readDWIdata {dti}R Documentation

Read Diffusion Weighted Data

Description

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.

Usage

  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))

Arguments

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

Details

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.

Value

An object of class "dtiData".

Author(s)

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

References

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

See Also

dti.smooth, dtiTensor-methods, dtiData

Examples

  ## Not run: demo(dti_art)

[Package dti version 0.6-0 Index]