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connectomestats

Synopsis

Connectome group-wise statistics at the edge level using non-parametric permutation testing

Usage

connectomestats [ options ]  input algorithm design contrast output
  • input: a text file listing the file names of the input connectomes
  • algorithm: the algorithm to use in network-based clustering/enhancement. Options are: nbs, nbse, none
  • 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

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: 0.4)
  • -tfce_h value tfce height exponent (default: 3)

Additional options for connectomestats

  • -threshold value the t-statistic value to use in threshold-based clustering algorithms

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).
  • -help display this information page and exit.
  • -version display version information and exit.

References

  • If using the NBS algorithm: Zalesky, A.; Fornito, A. & Bullmore, E. T. Network-based statistic: Identifying differences in brain networks. NeuroImage, 2010, 53, 1197-1207
  • If using the NBSE algorithm: Vinokur, L.; Zalesky, A.; Raffelt, D.; Smith, R.E. & Connelly, A. A Novel Threshold-Free Network-Based Statistics Method: Demonstration using Simulated Pathology. OHBM, 2015, 4144
  • 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: Robert E. Smith (robert.smith@florey.edu.au)

Copyright: Copyright (c) 2008-2018 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/

MRtrix3 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

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

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