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

  FT_HEADCOORDINATES returns the homogeneous coordinate transformation matrix
  that converts the specified fiducials in any coordinate system (e.g. MRI)
  into the rotated and translated headcoordinate system.
 
  Use as
    [h, coordsys] = ft_headcoordinates(fid1, fid2, fid3, coordsys)
  or
    [h, coordsys] = ft_headcoordinates(fid1, fid2, fid3, fid4, coordsys)
 
  Depending on the desired coordinate system, the order of the fiducials is
  interpreted as follows
 
    fid1 = nas
    fid2 = lpa
    fid3 = rpa
    fid4 = extra point (optional)
 
    fid1 = ac
    fid2 = pc
    fid3 = midsagittal
    fid4 = extra point (optional)
 
    fid1 = pt1
    fid2 = pt2
    fid3 = pt3
    fid4 = extra point (optional)
 
    fid1 = bregma
    fid2 = lambda
    fid3 = midsagittal
    fid4 = extra point (optional)
 
  The fourth argument fid4 is optional and can be specified as an an extra point
  which is assumed to have a positive Z-coordinate. It will be used to ensure correct
  orientation of the z-axis (ctf, 4d, yokogawa, itab, neuromag) or X-axis (tal, spm).
  The specification of this extra point may result in the handedness of the
  transformation to be changed, but ensures consistency with the handedness of the
  input coordinate system.
 
  The coordsys input argument is a string that determines how the location of the
  origin and the direction of the axis is to be defined relative to the fiducials
    according to CTF conventions:             coordsys = 'ctf'
    according to 4D conventions:              coordsys = '4d' or 'bti'
    according to YOKOGAWA conventions:        coordsys = 'yokogawa'
    according to ASA conventions:             coordsys = 'asa'
    according to NEUROMAG conventions:        coordsys = 'itab'
    according to ITAB conventions:            coordsys = 'neuromag'
    according to FTG conventions:             coordsys = 'ftg'
    according to Talairach conventions:       coordsys = 'tal'
    according to SPM conventions:             coordsys = 'spm'
    according to ACPC conventions:            coordsys = 'acpc'
    according to PAXINOS conventions:         coordsys = 'paxinos'
  If coordsys is not specified, it will default to 'ctf'.
 
  The CTF, 4D and YOKOGAWA coordinate systems are defined as follows:
    the origin is exactly between lpa and rpa
    the X-axis goes towards nas
    the Y-axis goes approximately towards lpa, orthogonal to X and in the plane spanned by the fiducials
    the Z-axis goes approximately towards the vertex, orthogonal to X and Y
 
  The TALAIRACH, SPM and ACPC coordinate systems are defined as:
    the origin corresponds with the anterior commissure
    the Y-axis is along the line from the posterior commissure to the anterior commissure
    the Z-axis is towards the vertex, in between the hemispheres
    the X-axis is orthogonal to the midsagittal-plane, positive to the right
 
  The NEUROMAG and ITAB coordinate systems are defined as follows:
    the X-axis is from the origin towards the RPA point (exactly through)
    the Y-axis is from the origin towards the nasion (exactly through)
    the Z-axis is from the origin upwards orthogonal to the XY-plane
    the origin is the intersection of the line through LPA and RPA and a line orthogonal to L passing through the nasion
 
  The ASA coordinate system is defined as follows:
    the origin is at the orthogonal intersection of the line from rpa-lpa and the line trough nas
    the X-axis goes towards nas
    the Y-axis goes through rpa and lpa
    the Z-axis goes approximately towards the vertex, orthogonal to X and Y
 
  The FTG coordinate system is defined as:
    the origin corresponds with pt1
    the x-axis is along the line from pt1 to pt2
    the z-axis is orthogonal to the plane spanned by pt1, pt2 and pt3
 
  The PAXINOS coordinate system is defined as:
    the origin is at bregma
    the x-axis extends along the Medial-Lateral direction, with positive towards the right
    the y-axis points from dorsal to ventral, i.e. from inferior to superior
    the z-axis passes through bregma and lambda and points from cranial to caudal, i.e. from anterior to posterior
 
  See also FT_ELECTRODEREALIGN, FT_VOLUMEREALIGN, FT_INTERACTIVEREALIGN, COORDSYS2LABEL