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reference:ft_megrealign [2018/08/23 14:43]
reference:ft_megrealign [2018/08/23 14:43] (current)
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 +=====  FT_MEGREALIGN =====
 +Note that this reference documentation is identical to the help that is displayed in MATLAB when you type "help ft_megrealign"​.
 +  <a href=/​reference/​ft_megrealign><​font color=green>​FT_MEGREALIGN</​font></​a>​ interpolates MEG data towards standard gradiometer locations by
 +  projecting the individual timelocked data towards a coarse source reconstructed
 +  representation and computing the magnetic field on the standard gradiometer
 +  locations.
 +  Use as
 +    [interp] = ft_megrealign(cfg,​ data)
 +  Required configuration options:
 +    cfg.template
 +    cfg.inwardshift
 +  The new gradiometer definition is obtained from a template dataset,
 +  or can be constructed by averaging the gradiometer positions over
 +  multiple datasets.
 +    cfg.template ​      = single dataset that serves as template
 +    cfg.template(1..N) = datasets that are averaged into the standard
 +  The realignment is done by computing a minumum norm estimate using a
 +  large number of dipoles that are placed in the upper layer of the brain
 +  surface, followed by a forward computation towards the template
 +  gradiometer array. This requires the specification of a volume conduction
 +  model of the head and of a source model.
 +  A volume conduction model of the head should be specified with
 +    cfg.headmodel ​  = structure, see <a href=/​reference/​ft_prepare_headmodel><​font color=green>​FT_PREPARE_HEADMODEL</​font></​a>​
 +  A source model (i.e. a superficial layer with distributed sources) can be
 +  constructed from a headshape file, or from the volume conduction model
 +    cfg.spheremesh ​ = number of dipoles in the source layer (default = 642)
 +    cfg.inwardshift = depth of the source layer relative to the headshape
 +                      surface or volume conduction model (no default
 +                      supplied, see below)
 +    cfg.headshape ​  = a filename containing headshape, a structure containing a
 +                      single triangulated boundary, or a Nx3 matrix with surface
 +                      points
 +  If you specify a headshape and it describes the skin surface, you should specify an
 +  inward shift of 2.5 cm.
 +  For a single-sphere or a local-spheres volume conduction model based on the skin
 +  surface, an inward shift of 2.5 cm is reasonable.
 +  For a single-sphere or a local-spheres volume conduction model based on the brain
 +  surface, you should probably use an inward shift of about 1 cm.
 +  For a realistic single-shell volume conduction model based on the brain surface, you
 +  should probably use an inward shift of about 1 cm.
 +  Other options are
 +  cfg.pruneratio ​ = for singular values, default is 1e-3
 +  cfg.verify ​     = '​yes'​ or '​no',​ show the percentage difference (default = '​yes'​)
 +  cfg.feedback ​   = '​yes'​ or '​no'​ (default = '​no'​)
 +  cfg.channel ​    ​= ​ Nx1 cell-array with selection of channels (default = '​MEG'​),​
 +                       see <a href=/​reference/​ft_channelselection><​font color=green>​FT_CHANNELSELECTION</​font></​a>​ for details
 +  cfg.trials ​     = '​all'​ or a selection given as a 1xN vector (default = '​all'​)
 +  This implements the method described by T.R. Knosche, Transformation
 +  of whole-head MEG recordings between different sensor positions.
 +  Biomed Tech (Berl). 2002 Mar;​47(3):​59-62. For more information and
 +  related methods, see Stolk et al., Online and offline tools for head
 +  movement compensation in MEG. NeuroImage, 2012.
 +  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.