plot-methods               package:dti               R Documentation

_M_e_t_h_o_d_s _f_o_r _F_u_n_c_t_i_o_n _p_l_o_t _i_n _P_a_c_k_a_g_e _d_t_i

_D_e_s_c_r_i_p_t_i_o_n:

     Visualization of objects of class '"dtiData"', '"dtiIndices"' and
     class '"dtiTensor"'

_U_s_a_g_e:

       ## S4 method for signature 'dtiData':
       plot(x, y, slice=1, gradient=NULL, view= "axial", show=TRUE, density=FALSE, xind=NULL, yind=NULL, zind=NULL, mar=c(3,3,3,.3), mgp=c(2,1,0), ...)
       ## S4 method for signature 'dtiTensor':
       plot(x, y, slice=1, view= "axial", method=1, quant=0, minanindex=NULL, show=TRUE, contrast.enh=1, what="FA", xind=NULL, yind=NULL, zind=NULL, mar=c(3,3,3,.3), mgp=c(2,1,0), ...)
       ## S4 method for signature 'dtiIndices':
       plot(x, y, slice=1, view="axial", quant=0, minanindex=NULL, show=TRUE, density=FALSE, contrast.enh=1,what="FA", qrange=c(.01,.99), xind=NULL, yind=NULL, zind=NULL, mar=c(2,2,2,.2), mgp=c(2,1,0), ...)

_A_r_g_u_m_e_n_t_s:

       x: Object of class '"dtiIndices"', '"dtiData"' or '"dtiTensor"'

       y: Not used 

   slice: Slice number 

    view: Choose '"sagittal"', '"coronal"', or '"axial"' view here 

gradient: Index of data cube to plot. Defaults to the first S0 image. 

  method: Method for color coding tensor indices. 

   quant: If 'is.null(minanindex)' specify 'minanindex' as
          corresponding quantile of the fractal anisotropy (FA) index.

minanindex: Display only information for voxel with 'FA>minanindex'

    show: Visualize information in a graphics device (for classes
          '"dtiData"' and '"dtiIndices"' only).  

 density: Show density of S0(Sb)-values (for class '"dtiData"') or
          densities of fractal anisotropy (FA) or geodesic anisotropy
          (GA) ( for class '"dtiIndices"').  

contrast.enh: Enhance image contrast using
          'min(1,x$anindex/contrast.enh' instead of the anisotropy
          index itself. Effective values are within the interval (0,1).

    what: If 'what="GA"' use geodesic anisotropy (GA) instead of
          fractional anisotropy (FA).  

     mar: Graphical parameter for 'par'. 

     mgp: Graphical parameter for 'par'. 

  qrange: Cut image intensity to these quantiles to avoid that outliers
          determine the dynamic range of the image. 

    xind: If provided restrict display to indices specified in 'xind'
          for x-direction.

    yind: If provided restrict display to indices specified in 'yind'
          for y-direction.

    zind: If provided restrict display to indices specified in 'zind'
          for z-direction.

     ...: currently not used 

_M_e_t_h_o_d_s:


     _x = "_A_N_Y" Generic function: see 'plot'. 

     _x =  "_d_t_i" Returns a warning. 

     _x = "_d_t_i_D_a_t_a" 'gradient' can be used to specify a specific data
          cube associated with the index of a gradient direction. For
          objects of class '"dtiData"' images are produces that are
          scaled by the maximal observed image value. This guarantees
          that subsequently produced images are on a comparable grey
          scale. The resulting image of class '"adimpro"' from package
          'adimpro' is returned. 

     _x = "_d_t_i_I_n_d_i_c_e_s" Color coded anisotropy maps are produced
          depending on the specification in 'method'. 'method==1',
          'method==2', 'method==4'  and 'method==5' specify three
          different color schemes for directional FA-maps. 'method==3'
          specifies visualization of dtiIndices using color coded shape
          parameters. The resulting image of class '"adimpro"' from
          package 'adimpro' is returned.

     _x = "_d_t_i_T_e_n_s_o_r" The tensor itself, fractional anisotropy (FA),
          mean diffusivity (MD) and a color coded anisotropy map are
          provided. 'NULL' is returned. 


_A_u_t_h_o_r(_s):

     Karsten Tabelow tabelow@wias-berlin.de
       J\"org Polzehl polzehl@wias-berlin.de

_S_e_e _A_l_s_o:

     'dtiIndices',  'dtiData',  'dtiTensor'

_E_x_a_m_p_l_e_s:

       ## Not run: demo(dti_art)

