Connectome group-wise statistics at the edge level using non-parametric permutation testing
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 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
- -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.
- 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 (firstname.lastname@example.org)
Copyright: Copyright (c) 2008-2018 the MRtrix3 contributors.
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