KAT.checkData: Checks and converts your data to the RData file format.

In KATforDCEMRI: Kinetic Analysis and Visualization of DCE-MRI Data

Description

Load your data into an R session and save as an RData file that can be analyzed by the KAT function. Also check that dimensions of vectors and arrays are consistent.

Usage

KAT.checkData(file.name, vector.times, map.CC, mask.ROI, vector.AIF, map.tlag=NULL,
write.data.to.file=TRUE)

Arguments

file.name	Give a name to the RData file that will be generated with this function. A .RData extension will automatically be added.
vector.times	The nt x 1 time vector; can have units of seconds or minutes. KAT will automatically assign units based on the following assumptions: units are minutes if tmax < 100 and seconds if tmax >= 100. Please make sure that these assumptions are consistent with your data. You will have to manually convert the time vector into seconds or minutes prior to running KAT.checkData if the time vector specified by vector.times has other units.
map.CC	The nx x ny x ns x nt contrast agent intensity/concentration array.
mask.ROI	The nx x ny x ns ROI mask array where voxels within the ROI are assigned a 1 and those outside assigned a 0.
vector.AIF	The nt x 1 arterial (vascular) input function.
map.tlag	The nx x ny x ns array that contains per-voxel tag times estimated outside of KAT, to be applied to the vascular input function. Units must be same as those used for vector.times. This argument is optional.
write.data.to.file	Should the original data, loaded into R, be saved in a single RData file for future use? Default=TRUE. NOTE: if set to FALSE, usage for this function must be exactly as follows: R> dcemri.data <- KAT.checkData(args) R> KAT(args) where the file argument is not specified when calling KAT().

Value

Returns an RData file that can be read by the KAT function.

Note

The KAT function can also read data stored as an uncompressed MATLAB 5 file.

Author(s)

Gregory Z. Ferl

See Also

KAT, KAT.plot, dcemri.data

Examples

## Create temporary directory for benchmark example code output files
temp_dir <- tempdir(check=FALSE)
##
current_dir <- getwd()
setwd(temp_dir)
##
## Run example code
data(dcemri.data, package="KATforDCEMRI")
a1=dcemri.data$vectorTimes
a2=dcemri.data$mapCC
a3=dcemri.data$maskROI
a4=dcemri.data$vectorAIF
KAT.checkData("f",vector.times=a1,map.CC=a2,mask.ROI=a3,vector.AIF=a4,write.data.to.file=TRUE)
##
setwd(current_dir)

KATforDCEMRI documentation built on Aug. 26, 2019, 9:03 a.m.