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    Metadata details:
    filename: spm_bias_ui.m
    path of file: ./repos/bspm/thirdparty/spm8
    
    the code of the file until where you have to start completion: function spm_bias_ui(P)
% Non-uniformity correct images.
%
% The objective function is related to minimising the entropy of
% the image histogram, but is modified slightly.
% This fixes the problem with the SPM99 non-uniformity correction
% algorithm, which tends to try to reduce the image intensities. As
% the field was constrainded to have an average value of one, then
% this caused the field to bend upwards in regions not included in
% computations of image non-uniformity.
%
%_______________________________________________________________________
% Ref:
% J Ashburner. 2002. "Another MRI Bias Correction Approach" [abstract].
% Presented at the 8th International Conference on Functional Mapping of
% the Human Brain, June 2-6, 2002, Sendai, Japan. Available on CD-Rom
% in NeuroImage, Vol. 16, No. 2.
%
%_______________________________________________________________________
%
%                        The Prompts Explained
%_______________________________________________________________________
%

    
function spm_bias_ui(P)
% Non-uniformity correct images.
%
% The objective function is related to minimising the entropy of
% the image histogram, but is modified slightly.
% This fixes the problem with the SPM99 non-uniformity correction
% algorithm, which tends to try to reduce the image intensities. As
% the field was constrainded to have an average value of one, then
% this caused the field to bend upwards in regions not included in
% computations of image non-uniformity.
%
%_______________________________________________________________________
% Ref:
% J Ashburner. 2002. "Another MRI Bias Correction Approach" [abstract].
% Presented at the 8th International Conference on Functional Mapping of
% the Human Brain, June 2-6, 2002, Sendai, Japan. Available on CD-Rom
% in NeuroImage, Vol. 16, No. 2.
%
%_______________________________________________________________________
%
%                        The Prompts Explained
%_______________________________________________________________________
%
% 'Scans to correct' - self explanatory
%
%_______________________________________________________________________
%
%                           Defaults Options
%_______________________________________________________________________
%[   things in square brackets indicate corresponding defaults field   ]
%
% 'Number of histogram bins?'
% The probability density of the image intensity is represented by a
% histogram. The optimum number of bins depends on the number of voxels
% in the image.  More voxels allows a more detailed representation.
% Another factor is any potential aliasing effect due to there being a
% discrete number of different intensities in the image.  Fewer bins
% should be used in this case.
% [defaults.bias.nbins]
%
% 'Regularisation?'
% The importance of smoothness for the estimated bias field. Without
% any regularisation, the algorithm will attempt to correct for
% different grey levels arising from different tissue types, rather than
% just correcting bias artifact.
% Bias correction uses a Bayesian framework (again) to model intensity
% inhomogeneities in the image(s).  The variance associated with each
% tissue class is assumed to be multiplicative (with the
% inhomogeneities).  The low frequency intensity variability is
% modelled by a linear combination of three dimensional DCT basis
% functions (again), using a fast algorithm (again) to generate the
% curvature matrix.  The regularization is based upon minimizing the
% integral of square of the fourth derivatives of the modulation field
% (the integral of the squares of the first and second derivs give the
% membrane and bending energies respectively).
% [defaults.bias.reg]
%
% 'Cutoff?'
% Cutoff of DCT bases.  Only DCT bases of periods longer than the
% cutoff are used to describe the warps. The number used will
% depend on the cutoff and the field of view of the image.
% [defaults.bias.cutoff]
%
%_______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging

% John Ashburner
% $Id: spm_bias_ui.m 3756 2010-03-05 18:43:37Z guillaume $


global defaults

if nargin==1 && strcmpi(P,'defaults');
    defaults.bias = edit_defaults(defaults.bias);
    return;
end