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reference:ft_headcoordinates [2018/08/23 14:43] (current)
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 +=====  FT_HEADCOORDINATES =====
 +
 +Note that this reference documentation is identical to the help that is displayed in MATLAB when you type "help ft_headcoordinates"​.
 +
 +<​html><​pre>​
 +  <a href=/​reference/​ft_headcoordinates><​font color=green>​FT_HEADCOORDINATES</​font></​a>​ 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 <a href=/​reference/​ft_electroderealign><​font color=green>​FT_ELECTRODEREALIGN</​font></​a>,​ <a href=/​reference/​ft_volumerealign><​font color=green>​FT_VOLUMEREALIGN</​font></​a>,​ <a href=/​reference/​ft_interactiverealign><​font color=green>​FT_INTERACTIVEREALIGN</​font></​a>,​ COORDSYS2LABEL
 +</​pre></​html>​