FieldTrip

Note that this reference documentation is identical to the help that is displayed in Matlab when you type “help ft_electroderealign”.

  FT_ELECTRODEREALIGN rotates and translates electrode positions to
  template electrode positions or towards the head surface. It can
  either perform a rigid body transformation, in which only the
  coordinate system is changed, or it can apply additional deformations
  to the input electrodes.
 
  Use as
    [elec] = ft_electroderealign(cfg)
 
  Different methods for aligning the input electrodes to the subjects head
  are implemented, which are described in detail below:
 
  TEMPLATE - You can apply a spatial transformation/deformation that
  automatically minimizes the distance between the electrodes and the
  template or standard electrode set. The warping methods use a non-linear
  search to minimize the error between the input electrodes and
  corresponding template electrodes or between the input electrodes and a
  head surface.
 
  FIDUCIAL - You can apply a rigid body realignment based on three fiducial
  locations. Realigning using the fiducials only ensures that the fiducials
  (typically nose, left and right ear) are along the same axes in the input
  eectrode set as in the template electrode set.
 
  INTERACTIVE - You can display the skin surface together with the
  electrode position, and manually (using the graphical user interface)
  adjust the rotation, translation and scaling parameters, so that the
  electrodes correspond with the skin.
 
  MANUAL - You can display the skin surface and manually determine the
  electrode positions by clicking on the skin surface.
 
  The configuration can contain the following options
    cfg.method         = string representing the method for aligning or placing the electrodes
                         'template'        realign the electrodes to a template electrode set
                         'fiducial'        realign using the NAS, LPA and RPA fiducials
                         'interactive'     realign manually using a graphical user interface
                         'manual'          manual positioning of the electrodes by clicking in a graphical user interface
    cfg.warp          = string describing the spatial transformation for the template method
                         'rigidbody'       apply a rigid-body warp (default)
                         'globalrescale'   apply a rigid-body warp with global rescaling
                         'traditional'     apply a rigid-body warp with individual axes rescaling
                         'nonlin1'         apply a 1st order non-linear warp
                         'nonlin2'         apply a 2nd order non-linear warp
                         'nonlin3'         apply a 3rd order non-linear warp
                         'nonlin4'         apply a 4th order non-linear warp
                         'nonlin5'         apply a 5th order non-linear warp
    cfg.channel        = Nx1 cell-array with selection of channels (default = 'all'),
                         see  FT_CHANNELSELECTION for details
    cfg.fiducial       = cell-array with the name of three fiducials used for
                         realigning (default = {'nasion', 'lpa', 'rpa'})
    cfg.casesensitive  = 'yes' or 'no', determines whether string comparisons
                         between electrode labels are case sensitive (default = 'yes')
    cfg.feedback       = 'yes' or 'no' (default = 'no')
 
  The electrode set that will be realigned is specified in the cfg, see
  FT_FETCH_SENS.
 
  If you want to align the electrodes to a single template electrode set
  or to multiple electrode sets (which will be averaged), you should
  specify the template electrode sets as
    cfg.template       = single electrode set that serves as standard
  or
    cfg.template{1..N} = list of electrode sets that are averaged into the standard
  The template electrode sets can be specified either as electrode
  structures (i.e. when they are already read in memory) or as electrode
  files.
 
  If you only want to realign using the fiducials, the template has to contain
  the three fiducials, e.g.
    cfg.template.chanpos(1,:) = [110 0 0]  % location of the nose
    cfg.template.chanpos(2,:) = [0  90 0]  % left ear
    cfg.template.chanpos(3,:) = [0 -90 0]  % right ear
    cfg.template.label    = {'nasion', 'lpa', 'rpa'}
 
  If you want to align existing electrodes to the head surface or position
  new electrodes on the head surface, you should specify the head surface as
    cfg.headshape      = a filename containing headshape, a structure containing a
                         single triangulated boundary, or a Nx3 matrix with surface
                         points
 
  See also FT_READ_SENS, FT_VOLUMEREALIGN