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faq:what_is_the_plotting_convention_for_anatomical_mris [2012/08/17 11:19]
robert spacing
faq:what_is_the_plotting_convention_for_anatomical_mris [2017/08/17 11:21] (current)
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 ===== What is the plotting convention for anatomical MRIs? ===== ===== What is the plotting convention for anatomical MRIs? =====
  
-The convention used in Fieldtrip for the plotting of anatomical MRI data in **[[reference:​ft_sourceplot|ft_sourceplot ]]** (when using cfg.method = '​ortho',​ or '​slice'​),​ and in **[[reference:​ft_volumerealign|ft_volumerealign]]** is to plot the data along the voxel-indices'​ axes, rather than along the world coordinate system'​s axes. Statements such as 'the image appears flipped',​ or 'the image is presented in neurological/​radiological convention'​ are basically dependent on the anatomical data. The question now of course is how it is possible to determine whether the data at hand is plotted in radiological/​neurological convention, or otherwise stated: '​whether left is left, or left is right'​.+The convention used in Fieldtrip for the plotting of anatomical MRI data in **[[reference:​ft_sourceplot|ft_sourceplot ]]** (when using cfg.method = '​ortho',​ or '​slice'​),​ and in **[[reference:​ft_volumerealign|ft_volumerealign]]** is to plot the data along the voxel-indices'​ axes, rather than along the world coordinate system'​s axes. Statements such as 'the image appears flipped',​ or 'the image is presented in neurological/​radiological convention'​ are basically dependent on the anatomical data. The question now of course is how it is possible to determine whether the data at hand is plotted in neurological/​radiological ​convention, or otherwise stated: '​whether left is left, or left is right'​.
  
 The key to the solution lies in the transformation-matrix that is attached to the data structure (in X.transform). This matrix maps the voxel indices to the world coordinate system, where the voxel indices start counting from 1. For more information about coordinate systems, see the following [[faq:​how_are_the_different_head_and_mri_coordinate_systems_defined|frequently asked question]]. The key to the solution lies in the transformation-matrix that is attached to the data structure (in X.transform). This matrix maps the voxel indices to the world coordinate system, where the voxel indices start counting from 1. For more information about coordinate systems, see the following [[faq:​how_are_the_different_head_and_mri_coordinate_systems_defined|frequently asked question]].