Perform calculations on linear transformation matrices


transformcalc [ options ]  inputs [ inputs ... ] operation output
  • inputs: the input(s) for the specified operation

  • operation: the operation to perform; one of: invert, half, rigid, header, average, interpolate, decompose, align_vertices_rigid, align_vertices_rigid_scale (see description section for details).

  • output: the output transformation matrix.

Example usages

  • Invert a transformation:

    $ transformcalc matrix_in.txt invert matrix_out.txt
  • Calculate the matrix square root of the input transformation (halfway transformation):

    $ transformcalc matrix_in.txt half matrix_out.txt
  • Calculate the rigid component of an affine input transformation:

    $ transformcalc affine_in.txt rigid rigid_out.txt
  • Calculate the transformation matrix from an original image and an image with modified header:

    $ transformcalc orig_image modified_image header output
  • Calculate the average affine matrix of a set of input matrices:

    $ transformcalc input1.txt ... inputN.txt average matrix_out.txt
  • Create interpolated transformation matrix between two inputs:

    $ transformcalc input1.txt input2.txt interpolate matrix_out.txt

    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:

  • Decompose transformation matrix M into translation, rotation and stretch and shear (M = T * R * S):

    $ transformcalc matrix_in.txt decompose matrixes_out.txt

    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

  • Calculate transformation that aligns two images based on sets of corresponding landmarks:

    $ transformcalc input moving.txt fixed.txt align_vertices_rigid rigid.txt

    Similary, ‘align_vertices_rigid_scale’ produces an affine matrix (rigid and global scale). 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


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: Max Pietsch (

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

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