readDWIdata               package:dti               R Documentation

_R_e_a_d _D_i_f_f_u_s_i_o_n _W_e_i_g_h_t_e_d _D_a_t_a

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

     The functions create a '"dtiData"' object from Diffusion Weighted
     Data from medicial imaging files in a list of directories or from
     an imagefile, where the diffusion weighted data is given as 2-byte
     integer.

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

       dtiData(gradient, imagefile, ddim, xind = NULL, yind = NULL, zind = NULL, level = 0, mins0value = 0, maxvalue = 10000, voxelext = c(1, 1, 1), orientation = c(1, 3, 5))
       readDWIdata(gradient, dirlist, format, nslice, order = NULL, xind = NULL, yind = NULL, zind = NULL, level = 0, mins0value = 0, maxvalue = 10000, voxelext = NULL, orientation = c(1, 3, 5))

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

gradient: matrix of diffusion gradients (including zero gradients for
          S0 images) 

imagefile: name of data image file (binary 2Byte integers)

    ddim: dimension of image cube (3D) 

 dirlist: list of directories containing the data files 

  format: string specifying the medical imaging format, one of
          ''DICOM'', ''NIFTI'', ''ANALYZE'', or ''AFNI'' 

  nslice: number of slices (usually z-direction) 

   order: vector, specifying a different order of the data files, i.e.
          other than alphabetic order in the directories given by
          'dirlist'. If not given, 1:n is used for n data files (no
          order change). 

    xind: subindex for x-direction 

    yind: subindex for y-direction 

    zind: subindex for z-direction 

   level: determine 'mins0value' as quantile of positive S0-values 

mins0value: set voxel in S0-images with values less than 'level'
          inactive 

maxvalue: set voxel with values larger than 'maxvalue' inactive 

voxelext: voxel extensions in coordinate directions 

orientation: orientations of data as coded in AFNI 

_D_e_t_a_i_l_s:

     The function 'dtiData' creates an object of class '"dtiData"' from
     an image file, where the diffusion weighted data is given as
     2-byte integer.  This image file has to be prepared by the user. 
     Use 'writeBin' to write out first all S0 images and than all Si
     images. The 'gradient' should be created according to this order.
     Run the demo in order to have an example, how to do this!

     The function 'readDWIdata' reads the data files given in the
     directories in 'dirlist' in alphabetic order. The order can be
     changed using the 'order' argument: If 'filelist' is the vector of
     files in alphabetic order, they are read in the order
     'filelist[order]'.  If order is not given 'order <- 1:n' is used
     (no change!).  The medical imaging format is given by 'format' and
     can be one of ''DICOM'', ''NIFTI'', ''ANALYZE'', or ''AFNI''.  The
     number of slices of the three dimensional data cube is given by
     'nslice'.  The diffusion gradients are provided as matrix
     'gradient'.

     'xind', 'yind', and 'zind' define a region of interest as indices.
      If not given '1:dim[i]' is used. 'level' determine 'mins0value'
     as quantile of positive S0-values.  'mins0value' sets voxel in
     S0-images with values less than 'level' inactive.  'maxvalue'
     sets voxel with values larger than 'maxvalue' inactive.

     'voxelext' defines the voxel extension, overwrites the values
     found in the imaging files.  'orientation' codes the data
     orientation in AFNI notation.

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

     An object of class '"dtiData"'.

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

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

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://afni.nimh.nih.gov/pub/dist/src/README.attributes>

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

     'dti.smooth',  'dtiTensor-methods',  'dtiData'

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

       ## Not run: demo(dti_art)

