FT_VOLUMEREALIGN

Note that this reference documentation is identical to the help that is displayed in MATLAB when you type “help ft_volumerealign”.

  FT_VOLUMEREALIGN spatially aligns an anatomical MRI with head coordinates based on
  external fiducials or anatomical landmarks. This function does not change the
  anatomical MRI volume itself, but only adjusts the homogeneous transformation
  matrix that describes the mapping from voxels to the coordinate system. It also
  appends a coordsys-field to the output data, or it updates it. This field specifies
  how the x/y/z-axes of the coordinate system should be interpreted.
 
  For spatial normalisation and deformation (i.e. warping) an MRI to a template brain
  you should use the FT_VOLUMENORMALISE function.
 
  Different methods for aligning the anatomical MRI to a coordinate system are
  implemented, which are described in detail below:
 
  INTERACTIVE - Use a graphical user interface to click on the location of anatomical
  fiducials. The coordinate system is updated according to the definition of the
  coordinates of these fiducials.
 
  FIDUCIAL - The coordinate system is updated according to the definition of the
  coordinates of fiducials that are specified in the configuration.
 
  HEADSHAPE - Match the head surface from the MRI with a measured head surface using
  an iterative closest point procedure. The MRI will be updated to match the measured
  head surface. This includes an optional manual coregistration of the two head
  surfaces.
 
  SPM - align the individual MRI to the coordinate system of a target or template MRI
  by matching the two volumes.
 
  FSL - align the individual MRI to the coordinate system of a target or template MRI
  by matching the two volumes.
 
  Use as
    [mri] = ft_volumerealign(cfg, mri)
  or
    [mri] = ft_volumerealign(cfg, mri, target)
  where the input mri should be an anatomical or functional MRI volume and the third
  input argument is the the target anatomical MRI for SPM or FSL.
 
  The configuration can contain the following options
    cfg.method         = string representing the method for aligning
                         'interactive' use the GUI to specify the fiducials
                         'fiducial'    use pre-specified fiducials
                         'headshape'   match the MRI surface to a headshape
                         'spm'         match to template anatomical MRI
                         'fsl'         match to template anatomical MRI
    cfg.coordsys       = string specifying the origin and the axes of the coordinate
                         system. Supported coordinate systems are 'ctf', '4d',
                         'bti', 'yokogawa', 'asa', 'itab', 'neuromag', 'spm',
                         'tal' and 'paxinos'. See http://tinyurl.com/ojkuhqz
    cfg.clim           = [min max], scaling of the anatomy color (default
                         is to adjust to the minimum and maximum)
    cfg.parameter      = 'anatomy' the parameter which is used for the
                          visualization
    cfg.viewresult     = string, 'yes' or 'no', whether or not to visualize aligned volume(s)
                         after realignment (default = 'no')
 
  When cfg.method = 'fiducial' and a coordinate system that is based on external
  facial anatomical landmarks (common for EEG and MEG), the following is required to
  specify the voxel indices of the fiducials:
    cfg.fiducial.nas    = [i j k], position of nasion
    cfg.fiducial.lpa    = [i j k], position of LPA
    cfg.fiducial.rpa    = [i j k], position of RPA
    cfg.fiducial.zpoint = [i j k], a point on the positive z-axis. This is
                          an optional 'fiducial', and can be used to determine
                          whether the input voxel coordinate axes are left-handed
                          (i.e. flipped in one of the dimensions). If this additional
                          point is specified, and the voxel coordinate axes are left
                          handed, the volume is flipped to yield right handed voxel
                          axes.
 
  When cfg.method = 'fiducial' and cfg.coordsys = 'spm' or 'tal', the following
  is required to specify the voxel indices of the fiducials:
    cfg.fiducial.ac      = [i j k], position of anterior commissure
    cfg.fiducial.pc      = [i j k], position of posterior commissure
    cfg.fiducial.xzpoint = [i j k], point on the midsagittal-plane with a
                           positive Z-coordinate, i.e. an interhemispheric
                           point above ac and pc
  The coordinate system will be according to the RAS_Tal convention i.e.
  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 YZ-plane, positive to the right
 
  When cfg.method = 'interactive', a user interface allows for the specification of
  the fiducials or landmarks using the mouse, cursor keys and keyboard.The fiducials
  can be specified by pressing the corresponding key on the keyboard (n/l/r or
  a/p/z). When pressing q the interactive mode will stop and the transformation
  matrix is computed. This method supports the following options:
    cfg.viewmode    = 'ortho' or 'surface', visualize the anatomical MRI as three
                       slices or visualize the extracted head surface (default = 'ortho')
    cfg.snapshot     = 'no' ('yes'), making a snapshot of the image once a
                       fiducial or landmark location is selected. The optional second
                       output argument to the function will contain the handles to these
                       figures.
    cfg.snapshotfile = 'ft_volumerealign_snapshot' or string, the root of
                       the filename for the snapshots, including the path. If no path
                       is given the files are saved to the pwd. The consecutive
                       figures will be numbered and saved as png-file.
 
  When cfg.method = 'headshape', the function extracts the scalp surface from the
  anatomical MRI, and aligns this surface with the user-supplied headshape.
  Additional options pertaining to this method should be defined in the subcfg
  cfg.headshape. The following option is required:
    cfg.headshape.headshape      = string pointing to a file describing a headshape or a
                                   FieldTrip-structure describing a headshape, see
                                   FT_READ_HEADSHAPE
  The following options are optional:
    cfg.headshape.scalpsmooth    = scalar, smoothing parameter for the scalp
                                   extraction (default = 2)
    cfg.headshape.scalpthreshold = scalar, threshold parameter for the scalp
                                   extraction (default = 0.1)
    cfg.headshape.interactive    = 'yes' or 'no', use interactive realignment to
                                   align headshape with scalp surface (default =
                                   'yes')
    cfg.headshape.icp            = 'yes' or 'no', use automatic realignment
                                   based on the icp-algorithm. If both 'interactive'
                                   and 'icp' are executed, the icp step follows the
                                   interactive realignment step (default = 'yes')
 
  When cfg.method = 'fsl', a third input argument is required. The input volume is
  coregistered to this target volume, using FSL-flirt. Additional options pertaining
  to this method should be defined in the subcfg cfg.fsl and can include:
    cfg.fsl.path         = string, specifying the path to fsl
    cfg.fsl.costfun      = string, specifying the cost-function used for
                           coregistration
    cfg.fsl.interpmethod = string, specifying the interpolation method, can be
                           'trilinear', 'nearestneighbour', or 'sinc'
    cfg.fsl.dof          = scalar, specifying the number of parameters for the
                           affine transformation. 6 (rigid body), 7 (global
                           rescale), 9 (traditional) or 12.
    cfg.fsl.reslice      = string, specifying whether the output image will be
                           resliced conform the target image (default = 'yes')
 
  When cfg.method = 'spm', a third input argument is required. The input volume is
  coregistered to this target volume, using SPM. Options pertaining to the
  behavior of spm can be defined in the subcfg cfg.spm and can include:
    cfg.spm.regtype = 'subj', 'rigid'
    cfg.spm.smosrc  = scalar value
    cfg.spm.smoref  = scalar value
  When cfg.spmversion = 'spm12', the following options apply:
    cfg.spm.sep     = optimisation sampling steps (mm), default: [4 2]
    cfg.spm.params  = starting estimates (6 elements), default: [0 0 0  0 0 0]
    cfg.spm.cost_fun = cost function string:
                        'mi'  - Mutual Information (default)
                        'nmi' - Normalised Mutual Information
                        'ecc' - Entropy Correlation Coefficient
                        'ncc' - Normalised Cross Correlation
    cfg.spm.tol     = tolerences for accuracy of each param, default: [0.02 0.02 0.02 0.001 0.001 0.001]
    cfg.spm.fwhm    = smoothing to apply to 256x256 joint histogram, default: [7 7]
 
  With the 'interactive' and 'fiducial' methods it is possible to define an
  additional point (with the key 'z'), which should be a point on the positive side
  of the xy-plane, i.e. with a positive z-coordinate in world coordinates. This point
  will subsequently be used to check whether the input coordinate system is left or
  right-handed. For the 'interactive' method you can also specify an additional
  control point (with the key 'r'), that should be a point with a positive coordinate
  on the left-right axis.
 
  To facilitate data-handling and distributed computing you can use
    cfg.inputfile   =  ...
    cfg.outputfile  =  ...
  If you specify one of these (or both) the input data will be read from a
  *.mat file on disk and/or the output data will be written to a *.mat
  file. These mat files should contain only a single variable,
  corresponding with the input/output structure.
 
  See also FT_READ_MRI, FT_ELECTRODEREALIGN, FT_DETERMINE_COORDSYS, SPM_AFFREG,
  SPM_NORMALISE, SPM_COREG

reference/ft_volumerealign.txt · Last modified: 2016/08/17 23:02 (external edit)

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