How your body function [head

• Have you ever wonder how you coordinate your self
• 
  Converting Neuromag head coordinates to
  Talairach coordinates
  K. Uutela
  November 19, 2000
  1 Introduction
  Neuromag software uses head coordinate system that is defined by three anatomical
  landmarks: nasion and preauricular points. To compare different brain locations,
  Talairach coordinate system, referring to the coordinate system used in
  Talairach and Tournoux brain atlas (1), where the anterior and posterior commissures
  (AC and PC) and the midline are used to define the coordinates. In both
  coordinate systems, x-axis increases from left to right, y-axis from posterior to
  anterior, and z-axis from inferior to superior, but the origins differ. The approach
  described here, used also in fMRI analysis software such as AFNI (2) also scales
  the coordinate system to match the extents of the Talairach standard brain.
  This document describes how to convert Neuromag head coordinates to Talairach
  coordinates by using the Matlab function coordtrans, included in the MEG
  toolbox. To use the function, the locations of the anterior and posterior commissure
  and the midline in the head coordinate system and the extents of the brain are
  needed.
  2 Getting Talairach information using MRILab
  To get the Talairach information for the magnetic resonance images (MRIs) of an
  individual subject, the MR images should have the head coordinate system defined.
  See the MRILab manual for details. Then, rotate the coordinate frame so
  that the midline (between two hemispheres) is shown. Find the anterior and posterior
  commissure and place points in crossing of the posterior and superior edge
  of the anterior commissure and at the inferior edge of the posterior commissure
  (Fig. 1). Place a third point more superior in the midline. Get the coordinates of
  1
  􀀀AC
  PC
  
  Corpus callosum
  Y
  Z
  Figure 1: The anterior and posterior commissures (AC and PC) and Talairach
  axes.
  these points either by the coordinate tool or by exporting the placed points in head
  coordinates.
  To find the extents of the brain (see Fig. 2), first rotate the stach so that the
  y axis is aligned with the landmarks of AC and PC. Then select a slice which
  includes the rightmost part of the cerebrum, and find the distance between ACPC
  line and the closest point in this slice using the coordinate tool. Calculate
  similarily the distance from AC-PC line to the leftmost part, from AC to the most
  anterior part in the frontal lobe, from PC to the most inferior part in the occipital
  lobe, from AC-PC line to the most superior part, and from AC-PC line to the most
  inferior part of the cerebrum (typically in the temporal lobes; cerebellum is not
  included).
  3 Using the coordtrans command
  Start Matlab with the command /usr/local/bin/matlab, load the head coordinate
  points (in meters) to be converted to matrix R (or create it manually using command
  like
  R=[0.010 ; 0.020 ; 0.030]’*0.001;
  Define the individual landmarks using a command like
  subjectNN=
  
  [AC x PC x ML x;AC y PC y ML y; AC z PC Z ML Z],
  ... [right left front back top bottom]
  
  ;
  where the values are
  2
  PC AC
  Midline
  X Y
  Z Z
  Figure 2: The extents of the brain.
  AC x x-coordinate of AC
  PX x x-coordinate of PC
  ML x x-coordinate of midline point
  AC y y-coordinate of AC
  PX y y-coordinate of PC
  ML y y-coordinate of midline point
  AC z z-coordinate of AC
  PX z z-coordinate of PC
  ML z z-coordinate of midline point
  right AC-right -distance
  left AC-left -distance
  front AC-front -distance
  back PC-back -distance
  top AC-top -distance
  bottom AC-bottom -distance .
  All values should be given in meters.
  You get the Talairach coordinates using the command
  R t=coordtrans(R,subjectNN,’talairach’);
  To obtain the individual coordinates from Talairach coordinates use the command
  R head=coordtrans(R t,’talairach’,subjectNN);
  3
  To convert from coordinates of subject NN to coordinates of subject MM, use
  the command line
  R mm=coordtrans(R nn,subjectNN,subjectBB); which will transform
  the coordinates first to Talairach coordinates and then to the second subject’s coordinates.
  The command line parameters are shown with the Matlab help command
  help coordtrans
  4 Saving the results
  You can save the individual talairach parameters by using the Matlab save command:
  save subjNN parameters.mat subjectNN
  You can save the converted points to an ascii file using the -ascii otion:
  save -ascii subjNN talairachpoints.txt R t
  5 Using Matlab scripts
  To spot errors and to automatize the procedure, it may be useful to create a Matlab
  script file which does the whole calculation. Simply creare a text file with a “.m”
  ending, such as “batch.m”, and include all the commands that you would give in
  the Matlab command line. You can run the batch script using the name of the file,
  e.g. bat