FT_PREPARE_HEADMODEL
Note that this reference documentation is identical to the help that is displayed in MATLAB when you type “help ft_prepare_headmodel”.
FT_PREPARE_HEADMODEL constructs a volume conduction model from the geometry of the head. The volume conduction model specifies how currents that are generated by sources in the brain, e.g. dipoles, are propagated through the tissue and how these result in externally measureable EEG potentials or MEG fields. FieldTrip implements a variety of forward solutions, partially with internal code and some of them using external toolboxes or executables. Each of the forward solutions requires a set of configuration options which are listed below. This function takes care of all the preparatory steps in the construction of the volume conduction model and sets it up so that subsequent computations are efficient and fast. Use as headmodel = ft_prepare_headmodel(cfg) or headmodel = ft_prepare_headmodel(cfg, mesh) with the output of FT_PREPARE_MESH or FT_READ_HEADSHAPE headmodel = ft_prepare_headmodel(cfg, seg) with the output of FT_VOLUMESEGMENT headmodel = ft_prepare_headmodel(cfg, elec) with the output of FT_READ_SENS headmodel = ft_prepare_headmodel(cfg, grid) with the output of FT_PREPARE_LEADFIELD In general the input to this function is a geometrical description of the shape of the head and a description of the electrical conductivity. The geometrical description can be a set of surface points obtained from fT_READ_HEADSHAPE, a surface mesh that was obtained from FT_PREPARE_MESH or a segmented anatomical MRI that was obtained from FT_VOLUMESEGMENT. The cfg argument is a structure that can contain: cfg.method string that specifies the forward solution, see below cfg.conductivity a number or a vector containing the conductivities of the compartments cfg.tissue a string or integer, to be used in combination with a 'seg' for the second intput. If 'brain', 'skull', and 'scalp' are fields present in 'seg', then cfg.tissue need not be specified, as these are defaults, depending on cfg.method. Otherwise, cfg.tissue should refer to which field(s) of seg should be used. For EEG the following methods are available: singlesphere analytical single sphere model concentricspheres analytical concentric sphere model with up to 4 spheres openmeeg boundary element method, based on the OpenMEEG software bemcp boundary element method, based on the implementation from Christophe Phillips dipoli boundary element method, based on the implementation from Thom Oostendorp asa boundary element method, based on the (commercial) ASA software simbio finite element method, based on the SimBio software fns finite difference method, based on the FNS software infinite electric dipole in an infinite homogenous medium halfspace infinite homogenous medium on one side, vacuum on the other besa finite element leadfield matrix from BESA interpolate interpolate the precomputed leadfield For MEG the following methods are available: openmeeg boundary element method, based on the OpenMEEG software singlesphere analytical single sphere model localspheres local spheres model for MEG, one sphere per channel singleshell realisically shaped single shell approximation, based on the implementation from Guido Nolte infinite magnetic dipole in an infinite vacuum Each specific method has its own specific configuration options which are listed below. BEMCP, DIPOLI, OPENMEEG cfg.tissue see above; in combination with 'seg' input cfg.isolatedsource (optional) CONCENTRICSPHERES cfg.tissue see above; in combination with 'seg' input cfg.fitind (optional) LOCALSPHERES cfg.grad cfg.tissue see above; in combination with 'seg' input; default options are 'brain' or 'scalp' cfg.feedback (optional) cfg.radius (optional) cfg.maxradius (optional) cfg.baseline (optional) SIMBIO cfg.conductivity SINGLESHELL cfg.tissue see above; in combination with 'seg' input; default options are 'brain' or 'scalp' SINGLESPHERE cfg.tissue see above; in combination with 'seg' input; default options are 'brain' or 'scalp'; must be only 1 value INTERPOLATE cfg.outputfile (required) string, filename prefix for the output files BESA cfg.headmodel (required) string, filename of precomputed FEM leadfield cfg.elecfile (required) string, filename of electrode configuration for the FEM leadfield cfg.outputfile (required) string, filename prefix for the output files FNS cfg.tissue cfg.tissueval cfg.conductivity cfg.elec cfg.grad cfg.transform cfg.unit HALFSPACE cfg.point cfg.submethod (optional) More details for each of the specific methods can be found in the corresponding low-level function which is called FT_HEADMODEL_XXX where XXX is the method of choise. See also FT_PREPARE_SOURCEMODEL, FT_PREPARE_LEADFIELD, FT_PREPARE_MESH, FT_HEADMODEL_BEMCP, FT_HEADMODEL_ASA, FT_HEADMODEL_DIPOLI, FT_HEADMODEL_SIMBIO, FT_HEADMODEL_FNS, FT_HEADMODEL_HALFSPACE, FT_HEADMODEL_INFINITE, FT_HEADMODEL_OPENMEEG, FT_HEADMODEL_SINGLESPHERE, FT_HEADMODEL_CONCENTRICSPHERES, FT_HEADMODEL_LOCALSPHERES, FT_HEADMODEL_SINGLESHELL, FT_HEADMODEL_INTERPOLATE