Directly edit the intensities within an image from the command-line


mredit [ options ]  input[ output ]
  • input: the input image

  • output: the (optional) output image


A range of options are provided to enable direct editing of voxel intensities based on voxel / real-space coordinates. If only one image path is provided, the image will be edited in-place (use at own risk); if input and output image paths are provided, the output will contain the edited image, and the original image will not be modified in any way.


  • -plane axis coord value (multiple uses permitted) fill one or more planes on a particular image axis

  • -sphere position radius value (multiple uses permitted) draw a sphere with radius in mm

  • -voxel position value (multiple uses permitted) change the image value within a single voxel

  • -scanner indicate that coordinates are specified in scanner space, rather than as voxel coordinates

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: Robert E. Smith (

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

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