FieldTrip

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 FT_SOURCEANALYSIS, FT_SOURCEGRANDAVERAGE or statistical
  values from FT_SOURCESTATISTICS.
 
  Use as
    ft_sourceplot(cfg, data)
  where the input data can contain an anatomical MRI, functional source
  reconstruction results and statistical data, which all have to be
  interpolated on the same 3-d grid.
 
  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
 
    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_PREPARE_ATLAS
                         for ROI masking (see "masking" below) or in interactive mode (see "ortho-plotting" below)
    cfg.coordsys      = 'mni' or 'tal', coordinate system of the input data, used to lookup the label from the atlas
 
  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' -> 'jet'
                          - funcolorlim: [min max] if min & max pos-> 'hot', neg-> 'cool', both-> 'jet'
    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(abs(funparameter))
                         'minzero', from min(abs(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 folowing 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 from anatomical MRI
                               'voxel', voxelcoordinates
    cfg.crosshair     = 'yes' or 'no' (default = 'yes')
    cfg.axis          = 'on' or 'off' (default = 'on')
    cfg.interactive   = 'yes' or 'no' (default = 'no')
                         in interactive mode cursor click determines location of cut
    cfg.queryrange    = number, in atlas voxels (default 3)
 
 
  The folowing 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
 
  The folowing parameters apply for surface-plotting
    cfg.surffile       = string, file that contains the surface (default = 'single_subj_T1.mat')
                         'single_subj_T1.mat' contains a triangulation that corresponds with the
                          SPM anatomical template in MNI coordinates
    cfg.surfinflated   = string, file that contains the inflated surface (default = [])
    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
    (cfg.projthresh = 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 = [])
    cfg.camlight       = 'yes' or 'no' (default = 'yes')
    cfg.renderer       = 'painters', 'zbuffer',' opengl' or 'none' (default = 'opengl')
                         When using opacity the OpenGL renderer is required.
 
  To facilitate data-handling and distributed computing with the peer-to-peer
  module, this function has the following option:
    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 named 'data',
  corresponding to the input structure.
 
  See also FT_SOURCEANALYSIS, FT_SOURCEGRANDAVERAGE, FT_SOURCESTATISTICS,
   FT_VOLUMELOOKUP, FT_PREPARE_ATLAS