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+ | ===== FT_SOURCEANALYSIS ===== | ||
+ | |||
+ | Note that this reference documentation is identical to the help that is displayed in MATLAB when you type "help ft_sourceanalysis". | ||
+ | |||
+ | <html><pre> | ||
+ | <a href=/reference/ft_sourceanalysis><font color=green>FT_SOURCEANALYSIS</font></a> performs beamformer dipole analysis on EEG or MEG data | ||
+ | after preprocessing and a timelocked or frequency analysis | ||
+ | |||
+ | Use as | ||
+ | [source] = ft_sourceanalysis(cfg, freq) | ||
+ | or | ||
+ | [source] = ft_sourceanalysis(cfg, timelock) | ||
+ | |||
+ | where the second input argument with the data should be organised in a structure | ||
+ | as obtained from the <a href=/reference/ft_freqanalysis><font color=green>FT_FREQANALYSIS</font></a> or <a href=/reference/ft_timelockanalysis><font color=green>FT_TIMELOCKANALYSIS</font></a> function. The | ||
+ | configuration "cfg" is a structure containing information about source positions | ||
+ | and other options. | ||
+ | |||
+ | The different source reconstruction algorithms that are implemented are | ||
+ | cfg.method = 'lcmv' linear constrained minimum variance beamformer | ||
+ | 'sam' synthetic aperture magnetometry | ||
+ | 'dics' dynamic imaging of coherent sources | ||
+ | 'pcc' partial cannonical correlation/coherence | ||
+ | 'mne' minimum norm estimation | ||
+ | 'rv' scan residual variance with single dipole | ||
+ | 'music' multiple signal classification | ||
+ | 'sloreta' standardized low-resolution electromagnetic tomography | ||
+ | 'eloreta' exact low-resolution electromagnetic tomography | ||
+ | The DICS and PCC methods are for frequency or time-frequency domain data, all other | ||
+ | methods are for time domain data. ELORETA can be used both for time, frequency and | ||
+ | time-frequency domain data. | ||
+ | |||
+ | The source model to use in the reconstruction should be specified as | ||
+ | cfg.grid = structure, see <a href=/reference/ft_prepare_sourcemodel><font color=green>FT_PREPARE_SOURCEMODEL</font></a> or <a href=/reference/ft_prepare_leadfield><font color=green>FT_PREPARE_LEADFIELD</font></a> | ||
+ | The positions of the dipoles can be specified as a regular 3-D | ||
+ | grid that is aligned with the axes of the head coordinate system | ||
+ | cfg.grid.xgrid = vector (e.g. -20:1:20) or 'auto' (default = 'auto') | ||
+ | cfg.grid.ygrid = vector (e.g. -20:1:20) or 'auto' (default = 'auto') | ||
+ | cfg.grid.zgrid = vector (e.g. 0:1:20) or 'auto' (default = 'auto') | ||
+ | cfg.grid.resolution = number (e.g. 1 cm) for automatic grid generation | ||
+ | cfg.grid.inside = N*1 vector with boolean value whether grid point is inside brain (optional) | ||
+ | cfg.grid.dim = [Nx Ny Nz] vector with dimensions in case of 3-D grid (optional) | ||
+ | If the source model destribes a triangulated cortical sheet, it is described as | ||
+ | cfg.grid.pos = N*3 matrix with the vertex positions of the cortical sheet | ||
+ | cfg.grid.tri = M*3 matrix that describes the triangles connecting the vertices | ||
+ | Alternatively the position of a few dipoles at locations of interest can be | ||
+ | specified, for example obtained from an anatomical or functional MRI | ||
+ | cfg.grid.pos = N*3 matrix with position of each source | ||
+ | |||
+ | Besides the source positions, you may also include previously computed | ||
+ | spatial filters and/or leadfields like this | ||
+ | cfg.grid.filter | ||
+ | cfg.grid.leadfield | ||
+ | |||
+ | The following strategies are supported to obtain statistics for the source parameters using | ||
+ | multiple trials in the data, either directly or through a resampling-based approach | ||
+ | cfg.rawtrial = 'no' or 'yes' construct filter from single trials, apply to single trials. Note that you also may want to set cfg.keeptrials='yes' to keep all trial information, especially if using in combination with grid.filter | ||
+ | cfg.jackknife = 'no' or 'yes' jackknife resampling of trials | ||
+ | cfg.pseudovalue = 'no' or 'yes' pseudovalue resampling of trials | ||
+ | cfg.bootstrap = 'no' or 'yes' bootstrap resampling of trials | ||
+ | cfg.numbootstrap = number of bootstrap replications (e.g. number of original trials) | ||
+ | If none of these options is specified, the average over the trials will | ||
+ | be computed prior to computing the source reconstruction. | ||
+ | |||
+ | To obtain statistics over the source parameters between two conditions, you | ||
+ | can also use a resampling procedure that reshuffles the trials over both | ||
+ | conditions. In that case, you should call the function with two datasets | ||
+ | containing single trial data like | ||
+ | [source] = ft_sourceanalysis(cfg, freqA, freqB) | ||
+ | [source] = ft_sourceanalysis(cfg, timelockA, timelockB) | ||
+ | and you should specify | ||
+ | cfg.randomization = 'no' or 'yes' | ||
+ | cfg.permutation = 'no' or 'yes' | ||
+ | cfg.numrandomization = number, e.g. 500 | ||
+ | cfg.numpermutation = number, e.g. 500 or 'all' | ||
+ | |||
+ | If you have not specified a grid with pre-computed leadfields, | ||
+ | the leadfield for each grid location will be computed on the fly. | ||
+ | In that case you can modify the leadfields by reducing the rank | ||
+ | (i.e. remove the weakest orientation), or by normalizing each | ||
+ | column. | ||
+ | cfg.reducerank = 'no', or number (default = 3 for EEG, 2 for MEG) | ||
+ | cfg.normalize = 'no' or 'yes' (default = 'no') | ||
+ | |||
+ | Other configuration options are | ||
+ | cfg.channel = Nx1 cell-array with selection of channels (default = 'all'), | ||
+ | see <a href=/reference/ft_channelselection><font color=green>FT_CHANNELSELECTION</font></a> for details | ||
+ | cfg.frequency = single number (in Hz) | ||
+ | cfg.latency = single number in seconds, for time-frequency analysis | ||
+ | cfg.lambda = number or empty for automatic default | ||
+ | cfg.refchan = reference channel label (for coherence) | ||
+ | cfg.refdip = reference dipole location (for coherence) | ||
+ | cfg.supchan = suppressed channel label(s) | ||
+ | cfg.supdip = suppressed dipole location(s) | ||
+ | cfg.keeptrials = 'no' or 'yes' | ||
+ | cfg.keepleadfield = 'no' or 'yes' | ||
+ | cfg.projectnoise = 'no' or 'yes' | ||
+ | cfg.keepfilter = 'no' or 'yes' | ||
+ | cfg.keepcsd = 'no' or 'yes' | ||
+ | cfg.keepmom = 'no' or 'yes' | ||
+ | cfg.feedback = 'no', 'text', 'textbar', 'gui' (default = 'text') | ||
+ | |||
+ | The volume conduction model of the head should be specified as | ||
+ | cfg.headmodel = structure with volume conduction model, see <a href=/reference/ft_prepare_headmodel><font color=green>FT_PREPARE_HEADMODEL</font></a> | ||
+ | |||
+ | The EEG or MEG sensor positions can be present in the data or can be specified as | ||
+ | cfg.elec = structure with electrode positions, see <a href=/reference/ft_datatype_sens><font color=green>FT_DATATYPE_SENS</font></a> | ||
+ | cfg.grad = structure with gradiometer definition, see <a href=/reference/ft_datatype_sens><font color=green>FT_DATATYPE_SENS</font></a> | ||
+ | cfg.elecfile = name of file containing the electrode positions, see <a href=/reference/ft_read_sens><font color=green>FT_READ_SENS</font></a> | ||
+ | cfg.gradfile = name of file containing the gradiometer definition, see <a href=/reference/ft_read_sens><font color=green>FT_READ_SENS</font></a> | ||
+ | |||
+ | To facilitate data-handling and distributed computing you can use | ||
+ | cfg.inputfile = ... | ||
+ | cfg.outputfile = ... | ||
+ | If you specify one of these (or both) the input data will be read from a *.mat | ||
+ | file on disk and/or the output data will be written to a *.mat file. These mat | ||
+ | files should contain only a single variable, corresponding with the | ||
+ | input/output structure. | ||
+ | |||
+ | See also <a href=/reference/ft_sourcedescriptives><font color=green>FT_SOURCEDESCRIPTIVES</font></a>, <a href=/reference/ft_sourcestatistics><font color=green>FT_SOURCESTATISTICS</font></a>, <a href=/reference/ft_prepare_leadfield><font color=green>FT_PREPARE_LEADFIELD</font></a>, | ||
+ | <a href=/reference/ft_prepare_headmodel><font color=green>FT_PREPARE_HEADMODEL</font></a>, <a href=/reference/ft_prepare_sourcemodel><font color=green>FT_PREPARE_SOURCEMODEL</font></a> | ||
+ | </pre></html> | ||