SLM¶
Synopsis¶
The core object of the MATLAB BrainStat statistics module (source code).
Usage¶
obj = SLM(model, contrast, varargin);
obj.fit(data);
obj: the SLM object.
model: the input model, either a FixedEffect or MixedEffect object.
contrast: a contrast in observations of the model.
varargin: a set of name-value pairs (see below).
Initialization¶
A basic SLM object can initialized by simply running it with only a model and contrast
i.e. obj = SLM(model, contrast);
. However, several name-value pairs can
be provided to alter its behavior.
- ‘cluster_threshold’
P-value threshold or statistic threshold for defining clusters, Defaults to 0.001.
- ‘correction’
A cell array containing ‘rft’, ‘fdr’, or both. If ‘rft’ is included, then a random field theory correction will be run. If ‘fdr’ is included, then a false discovery rate correction will be run. Defaults to [].
- ‘drlim’
Step of ratio of variance coefficients, in sd’s. Defaults 0.1.
- ‘mask’
A logical vector containing true for vertices that should be kept during the analysis. Defaults to [].
- ‘surf’
A char array containing a path to a surface, a cell/string array of the aforementioned, or a loaded surface in SurfStat format. Defaults to struct().
- ‘thetalim’
Lower limit on variance coefficients, in sd’s. Defaults 0.01
- ‘two_tailed’
Whether to run one-tailed or two-tailed significance tests. Defaults to true. Note that multivariate models only support two-tailed tests.
Properties¶
- ‘cluster_threshold’
P-value threshold or statistic threshold for defining clusters, Defaults to 0.001.
- ‘coef’
The coefficients of the model.
- ‘contrast’
The contrast of the model.
- ‘coord’
Vertex coordinates.
- ‘correction’
Correction method for multiple comparisons.
- ‘df’
Degrees of freedom.
- ‘drlim’
Step of ratio of variance coefficients, in sd’s. Defaults 0.1.
- ‘lat’
Lattice structure.
- ‘mask’
A logical vector containing true for vertices that should be kept during the analysis. Defaults to [].
- ‘model’
The model of the SLM.
- ‘P’
The p-values corrected for random field theory.
- ‘Q’
The p-values corrected for false discovery rate.
- ‘SSE’
The sum of squared errors.
- ‘surf’
The surface of the model.
- ‘t’
The t-statistic.
- ‘thetalim’
Lower limit on variance coefficients, in sd’s. Defaults 0.01
- ‘tri’
The surface triangles.
- ‘two_tailed’
Whether to run one-tailed or two-tailed significance tests. Defaults to true. Note that multivariate models only support two-tailed tests.
- ‘X’
The design matrix.