DATforDCEMRI (version 0.5)

DAT: Deconvolution Analysis Tool

Description

Calculates the Impulse Response Function on a per-voxel basis for DCE-MRI data using numerical deconvolution, yielding the Impulse Response Function for each voxel analyzed. The Area Under the Curve and ratio of AUC to Mean Residence Time provide estimates of the kinetic model parameters ve and Ktrans. A visualization tool is also included that allows the user to explore voxel-wise data in an interactive manner.

Usage

DAT(file = "nodata", slice = 0, vp = 0, border = 20, maxCt = 0.66, 
parameter.plot = "AUCMRT", cutoff.map = 0.85, range.map = 1.5, 
export.matlab = FALSE, batch.mode = FALSE, alpha.AIF=c(0,0,2000), 
correct.trunc=TRUE, kep.nom=0.5, ...)

Arguments

file

RData file containing DCE-MRI data. May be generated manually or by the function DAT.checkData.

slice

Image slice to be extracted for analysis.

vp

Fractional plasma volume of tissue within Region of Interest. Default value is zero.

border

A border of image voxels around the Field of View to be excluded from analysis. Default is 20 voxels.

maxCt

Voxels will be excluded from analysis if the maximum contrast agent concentration exceed a threshold of maxCt times the maximum contrast agent concentration within the Arterial Input Function vector. Default value is 0.66.

parameter.plot

Which parameter will be described in the parametric maps? Two possible values are AUC and AUCMRT for the Area Under the Curve (AUC) and AUC divided by the Mean Residence Time of the Impulse Response Function. AUC i

cutoff.map

Typically a number between 0.5 and 1. Represents the quantile at which parametric map values will be truncated in order to suppress very large AUC or AUCMRT values within the parametric maps. Default value is 0.85.

range.map

Typically a number between 1 and 2. The range of the color bar associated with the parametric map is set to the maximum value within the map times range.map. Default value is 1.5.

export.matlab

Will the deconvolution results be export as a matlab file in addition to an RData file? Default value is FALSE.

batch.mode

Will the interactive parametric maps normally displayed at the end of each run be suppressed? Default value is FALSE.

alpha.AIF

Vector of smoothing parameters utilized by the locfit function when smoothing the arterial input function. Default value is c(0,0,2000).

correct.trunc

Will a rough approximation of truncation error correction be performed on parametric maps of AUC and AUC/MRT? Default value is TRUE.

kep.nom

A nominal value of kep to be used for truncation correction, i.e., to estimate the AUC of the IRF from the end of the scanning period to infinity? Default value is 0.5.

...

Pass arguments.

References

Ferl GZ (2011) DATforDCEMRI: An R Package for Deconvolution Analysis and Visualization of DCE-MRI Data. Journal of Statistical Software 44, 1-18.

Ferl GZ, Xu L, Friesenhahn M, Bernstein LJ, Barboriak DP, Port RE. (2010) An automated method for nonparametric kinetic analysis of clinical DCE-MRI data: application to glioblastoma treated with bevacizumab. Magn Reson Med. 63, 1366-1375.

See Also

See also DAT.checkData

Examples

data(DAT.simData, package="DATforDCEMRI")
myccarray <- (DAT.simData$mapCC)
mytimevector <- (DAT.simData$vectorTimes)
myroiarray <- (DAT.simData$maskROI)
myaifvector <- (DAT.simData$vectorAIF)
DAT.checkData(file.name="mydcemridata", vector.times=mytimevector, map.CC=myccarray, 
mask.ROI=myroiarray, vector.AIF=myaifvector, slice.stop=1)
DAT(file="mydcemridata_s1-s1.RData", slice=1, range.map=1.05, cutoff.map=0.95, 
batch.mode=TRUE)