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.
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)
An object of class "dtiData"
.
matrix of diffusion gradients (including zero gradients for S0 images)
name of data image file (binary 2Byte integers)
dimension of image cube (3D)
list of directories containing the data files or name of a single data file (e.g. 4D NIFTI)
string specifying the medical imaging format, one of ''DICOM'', ''NIFTI'', ''ANALYZE'', or ''AFNI''
number of slices (usually z-direction)
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).
vector of b-values (default 0 for S0 and 1 for Si)
subindex for x-direction
subindex for y-direction
subindex for z-direction
determine mins0value
as quantile of positive S0-values
set voxel in S0-images with values less than level
“inactive”
set voxel with values larger than maxvalue
inactive
voxel extensions in coordinate directions
orientations of data as coded in AFNI
optional rotation matrix for the coordinate system.
pattern for file matching in the directories dirlist
.
Enable some non-standard NIfTI files produced by SPM to be readable.
some progress reports if TRUE
Karsten Tabelow tabelow@wias-berlin.de
J\"org Polzehl polzehl@wias-berlin.de
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.
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.
dti.smooth
,
dtiTensor-methods
,
dtiData