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{{tag>faq coordinate}} ====== How do homogenous coordinate transformation matrices work? ====== The documentation of the [[http://bishopw.loni.ucla.edu/AIR5|AIR]] software by Roger P. Woods provides a very nice description of [[http://bishopw.loni.ucla.edu/air5/homogenous.html|homogenous coordinates]]. In FieldTrip, as in many other software packages that deal with anatomical and functional MRI data, we use the homogenous coordinate transformation matrix do describe the relation between voxel coordinates, where the first voxel in the volume is described as [1,1,1], and the [[:faq:how_are_the_different_head_and_mri_coordinate_systems_defined|head-coordinate system]] where coordinates are expressed in mm, cm or m relative to some anatomical landmarks. Following **[[:reference:ft_read_mri]]** the mri.transform field contains the transformation matrix. Following **[[:reference:ft_volumerealign]]** that matrix is updated.