headcoordinates.m

function [h] = headcoordinates(nas, lpa, rpa, flag);

% HEADCOORDINATES returns the homogenous coordinate transformation matrix
% that converts the specified fiducials in any coordinate system (e.g. MRI)
% into the rotated and translated headccordinate system.
%
% [h] = headcoordinates(nas, lpa, rpa, flag) or
% [h] = headcoordinates(pt1, pt2, pt3, flag)
%
% The optional flag determines how the origin should be specified 
% according to CTF conventions: flag = 0 (default)
% according to ASA conventions: flag = 1 
% according to FTG conventions: flag = 2 
% 
% The headcoordinate system in CTF is 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 headcoordinate system in ASA is defined as follows:
% the origin is at the orthogonal intersection of the line from rpa-rpa 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 headcoordinate system in FTG is defines 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
% 
% See also WARPING, WARP3D

% Copyright (C) 2003 Robert Oostenveld
%
if nargin<4
  flag=0;
end

% ensure that they are row vectors
lpa = lpa(:)';
rpa = rpa(:)';
nas = nas(:)';

% compute the origin and direction of the coordinate axes in MRI coordinates
if flag==0
  % follow CTF convention
  origin = [lpa+rpa]/2;
  dirx = nas-origin;
  dirx = dirx/norm(dirx);
  dirz = cross(dirx,lpa-rpa);
  dirz = dirz/norm(dirz);
  diry = cross(dirz,dirx);
elseif flag==1
  % follow ASA convention
  dirz = cross(nas-rpa, lpa-rpa);
  diry = lpa-rpa;
  dirx = cross(diry,dirz);
  dirz = dirz/norm(dirz);
  diry = diry/norm(diry);
  dirx = dirx/norm(dirx);
  origin = rpa + dot(nas-rpa,diry)*diry;
elseif flag==2
  % rename the marker points for convenience
  pt1 = nas; pt2 = lpa; pt3 = rpa;
  % follow FTG conventions
  origin = pt1;
  dirx = pt2-origin;
  dirx = dirx/norm(dirx);
  diry = pt3-origin;
  dirz = cross(dirx,diry);
  dirz = dirz/norm(dirz);
  diry = cross(dirz,dirx);
end

% compute the rotation matrix
rot = eye(4);
rot(1:3,1:3) = inv(eye(3) / [dirx; diry; dirz]);
% compute the translation matrix
tra = eye(4);
tra(1:4,4)   = [-origin(:); 1];
% compute the full homogenous transformation matrix from these two
h = rot * tra;