# 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)

• -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).
• -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)