dti (version 0.8-1)

readDWIdata: 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

Value

• An object of class "dtiData".

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.

References

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

See Also

dti.smooth, dtiTensor-methods, dtiData

Examples

demo(dti_art)