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+ | ===== 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". | ||
+ | |||
+ | <html><pre> | ||
+ | <a href=/reference/ft_prepare_headmodel><font color=green>FT_PREPARE_HEADMODEL</font></a> 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 <a href=/reference/ft_prepare_mesh><font color=green>FT_PREPARE_MESH</font></a> or <a href=/reference/ft_read_headshape><font color=green>FT_READ_HEADSHAPE</font></a> | ||
+ | headmodel = ft_prepare_headmodel(cfg, seg) with the output of <a href=/reference/ft_volumesegment><font color=green>FT_VOLUMESEGMENT</font></a> | ||
+ | headmodel = ft_prepare_headmodel(cfg, elec) with the output of <a href=/reference/ft_read_sens><font color=green>FT_READ_SENS</font></a> | ||
+ | headmodel = ft_prepare_headmodel(cfg, grid) with the output of <a href=/reference/ft_prepare_leadfield><font color=green>FT_PREPARE_LEADFIELD</font></a> | ||
+ | |||
+ | 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 <a href=/reference/ft_prepare_mesh><font color=green>FT_PREPARE_MESH</font></a> or | ||
+ | a segmented anatomical MRI that was obtained from <a href=/reference/ft_volumesegment><font color=green>FT_VOLUMESEGMENT</font></a>. | ||
+ | |||
+ | 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 <a href=/reference/ft_prepare_sourcemodel><font color=green>FT_PREPARE_SOURCEMODEL</font></a>, <a href=/reference/ft_prepare_leadfield><font color=green>FT_PREPARE_LEADFIELD</font></a>, <a href=/reference/ft_prepare_mesh><font color=green>FT_PREPARE_MESH</font></a>, | ||
+ | <a href=/reference/ft_headmodel_bemcp><font color=green>FT_HEADMODEL_BEMCP</font></a>, <a href=/reference/ft_headmodel_asa><font color=green>FT_HEADMODEL_ASA</font></a>, <a href=/reference/ft_headmodel_dipoli><font color=green>FT_HEADMODEL_DIPOLI</font></a>, | ||
+ | <a href=/reference/ft_headmodel_simbio><font color=green>FT_HEADMODEL_SIMBIO</font></a>, <a href=/reference/ft_headmodel_fns><font color=green>FT_HEADMODEL_FNS</font></a>, <a href=/reference/ft_headmodel_halfspace><font color=green>FT_HEADMODEL_HALFSPACE</font></a>, | ||
+ | <a href=/reference/ft_headmodel_infinite><font color=green>FT_HEADMODEL_INFINITE</font></a>, <a href=/reference/ft_headmodel_openmeeg><font color=green>FT_HEADMODEL_OPENMEEG</font></a>, <a href=/reference/ft_headmodel_singlesphere><font color=green>FT_HEADMODEL_SINGLESPHERE</font></a>, | ||
+ | <a href=/reference/ft_headmodel_concentricspheres><font color=green>FT_HEADMODEL_CONCENTRICSPHERES</font></a>, <a href=/reference/ft_headmodel_localspheres><font color=green>FT_HEADMODEL_LOCALSPHERES</font></a>, | ||
+ | <a href=/reference/ft_headmodel_singleshell><font color=green>FT_HEADMODEL_SINGLESHELL</font></a>, <a href=/reference/ft_headmodel_interpolate><font color=green>FT_HEADMODEL_INTERPOLATE</font></a> | ||
+ | </pre></html> | ||