Clean up residual temporary files & scratch directories from MRtrix3 commands


mrtrix_cleanup path [ options ]
  • path: Directory from which to commence filesystem search


This script will search the file system at the specified location (and in sub-directories thereof) for any temporary files or directories that have been left behind by failed or terminated MRtrix3 commands, and attempt to delete them.

Note that the script’s search for temporary items will not extend beyond the user-specified filesystem location. This means that any built-in or user-specified default location for MRtrix3 piped data and scripts will not be automatically searched. Cleanup of such locations should instead be performed explicitly: e.g. “mrtrix_cleanup /tmp/” to remove residual piped images from /tmp/.

This script should not be run while other MRtrix3 commands are being executed: it may delete temporary items during operation that may lead to unexpected behaviour.


  • -test Run script in test mode: will list identified files / directories, but not attempt to delete them

  • -failed file Write list of items that the script failed to delete to a text file

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: Robert E. Smith (

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

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