# Differences

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 reference:ft_headcoordinates [2018/08/23 14:43] reference:ft_headcoordinates [2018/08/23 14:43] (current) Line 1: Line 1: + =====  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>​ + <​font color=green>​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 <​font color=green>​FT_ELECTRODEREALIGN,​ <​font color=green>​FT_VOLUMEREALIGN,​ <​font color=green>​FT_INTERACTIVEREALIGN,​ COORDSYS2LABEL +