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Statistical analysis using CFE is performed separately for each metric
(FD, log(FC), and FDC) as follows::
fixelcfestats fd_smooth/ files.txt design_matrix.txt contrast_matrix.txt matrix/ stats_fd/
fixelcfestats log_fc_smooth/ files.txt design_matrix.txt contrast_matrix.txt matrix/ stats_log_fc/
fixelcfestats fdc_smooth/ files.txt design_matrix.txt contrast_matrix.txt matrix/ stats_fdc/
The input :code:`files.txt` is a text file containing the filename of each
file (i.e. *not* the full path) to be analysed inside the input fixel
directory, each filename on a separate line. The line ordering should
correspond to the lines in the file :code:`design_matrix.txt`.
.. NOTE:: While previous versions of :ref:`fixelcfestats` performed smoothing
of the input fixel data as those data were imported, this is *no longer the case*.
It is expected that the fixel data provided as input to :ref:`fixelcfestats`
will already have been appropriately smoothed; e.g. using :ref:`fixelfilter`.
.. NOTE:: Unlike some other software packages providing a GLM (e.g. FSL
:code:`randomise`), a column of 1's (corresponding to the "global intercept":
the mean image value when all other design matrix factors are zero) will
*not be automatically included*. If the model for your experiment requires
such a factor, it is necessary to include it explicitly in the design matrix.
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