readDWIdata: Read Diffusion Weighted Data
In WIAS-BERLIN/dti: Analysis of Diffusion Weighted Imaging (DWI) Data

readDWIdata

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, bvalue = NULL, xind = NULL, yind = NULL, zind = NULL,
        level = 0, mins0value = 1, maxvalue = 32000, voxelext = c(1, 1, 1),
        orientation = c(0L, 2L, 5L), rotation = diag(3))
readDWIdata(gradient, dirlist, format = c("DICOM", "NIFTI", "ANALYZE", "AFNI"),
        nslice = NULL, order = NULL, bvalue = NULL,
        xind = NULL, yind = NULL, zind = NULL, level = 0, mins0value = 1,
        maxvalue = 32000, voxelext = NULL, orientation = c(0L, 2L, 5L),
        rotation = NULL, pattern = NULL, SPM2=TRUE, verbose = FALSE)

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 or name of a single data file (e.g. 4D NIFTI)
`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).
`bvalue`	vector of b-values (default 0 for S0 and 1 for Si)
`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
`rotation`	optional rotation matrix for the coordinate system.
`pattern`	pattern for file matching in the directories `dirlist`.
`SPM2`	Enable some non-standard NIfTI files produced by SPM to be readable.
`verbose`	some progress reports if TRUE

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

J. Polzehl, K. Tabelow (2019). Magnetic Resonance Brain Imaging: Modeling and Data Analysis Using R. Springer, Use R! series. Doi:10.1007/978-3-030-29184-6.

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