fixelcfestats [ options ]  input template design contrast tracks output
  • input: a text file listing the file names of the input fixel images
  • template: the fixel mask used to define fixels of interest. This can be generated by thresholding the group average AFD fixel image.
  • 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
  • tracks: the tracks used to determine fixel-fixel connectivity
  • output: the filename prefix for all output.


Fixel-based analysis using connectivity-based fixel enhancement and non-parametric permutation testing.


  • -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).
  • -cfe_dh value the height increment used in the cfe integration (default: 0.1)
  • -cfe_e value cfe extent exponent (default: 2)
  • -cfe_h value cfe height exponent (default: 3)
  • -cfe_c value cfe connectivity exponent (default: 0.5)
  • -angle value the max angle threshold for computing inter-subject fixel correspondence (Default: 45 degrees)
  • -connectivity threshold a threshold to define the required fraction of shared connections to be included in the neighbourhood (default: 0.01)
  • -smooth FWHM smooth the fixel value along the fibre tracts using a Gaussian kernel with the supplied FWHM (default: 10mm)
  • -nonstationary do adjustment for non-stationarity
  • -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.


Raffelt, D.; Smith, RE.; Ridgway, GR.; Tournier, JD.; Vaughan, DN.; Rose, S.; Henderson, R.; Connelly, A.Connectivity-based fixel enhancement: Whole-brain statistical analysis of diffusion MRI measures in the presence of crossing fibres. Neuroimage, 2015, 15(117):40-55

  • 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 (

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