Statistical testing of vector data using non-parametric permutation testing


vectorstats [ options ]  input design contrast output
  • input: a text file listing the file names of the input subject data
  • design: the design matrix. Note that a column of 1’s will need to be added for correlations.
  • contrast: the contrast vector, specified as a single row of weights
  • output: the filename prefix for all output.


Options for permutation testing

  • -notest don’t perform permutation testing and only output population statistics (effect size, stdev etc)
  • -nperms num the number of permutations (Default: 5000)
  • -permutations file manually define the permutations (relabelling). The input should be a text file defining a m x n matrix, where each relabelling is defined as a column vector of size m, and the number of columns, n, defines the number of permutations. Can be generated with the palm_quickperms function in PALM ( Overrides the nperms option.

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.

Author: Robert E. Smith (

Copyright: Copyright (c) 2008-2019 the MRtrix3 contributors.

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