FieldTrip

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

  FT_SENSORREALIGN rotates and translates electrode and gradiometer
  sensor 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 sensors. Different methods for aligning the input electrodes
  to the subjects head are implemented, which are described in detail
  below.
 
  FIDUCIAL - You can apply a rigid body realignment based on three fiducial
  locations. After realigning, the fiducials in the input electrode set
  (typically nose, left and right ear) are along the same axes as the
  fiducials in the template electrode set.
 
  TEMPLATE - You can apply a spatial transformation/deformation that
  automatically minimizes the distance between the electrodes or
  gradiometers and a template or sensor array. The warping methods use a
  non-linear search to minimize the distance between the input sensor
  positions and the corresponding template sensors.
 
  HEADSHAPE - You can apply a spatial transformation/deformation that
  automatically minimizes the distance between the electrodes and the head
  surface. The warping methods use a non-linear search to minimize the
  distance between the input sensor positions and the projection of the
  electrodes on the head surface.
 
  INTERACTIVE - You can display the skin surface together with the
  electrode or gradiometer positions, 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.
 
  Use as
    [sensor] = ft_sensorrealign(cfg) or
    [sensor] = ft_sensorrealign(cfg, sensor)
  where you specify the electrodes or gradiometers in the configuration
  structure (see below) or as the second input argument.
 
  The configuration can contain the following options
    cfg.method         = string representing the method for aligning or placing the electrodes
                         'fiducial'        realign using three fiducials (e.g. NAS, LPA and RPA)
                         'template'        realign the sensors to match a template set
                         'headshape'       realign the sensors to fit the head surface
                         '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 electrodes or the gradiometers that will be realigned can be
  specified in the second input argument, or optionally as specified in the
  cfg. See FT_FETCH_SENS.
 
  To realign the sensors using the fiducials, the target has to contain the
  three template fiducials, e.g.
    cfg.target.pnt(1,:) = [110 0 0]     % location of the nose
    cfg.target.pnt(2,:) = [0  90 0]     % location of the left ear
    cfg.target.pnt(3,:) = [0 -90 0]     % location of the right ear
    cfg.target.label    = {'NAS', 'LPA', 'RPA'}
 
  To align the sensors to a single template set or to multiple electrode
  sets (which will be averaged), you should specify the target as
    cfg.target          = single electrode or gradiometer set that serves as standard
  or
    cfg.target(1..N)    = list of electrode or gradiometer sets that are averaged into the standard
  The target electrode or gradiometer sets can be specified either as
  structures (i.e. when they are already read in memory) or as file names.
 
  To align existing electrodes to the head surface, or to manually position
  new electrodes using the head surface, you should specify
    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, FT_INTERACTIVEREALIGN,
  FT_FETCH_SENS