Crop an image to a reduced field of view


mrcrop [ options ]  image_in image_out
  • image_in: the image to be cropped
  • image_out: the output path for the resulting cropped image


Extent of cropping can be determined using either manual setting of axis dimensions, or a computed mask image corresponding to the brain.

If using a mask, a gap of 1 voxel will be left at all 6 edges of the image such that trilinear interpolation upon the resulting images is still valid.

This is useful for axially-acquired brain images, where the image size can be reduced by a factor of 2 by removing the empty space on either side of the brain.


  • -mask image crop the input image according to the spatial extent of a mask image
  • -axis index start end crop the input image in the provided axis

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: Robert E. Smith (

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

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MRtrix3 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

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