Create a glass brain from mask input


mask2glass input output [ options ]
  • input: The input mask image

  • output: The output glass brain image


The output of this command is a glass brain image, which can be viewed using the volume render option in mrview, and used for visualisation purposes to view results in 3D.

While the name of this script indicates that a binary mask image is required as input, it can also operate on a floating-point image. One way in which this can be exploited is to compute the mean of all subject masks within template space, in which case this script will produce a smoother result than if a binary template mask were to be used as input.


  • -dilate iterations Provide number of iterations for dilation step; default = 2

  • -scale value Provide resolution upscaling value; default = 2.0

  • -smooth value Provide standard deviation of smoothing (in mm); default = 1.0

Additional standard options for Python scripts

  • -nocleanup do not delete intermediate files during script execution, and do not delete scratch directory at script completion.

  • -scratch /path/to/scratch/ manually specify an existing directory in which to generate the scratch directory.

  • -continue ScratchDir LastFile continue the script from a previous execution; must provide the scratch directory path, and the name of the last successfully-generated file.

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.

  • -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: Remika Mito ( and Robert E. Smith (

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

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