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reference:ft_prepare_headmodel [2018/08/23 14:43] (current)
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 +Note that this reference documentation is identical to the help that is displayed in MATLAB when you type "help ft_prepare_headmodel"​.
 +  <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.
 +    cfg.tissue ​           see above; in combination with '​seg'​ input
 +    cfg.isolatedsource ​   (optional)
 +    cfg.tissue ​           see above; in combination with '​seg'​ input
 +    cfg.fitind ​           (optional)
 +    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)
 +    cfg.conductivity
 +    cfg.tissue ​           see above; in combination with '​seg'​ input; default options are '​brain'​ or '​scalp'​
 +    cfg.tissue ​           see above; in combination with '​seg'​ input; default options are '​brain'​ or '​scalp';​ must be only 1 value
 +     ​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
 +    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>​