Convert linear transformation matrices


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

  • operation: the operation to perform, one of:
    flirt_import, itk_import

  • output: the output transformation matrix.


This command allows to convert transformation matrices provided by other registration softwares to a format usable in MRtrix3. Example usages are provided below.

Example usages

  • Convert a transformation matrix produced by FSL’s flirt command into a format usable by MRtrix3:

    $ transformconvert transform_flirt.mat flirt_in.nii flirt_ref.nii flirt_import transform_mrtrix.txt

    The two images provided as inputs for this operation must be in the correct order: first the image that was provided to flirt via the -in option, second the image that was provided to flirt via the -ref option.

  • Convert a plain text transformation matrix file produced by ITK’s affine registration (e.g. ANTS, Slicer) into a format usable by MRtrix3:

    $ transformconvert transform_itk.txt itk_import transform_mrtrix.txt


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 (

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