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reference:ft_omri_align_init [2018/08/23 14:43] (current)
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 +=====  FT_OMRI_ALIGN_INIT =====
 +
 +Note that this reference documentation is identical to the help that is displayed in MATLAB when you type "help ft_omri_align_init"​.
 +
 +<​html><​pre>​
 +  function model = ft_omri_align_init(Vr,​flags)
 + 
 +  Ripped out of SPM 8 and modified (2010, S.Klanke)
 + 
 +  Estimation of within modality rigid body movement parameters
 +  FORMAT P = spm_realign(P,​flags)
 + 
 +  P     - matrix of filenames {one string per row}
 +          All operations are performed relative to the first image.
 +          ie. Coregistration is to the first image, and resampling
 +          of images is into the space of the first image.
 +          For multiple sessions, P should be a cell array, where each
 +          cell should be a matrix of filenames.
 + 
 +  flags - a structure containing various options. ​ The fields are:
 +          quality - Quality versus speed trade-off. ​ Highest quality
 +                    (1) gives most precise results, whereas lower
 +                    qualities gives faster realignment.
 +                    The idea is that some voxels contribute little to
 +                    the estimation of the realignment parameters.
 +                    This parameter is involved in selecting the number
 +                    of voxels that are used.
 + 
 +          fwhm    - The FWHM of the Gaussian smoothing kernel (mm)
 +                    applied to the images before estimating the
 +                    realignment parameters.
 + 
 +          sep     - the default separation (mm) to sample the images.
 + 
 +          PW      - a filename of a weighting image (reciprocal of
 +                    standard deviation). ​ If field does not exist, then
 +                    no weighting is done.
 + 
 +          interp ​ - B-spline degree used for interpolation
 + 
 + ​__________________________________________________________________________
 + 
 +  Inputs
 +  A series of *.img conforming to SPM data format (see 'Data Format'​).
 + 
 +  Outputs
 +  If no output argument, then an updated voxel to world matrix is written
 +  to the headers of the images (a .mat file is created for 4D images).
 +  The details of the transformation are displayed in the
 +  results window as plots of translation and rotation.
 +  A set of realignment parameters are saved for each session, named:
 +  rp_*.txt.
 + ​__________________________________________________________________________
 + 
 +  The voxel to world mappings.
 + 
 +  These are simply 4x4 affine transformation matrices represented in the
 +  NIFTI headers (see http://​nifti.nimh.nih.gov/​nifti-1 ).
 +  These are normally modified by the `realignment'​ and `coregistration'​
 +  modules. ​ What these matrixes represent is a mapping from
 +  the voxel coordinates (x0,y0,z0) (where the first voxel is at coordinate
 +  (1,1,1)), to coordinates in millimeters (x1,y1,z1).
 +   
 +  x1 = M(1,1)*x0 + M(1,2)*y0 + M(1,3)*z0 + M(1,4)
 +  y1 = M(2,1)*x0 + M(2,2)*y0 + M(2,3)*z0 + M(2,4)
 +  z1 = M(3,1)*x0 + M(3,2)*y0 + M(3,3)*z0 + M(3,4)
 + 
 +  Assuming that image1 has a transformation matrix M1, and image2 has a
 +  transformation matrix M2, the mapping from image1 to image2 is: M2\M1
 +  (ie. from the coordinate system of image1 into millimeters,​ followed
 +  by a mapping from millimeters into the space of image2).
 + 
 +  These matrices allow several realignment or coregistration steps to be
 +  combined into a single operation (without the necessity of resampling the
 +  images several times). ​ The `.mat' files are also used by the spatial
 +  normalisation module.
 + ​__________________________________________________________________________
 +  Ref:
 +  Friston KJ, Ashburner J, Frith CD, Poline J-B, Heather JD & Frackowiak
 +  RSJ (1995) Spatial registration and normalization of images Hum. Brain
 +  Map. 2:165-189
 + ​__________________________________________________________________________
 +  Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 +</​pre></​html>​