mrclusterstats¶
Synopsis¶
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.
Description¶
Voxel-based analysis using permutation testing and threshold-free cluster enhancement.
Options¶
- -notest don’t perform permutation testing and only output population statistics (effect size, stdev etc)
- -negative automatically test the negative (opposite) contrast. By computing the opposite contrast simultaneously the computation time is reduced.
- -nperms num the number of permutations (default = 5000).
- -threshold value the cluster-forming threshold to use for a standard cluster-based analysis. This disables TFCE, which is the default otherwise.
- -tfce_dh value the height increment used in the TFCE integration (default = 0.1)
- -tfce_e value TFCE extent parameter (default = 0.5)
- -tfce_h value TFCE height parameter (default = 2)
- -connectivity use 26-voxel-neighbourhood connectivity (Default: 6)
- -nonstationary perform non-stationarity correction (currently only implemented with tfce)
- -nperms_nonstationary num the number of permutations used when precomputing the empirical statistic image for nonstationary correction (Default: 5000)
Standard options¶
- -info display information messages.
- -quiet do not display information messages or progress status.
- -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)
- -failonwarn terminate program if a warning is produced
- -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) 2008-2016 the MRtrix3 contributors
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