extract-methods             package:dti             R Documentation

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

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

     The methods extract and/or compute specified statistics from
     object of class '"dtiData"', '"dtiTensor"', and '"dtiIndices"'.
     This can be restricted to a subset of voxel.

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

       ## S4 method for signature 'dtiData':
       extract(x, what="data", xind, yind, zind)
       ## S4 method for signature 'dtiTensor':
       extract(x, what="tensor", xind, yind, zind)
       ## S4 method for signature 'dtiIndices':
       extract(x, what=c("fa","andir"), xind, yind, zind)
       ## S4 method for signature 'dtiData':
       x[i, j, k, drop=FALSE]
       ## S4 method for signature 'dtiTensor':
       x[i, j, k, drop=FALSE]
       ## S4 method for signature 'dtiIndices':
       x[i, j, k, drop=FALSE]

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

       x: Object of class 'dti' 

       i: vector of x-coordinates, defaults to whole range. 

       j: vector of y-coordinates, defaults to whole range. 

       k: vector of z-coordinates, defaults to whole range. 

    xind: vector of x-coordinates, defaults to whole range. 

    yind: vector of y-coordinates, defaults to whole range. 

    zind: vector of z-coordinates, defaults to whole range. 

    what: Statistic to extract. See Methods Section for details. 

    drop: unused. 

_V_a_l_u_e:

     For function 'extract' a list with components carrying the names
     of the options specified in argument 'what'.  For indexing
     function, the cutted object.

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


          The generic extract function '"["' does what it is expected
          to do: it extracts parts of the object specified by 'i', 'j',
          and 'k'.

     _x = "_A_N_Y" Returns a warning for 'extract'. Generic funtion for
          '"["' returns an object of same class with data clipped to
          the indices specified in arguments 'i', 'j' and 'k'.

     _x = "_d_t_i_D_a_t_a" Extraction of squared gradient matrix (btb) or of S0
          (S0), Sb (Sb) or all images (Si) restricted to the cube
          defined by arguments 'i', 'j' and 'k'.

     _x = "_d_t_i_I_n_d_i_c_e_s" Returns an array containing the specified
          statistics, i.e. fractional anisotropy (fa), geodesic
          anisotropy (ga), mean diffusivity (md), main direction of
          anisotropy (andir) and/or shape parameters (bary), as
          specified in argument 'what'. Information is extracted for
          voxel within the cube defined by 'xind', 'yind', and 'zind'. 

     _x = "_d_t_i_T_e_n_s_o_r" Returns an array containing the specified
          statistics, i.e. fractional anisotropy (fa), geodesic
          anisotropy (ga), mean diffusivity (md), eigenvalues
          (evalues), main direction of anisotropy (andir), the tensor
          (tensor) the estimated S0 image (s0) and/or the mask used to
          restrict computations (mask), as specified in argument
          'what'. Information is extracted for voxel within the  cube
          defined by arguments 'xind', 'yind' and 'zind'. 

_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:

     'dtiData',  'dtiTensor',  'dtiIndices'

