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


fixelcfestats [ options ]  in_fixel_directory subjects design contrast connectivity out_fixel_directory
  • in_fixel_directory: the fixel directory containing the data files for each subject (after obtaining fixel correspondence
  • subjects: a text file listing the subject identifiers (one per line). This should correspond with the filenames in the fixel directory (including the file extension), and be listed in the same order as the rows of the design matrix.
  • design: the design matrix
  • contrast: the contrast matrix, specified as rows of weights
  • connectivity: the fixel-fixel connectivity matrix
  • out_fixel_directory: the output directory where results will be saved. Will be created if it does not exist


Unlike previous versions of this command, where a whole-brain tractogram file would be provided as input in order to generate the fixel-fixel connectivity matrix and smooth fixel data, this version expects to be provided with the directory path to a pre-calculated fixel-fixel connectivity matrix (likely generated using the MRtrix3 command fixelconnectivity), and for the input fixel data to have already been smoothed (likely using the MRtrix3 command fixelfilter).

Note that if the -mask option is used, the output fixel directory will still contain the same set of fixels as that present in the input fixel template, in order to retain fixel correspondence. However a consequence of this is that all fixels in the template will be initialy visible when the output fixel directory is loaded in mrview. Those fixels outside the processing mask will immediately disappear from view as soon as any data-file-based fixel colouring or thresholding is applied.

In some software packages, a column of ones is automatically added to the GLM design matrix; the purpose of this column is to estimate the “global intercept”, which is the predicted value of the observed variable if all explanatory variables were to be zero. However there are rare situations where including such a column would not be appropriate for a particular experimental design. Hence, in MRtrix3 statistical inference commands, it is up to the user to determine whether or not this column of ones should be included in their design matrix, and add it explicitly if necessary. The contrast matrix must also reflect the presence of this additional column.


  • -mask file provide a fixel data file containing a mask of those fixels to be used during processing

Options relating to shuffling of data for nonparametric statistical inference

  • -notest don’t perform statistical inference; only output population statistics (effect size, stdev etc)
  • -errors spec specify nature of errors for shuffling; options are: ee,ise,both (default: ee)
  • -exchange_within file specify blocks of observations within each of which data may undergo restricted exchange
  • -exchange_whole file specify blocks of observations that may be exchanged with one another (for independent and symmetric errors, sign-flipping will occur block-wise)
  • -strong use strong familywise error control across multiple hypotheses
  • -nshuffles number the number of shuffles (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 ( Overrides the -nshuffles option.
  • -nonstationarity perform non-stationarity correction
  • -skew_nonstationarity value specify the skew parameter for empirical statistic calculation (default for this command is 1)
  • -nshuffles_nonstationarity number the number of shuffles to use when precomputing the empirical statistic image for non-stationarity correction (default: 5000)
  • -permutations_nonstationarity file manually define the permutations (relabelling) for computing the emprical statistics for non-stationarity 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 ( Overrides the -nshuffles_nonstationarity option.

Parameters for the Connectivity-based Fixel Enhancement algorithm

  • -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)
  • -cfe_legacy use the legacy (non-normalised) form of the cfe equation

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).
  • -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.


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 not using the -cfe_legacy option: Smith, RE.; Dimond, D; Vaughan, D.; Parker, D.; Dhollander, T.; Jackson, G.; Connelly, A. Intrinsic non-stationarity correction for Fixel-Based Analysis. In Proc OHBM 2019 M789
  • 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

Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch, M.; Christiaens, D.; Jeurissen, B.; Yeh, C.-H. & Connelly, A. MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 2019, 202, 116137

Author: David Raffelt ( and Robert E. Smith (

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