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reference:ft_prepare_layout [2018/08/23 14:43] (current)
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 +=====  FT_PREPARE_LAYOUT =====
 +
 +Note that this reference documentation is identical to the help that is displayed in MATLAB when you type "help ft_prepare_layout"​.
 +
 +<​html><​pre>​
 +  <a href=/​reference/​ft_prepare_layout><​font color=green>​FT_PREPARE_LAYOUT</​font></​a>​ loads or creates a 2-D layout of the channel locations. This
 +  layout is required for plotting the topographical distribution of the potential or
 +  field distribution,​ or for plotting timecourses in a topographical arrangement.
 + 
 +  Use as
 +    layout = ft_prepare_layout(cfg,​ data)
 + 
 +  There are several ways in which a 2-D layout can be made: 1) it can be read
 +  directly from a layout file, 2) it can be created on basis of an image or photo, 3)
 +  it can be created based on 3-D sensor positions in the configuration,​ in the data,
 +  or in an electrode or gradiometer file.
 + 
 +  Layout files are MATLAB files with a single variable representing the layout (see
 +  below). The layout file can also be an ASCII *.lay file, but this type of layout is
 +  no longer recommended,​ since the outline of the head and the mask within which the
 +  interpolation is done is less refined for an ASCII layout. A large number of
 +  template layout files is provided in the fieldtrip/​template/​layout directory. See
 +  also http://​fieldtriptoolbox.org/​template/​layout
 + 
 +  You can specify any one of the following configuration options
 +    cfg.layout ​     = filename containg the input layout (*.mat or *.lay file), this can also be a layout
 +                      structure, which is simply returned as-is (see below for details)
 +    cfg.output ​     = filename (ending in .mat or .lay) to which the layout will be written (default = [])
 +    cfg.elec ​       = structure with electrode definition, or
 +    cfg.elecfile ​   = filename containing electrode definition
 +    cfg.grad ​       = structure with gradiometer definition, or
 +    cfg.gradfile ​   = filename containing gradiometer definition
 +    cfg.opto ​       = structure with optode structure definition, or
 +    cfg.optofile ​   = filename containing optode structure definition
 +    cfg.rotate ​     = number, rotation around the z-axis in degrees (default = [], which means automatic)
 +    cfg.projection ​ = string, 2D projection method can be '​stereographic',​ '​orthographic',​ '​polar'​ or '​gnomic'​ (default = '​polar'​)
 +                      When '​orthographic',​ cfg.viewpoint can be used to indicate to specificy projection (keep empty for legacy projection)
 +    cfg.viewpoint ​  = string indicating the view point that is used for orthographic projection of 3-D sensor
 +                      positions to the 2-D plane. The possible viewpoints are
 +                      '​left' ​     - left  sagittal view,    L=anterior, R=posterior,​ top=top, bottom=bottom
 +                      '​right' ​    - right sagittal view,    L=posterior,​ R=anterior, top=top, bottom=bottom
 +                      '​inferior' ​ - inferior axial view,    L=R, R=L, top=anterior,​ bottom=posterior
 +                      '​superior' ​ - superior axial view,    L=L, R=R, top=anterior,​ bottom=posterior
 +                      '​anterior' ​ - anterior ​ coronal view, L=R, R=L, top=top, bottom=bottom
 +                      '​posterior'​ - posterior coronal view, L=L, R=R, top=top, bottom=bottom
 +                      '​auto' ​     - automatic guess of the most optimal of the above
 +                       tip: use cfg.viewpoint = '​auto'​ per iEEG electrode grid/​strip/​depth for more accurate results
 +                       tip: to obtain an overview of all iEEG electrodes, choose superior/​inferior,​ use cfg.headshape/​mri,​ and plot using <a href=/​reference/​ft_layoutplot><​font color=green>​FT_LAYOUTPLOT</​font></​a>​ with cfg.box/​mask = '​no'​
 +    cfg.outline ​    = string, how to create the outline, can be '​circle',​ '​convex',​ '​headshape',​ '​mri'​ or '​no'​ (default is automatic)
 +    cfg.mask ​       = string, how to create the mask, can be '​circle',​ '​convex',​ '​headshape',​ '​mri'​ or '​no'​ (default is automatic)
 +    cfg.headshape ​  = surface mesh (e.g. pial, head, etc) to be used for generating an outline, see <a href=/​reference/​ft_read_headshape><​font color=green>​FT_READ_HEADSHAPE</​font></​a>​ for details
 +    cfg.mri ​        = segmented anatomical MRI to be used for generating an outline, see <a href=/​reference/​ft_read_mri><​font color=green>​FT_READ_MRI</​font></​a>​ and <a href=/​reference/​ft_volumesegment><​font color=green>​FT_VOLUMESEGMENT</​font></​a>​ for details
 +    cfg.montage ​    = '​no'​ or a montage structure (default = '​no'​)
 +    cfg.image ​      = filename, use an image to construct a layout (e.g. useful for ECoG grids)
 +    cfg.bw ​         = '​yes'​ or '​no',​ if an image is used and this option is true, the image is transformed in black and white (default = '​no',​ i.e. do not transform)
 +    cfg.overlap ​    = string, how to deal with overlapping channels when the layout is constructed from a sensor configuration structure. This can be
 +                      '​shift' ​ - shift the positions in 2D space to remove the overlap (default)
 +                      '​keep' ​  - do not shift, retain the overlap
 +                      '​no' ​    - throw an error when overlap is present
 +    cfg.channel ​    = '​all',​ or Nx1 cell-array with selection of channels, see <a href=/​reference/​ft_channelselection><​font color=green>​FT_CHANNELSELECTION</​font></​a>​ for details
 +    cfg.boxchannel ​ = '​all',​ or Nx1 cell-array with selection of channels, see <a href=/​reference/​ft_channelselection><​font color=green>​FT_CHANNELSELECTION</​font></​a>​ for details
 +                       ​specificies channels to use for determining channel box size (default = '​all',​ recommended for MEG/EEG, a selection is recommended for iEEG)
 +    cfg.skipscale ​  = '​yes'​ or '​no',​ whether the scale should be included in the layout or not (default = '​no'​)
 +    cfg.skipcomnt ​  = '​yes'​ or '​no',​ whether the comment should be included in the layout or not (default = '​no'​)
 + 
 +  If you use cfg.headshape or cfg.mri to create a headshape outline, the input
 +  geometry should be expressed in the same units and coordinate system as the input
 +  sensors.
 + 
 +  Alternatively the layout can be constructed from either one of these in the input data structure:
 +    data.elec ​    = structure with electrode positions
 +    data.grad ​    = structure with gradiometer definition
 +    data.opto ​    = structure with optode structure definition
 + 
 +  Alternatively you can specify the following systematic layouts which will be
 +  generated for all channels present in the data. Note that these layouts are only
 +  suitable for multiplotting,​ not for topoplotting.
 +    cfg.layout = '​ordered' ​   will give you a NxN ordered layout
 +    cfg.layout = '​vertical' ​  will give you a Nx1 ordered layout
 +    cfg.layout = '​horizontal'​ will give you a 1xN ordered layout
 +    cfg.layout = '​butterfly' ​ will give you a layout with all channels on top of each other
 +    cfg.layout = '​circular' ​  will distribute the channels on a circle
 + 
 +  The output layout structure will contain the following fields
 +    layout.label ​  = Nx1 cell-array with channel labels
 +    layout.pos ​    = Nx2 matrix with channel positions
 +    layout.width ​  = Nx1 vector with the width of each box for multiplotting
 +    layout.height ​ = Nx1 matrix with the height of each box for multiplotting
 +    layout.mask ​   = optional cell-array with line segments that determine the area for topographic interpolation
 +    layout.outline = optional cell-array with line segments that represent the head, nose, ears, sulci or other anatomical features
 + 
 +  See also <a href=/​reference/​ft_topoplotER><​font color=green>​FT_TOPOPLOTER</​font></​a>,​ <a href=/​reference/​ft_topoplotTFR><​font color=green>​FT_TOPOPLOTTFR</​font></​a>,​ <a href=/​reference/​ft_multiplotER><​font color=green>​FT_MULTIPLOTER</​font></​a>,​ <a href=/​reference/​ft_multiplotTFR><​font color=green>​FT_MULTIPLOTTFR</​font></​a>,​ <a href=/​reference/​ft_plot_lay><​font color=green>​FT_PLOT_LAY</​font></​a>​
 +</​pre></​html>​