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

  FT_SOURCEPLOT plots functional source reconstruction data on slices or on a
  surface, optionally as an overlay on anatomical MRI data, where statistical data
  can be used to determine the opacity of the mask. Input data comes from
  Use as
    ft_sourceplot(cfg, data)
  where the input data can contain an anatomical MRI, functional source
  reconstruction results and/or statistical data. If both anatomical and
  functional/statistical data is provided as input, they should be represented or
  interpolated on the same same 3-D grid, e.g. using FT_SOURCEINTERPOLATE.
  The slice and ortho visualization plot the data in the input data voxel
  arrangement, i.e. the three ortho views are the 1st, 2nd and 3rd dimension of
  the 3-D data matrix, not of the head coordinate system. The specification of the
  coordinate for slice intersection is specified in head coordinates, i.e.
  relative to the fiducials and in mm or cm. If you want the visualisation to be
  consistent with the head coordinate system, you can reslice the data using
  The configuration should contain:
    cfg.method        = 'slice',      plots the data on a number of slices in the same plane
                        'ortho',      plots the data on three orthogonal slices
                        'surface',    plots the data on a 3D brain surface
                        'glassbrain', plots a max-projection through the brain
                        'vertex',     plots the grid points or vertices scaled according to the functional value
    cfg.anaparameter  = string, field in data with the anatomical data (default = 'anatomy' if present in data)
    cfg.funparameter  = string, field in data with the functional parameter of interest (default = [])
    cfg.maskparameter = string, field in the data to be used for opacity masking of fun data (default = [])
                         If values are between 0 and 1, zero is fully transparant and one is fully opaque.
                         If values in the field are not between 0 and 1 they will be scaled depending on the values
                         of cfg.opacitymap and cfg.opacitylim (see below)
                         You can use masking in several ways, f.i.
                         - use outcome of statistics to show only the significant values and mask the insignificant
                           NB see also cfg.opacitymap and cfg.opacitylim below
                         - use the functional data itself as mask, the highest value (and/or lowest when negative)
                           will be opaque and the value closest to zero transparent
                         - Make your own field in the data with values between 0 and 1 to control opacity directly
  The following parameters can be used in all methods:
    cfg.downsample    = downsampling for resolution reduction, integer value (default = 1) (orig: from surface)
    cfg.atlas         = string, filename of atlas to use (default = []) see FT_READ_ATLAS
                         for ROI masking (see "masking" below) or in "ortho-plotting" mode (see "ortho-plotting" below)
  The following parameters can be used for the functional data:
    cfg.funcolormap   = colormap for functional data, see COLORMAP (default = 'auto')
                        'auto', depends structure funparameter, or on funcolorlim
                          - funparameter: only positive values, or funcolorlim:'zeromax' -> 'hot'
                          - funparameter: only negative values, or funcolorlim:'minzero' -> 'cool'
                          - funparameter: both pos and neg values, or funcolorlim:'maxabs' -> 'default'
                          - funcolorlim: [min max] if min & max pos-> 'hot', neg-> 'cool', both-> 'default'
    cfg.funcolorlim   = color range of the functional data (default = 'auto')
                         [min max]
                         'maxabs', from -max(abs(funparameter)) to +max(abs(funparameter))
                         'zeromax', from 0 to max(funparameter)
                         'minzero', from min(funparameter) to 0
                         'auto', if funparameter values are all positive: 'zeromax',
                           all negative: 'minzero', both possitive and negative: 'maxabs'
    cfg.colorbar      = 'yes' or 'no' (default = 'yes')
  The following parameters can be used for the masking data:
    cfg.opacitymap    = opacitymap for mask data, see ALPHAMAP (default = 'auto')
                        'auto', depends structure maskparameter, or on opacitylim
                          - maskparameter: only positive values, or opacitylim:'zeromax' -> 'rampup'
                          - maskparameter: only negative values, or opacitylim:'minzero' -> 'rampdown'
                          - maskparameter: both pos and neg values, or opacitylim:'maxabs' -> 'vdown'
                          - opacitylim: [min max] if min & max pos-> 'rampup', neg-> 'rampdown', both-> 'vdown'
                          - NB. to use p-values use 'rampdown' to get lowest p-values opaque and highest transparent
    cfg.opacitylim    = range of mask values to which opacitymap is scaled (default = 'auto')
                         [min max]
                         'maxabs', from -max(abs(maskparameter)) to +max(abs(maskparameter))
                         'zeromax', from 0 to max(abs(maskparameter))
                         'minzero', from min(abs(maskparameter)) to 0
                         'auto', if maskparameter values are all positive: 'zeromax',
                           all negative: 'minzero', both possitive and negative: 'maxabs'
    cfg.roi           = string or cell of strings, region(s) of interest from anatomical atlas (see cfg.atlas above)
                         everything is masked except for ROI
  The following parameters apply for ortho-plotting
    cfg.location      = location of cut, (default = 'auto')
                         'auto', 'center' if only anatomy, 'max' if functional data
                         'min' and 'max' position of min/max funparameter
                         'center' of the brain
                         [x y z], coordinates in voxels or head, see cfg.locationcoordinates
    cfg.locationcoordinates = coordinate system used in cfg.location, 'head' or 'voxel' (default = 'head')
                               'head', headcoordinates as mm or cm
                               'voxel', voxelcoordinates as indices
    cfg.crosshair     = 'yes' or 'no' (default = 'yes')
    cfg.axis          = 'on' or 'off' (default = 'on')
    cfg.queryrange    = number, in atlas voxels (default 3)
  The following parameters apply for slice-plotting
    cfg.nslices       = number of slices, (default = 20)
    cfg.slicerange    = range of slices in data, (default = 'auto')
                        'auto', full range of data
                        [min max], coordinates of first and last slice in voxels
    cfg.slicedim      = dimension to slice 1 (x-axis) 2(y-axis) 3(z-axis) (default = 3)
    cfg.title         = string, title of the figure window
  When cfg.method = 'surface', the functional data will be rendered onto a cortical
  mesh (can be an inflated mesh). If the input source data contains a tri-field (i.e.
  a description of a mesh), no interpolation is needed. If the input source data does
  not contain a tri-field, an interpolation is performed onto a specified surface.
  Note that the coordinate system in which the surface is defined should be the same
  as the coordinate system that is represented in source.pos.
  The following parameters apply to surface-plotting when an interpolation
  is required
    cfg.surffile       = string, file that contains the surface (default = 'surface_white_both.mat')
                         'surface_white_both.mat' contains a triangulation that corresponds with the
                          SPM anatomical template in MNI coordinates
    cfg.surfinflated   = string, file that contains the inflated surface (default = [])
                         may require specifying a point-matching (uninflated) surffile
    cfg.surfdownsample = number (default = 1, i.e. no downsampling)
    cfg.projmethod     = projection method, how functional volume data is projected onto surface
                         'nearest', 'project', 'sphere_avg', 'sphere_weighteddistance'
    cfg.projvec        = vector (in mm) to allow different projections that
                         are combined with the method specified in cfg.projcomb
    cfg.projcomb       = 'mean', 'max', method to combine the different projections
    cfg.projweight     = vector of weights for the different projections (default = 1)
    cfg.projthresh     = implements thresholding on the surface level
                         for example, 0.7 means 70% of maximum
    cfg.sphereradius   = maximum distance from each voxel to the surface to be
                         included in the sphere projection methods, expressed in mm
    cfg.distmat        = precomputed distance matrix (default = [])
  The following parameters apply to surface-plotting independent of whether
  an interpolation is required
    cfg.camlight       = 'yes' or 'no' (default = 'yes')
    cfg.renderer       = 'painters', 'zbuffer', ' opengl' or 'none' (default = 'opengl')
                         note that when using opacity the OpenGL renderer is required.
  To facilitate data-handling and distributed computing you can use
    cfg.inputfile   =  ...
  If you specify this option the input data will be read from a *.mat file on
  disk. This mat files should contain only a single variable corresponding to the
  input structure.

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

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