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
  • contrast: the contrast matrix
  • output: the filename prefix for all output


This command can be used to perform permutation testing of any form of data. The data for each input subject must be stored in a text file, with one value per row. The data for each row across subjects will be tested independently, i.e. there is no statistical enhancement that occurs between the data; however family-wise error control will be used.

In some software packages, a column of ones is automatically added to the GLM design matrix; the purpose of this column is to estimate the “global intercept”, which is the predicted value of the observed variable if all explanatory variables were to be zero. However there are rare situations where including such a column would not be appropriate for a particular experimental design. Hence, in MRtrix3 statistical inference commands, it is up to the user to determine whether or not this column of ones should be included in their design matrix, and add it explicitly if necessary. The contrast matrix must also reflect the presence of this additional column.


Options relating to shuffling of data for nonparametric statistical inference

  • -notest don’t perform statistical inference; only output population statistics (effect size, stdev etc)
  • -errors spec specify nature of errors for shuffling; options are: ee,ise,both (default: ee)
  • -exchange_within file specify blocks of observations within each of which data may undergo restricted exchange
  • -exchange_whole file specify blocks of observations that may be exchanged with one another (for independent and symmetric errors, sign-flipping will occur block-wise)
  • -strong use strong familywise error control across multiple hypotheses
  • -nshuffles number the number of shuffles (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 -nshuffles 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.


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) 2008-2019 the MRtrix3 contributors.

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