mrclusterstats

Synopsis

Voxel-based analysis using permutation testing and threshold-free cluster enhancement

Usage

mrclusterstats [ options ]  input design contrast mask output
  • input: a text file containing the file names of the input images, one file per line
  • design: the design matrix, rows should correspond with images in the input image text file
  • contrast: the contrast matrix, only specify one contrast as it will automatically compute the opposite contrast.
  • mask: a mask used to define voxels included in the analysis.
  • output: the filename prefix for all output.

Options

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 (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM). Overrides the nperms option.
  • -nonstationary perform non-stationarity correction
  • -nperms_nonstationary num the number of permutations used when precomputing the empirical statistic image for nonstationary correction (Default: 5000)
  • -permutations_nonstationary file manually define the permutations (relabelling) for computing the emprical statistic image for nonstationary correction. 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 (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM) Overrides the nperms_nonstationary option.

Options for controlling TFCE behaviour

  • -tfce_dh value the height increment used in the tfce integration (default: 0.1)
  • -tfce_e value tfce extent exponent (default: 0.5)
  • -tfce_h value tfce height exponent (default: 2)

Additional options for mrclusterstats

  • -negative automatically test the negative (opposite) contrast. By computing the opposite contrast simultaneously the computation time is reduced.
  • -threshold value the cluster-forming threshold to use for a standard cluster-based analysis. This disables TFCE, which is the default otherwise.
  • -connectivity use 26-voxel-neighbourhood connectivity (Default: 6)

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.

References

  • If not using the -threshold command-line option:Smith, S. M. & Nichols, T. E. Threshold-free cluster enhancement: Addressing problems of smoothing, threshold dependence and localisation in cluster inference. NeuroImage, 2009, 44, 83-98
  • If using the -nonstationary option:Salimi-Khorshidi, G. Smith, S.M. Nichols, T.E. Adjusting the effect of nonstationarity in cluster-based and TFCE inference. Neuroimage, 2011, 54(3), 2006-19

Author: David Raffelt (david.raffelt@florey.edu.au)

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

This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/.

Covered Software is provided under this License on an “as is” basis, without warranty of any kind, either expressed, implied, or statutory, including, without limitation, warranties that the Covered Software is free of defects, merchantable, fit for a particular purpose or non-infringing. See the Mozilla Public License v. 2.0 for more details.

For more details, see http://www.mrtrix.org/.