in mm; R: composed roation matrix (R = rot_x * rot_y * rot_z); S: composed scaling and shear matrix:

matrix_in decompose output

align_vertices_rigid: align two sets of landmarks using a rigid transformation. Vertex coordinates are in scanner space, corresponding vertices must be stored in the same row of moving.txt and fixed.txt. Requires 3 or more vertices in each file. Algorithm: Kabsch ‘A solution for the best rotation to relate two sets of vectors’ DOI:10.1107/S0567739476001873:

input moving.txt fixed.txt align_vertices_rigid output


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).
  • -help display this information page and exit.
  • -version display version information and exit.

Author: Max Pietsch (

Copyright: Copyright (c) 2008-2018 the MRtrix3 contributors.

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