dcemri: Pharmacokinetic Models for Dynamic Contrast-Enhanced MRI Data
In dcemri: A Package for Medical Image Analysis

Description Usage Arguments Details Value Author(s) References See Also Examples

Parameter estimation for single compartment models is performed using literature-based or user-specified arterial input functions. The Levenburg-Marquardt algorithm does the heavy lifting.

1 2	dcemri.lm(conc, time, img.mask, model="extended", aif=NULL, nprint=0, user=NULL, verbose=FALSE, ...)

`conc`	is a multidimensional (1D-4D) array of contrast agent concentrations. The last dimension is assumed to be temporal, while the previous dimensions are assued to be spatial.
`time`	is a vector of acquisition times (in minutes) relative to injection of the contrast agent. Negative values should be used prior to the injection.
`img.mask`	is a (logical) multidimensional array that identifies the voxels to be analyzed. Has to have same dimension as `conc` minus temporal dimension.
`model`	is a character string that identifies the type of compartmental model to be used. Acceptable models include: “weinmann”Tofts & Kermode AIF convolved with single compartment model “extended”Weinmann model extended with additional vascular compartment (default) “orton.exp”Extended model using Orton's exponential AIF “orton.cos”Extended model using Orton's raised cosine AIF
`aif`	is a character string that identifies the parameters of the type of arterial input function (AIF) used with the above model. Acceptable values are: `tofts.kermode` (default) or `fritz.hansen` for the `weinmann` and `extended` models; `orton.exp` (default) and `user` for the `orton.exp` model; `orton.cos` (default) and `user` for the `orton.cos` model. All AIF models set the parametric form and parameter values – except `user` where a set of user-defined parameter values are allowed.
`nprint`	is an integer, that enables controlled printing of iterates if it is positive. In this case, estimates of `par` are printed at the beginning of the first iteration and every `nprint` iterations thereafter and immediately prior to return. If `nprint` is not positive, no tracing information on the progress of the optimization is produced.
`user`	is a list with the following paramters required: D, AB, muB, AG, muG.
`verbose`	.
`...`	Additional parameters to the function.

Compartmental models are the solution to the modified general rate equation (Kety 1951). The specific parametric models considered here include the basic Kety model

C_t(t)=K^{trans}≤ft[C_p(t)\otimes\exp(-k_{ep}t)\right],

where \otimes is the convoluation operator, and the so-called extended Kety model

C_t(t)=v_pC_p(t)+K^{trans}≤ft[C_p(t)\otimes\exp(-k_{ep}t)\right].

The arterial input function must be either literature-based (with fixed parameters) or the exponential AIF from Orton et al. (2008) with user-defined parameters.

Parameter estimates and their standard errors are provided for the masked region of the multidimensional array. They include

`ktrans`	Transfer rate from plasma to the extracellular, extravascular space (EES).
`kep`	Rate parameter for transport from the EES to plasma.
`ve`	Fractional occupancy by EES (the ratio between ktrans and kep).
`vp`	Fractional occupancy by plasma.
`ktranserror`	Standard error for ktrans.
`keperror`	Standard error for kep.
`vperror`	Standard error for vp.

The residual sum-of-squares is also provided, along with the original acquisition times (for plotting purposes).

Brandon Whitcher, Volker Schmid

Ahearn, T.S., Staff, R.T., Redpath, T.W. and Semple, S.I.K. (2005) The use of the Levenburg-Marquardt curve-fitting algorithm in pharmacokinetic modelling of DCE-MRI data, Physics in Medicine and Biology, 50, N85-N92.

Fritz-Hansen, T., Rostrup, E., Larsson, H.B.W, Sondergaard, L., Ring, P. and Henriksen, O. (1993) Measurement of the arterial concentration of Gd-DTPA using MRI: A step toward quantitative perfusion imaging, Magnetic Resonance in Medicine, 36, 225-231.

Orton, M.R., Collins, D.J., Walker-Samuel, S., d'Arcy, J.A., Hawkes, D.J., Atkinson, D. and Leach, M.O. (2007) Bayesian estimation of pharmacokinetic parameters for DCE-MRI with a robust treatment of enhancement onset time, Physics in Medicine and Biology 52, 2393-2408.

Orton, M.R., d'Arcy, J.A., Walker-Samuel, S., Hawkes, D.J., Atkinson, D., Collins, D.J. and Leach, M.O. (2008) Computationally efficient vascular input function models for quantitative kinetic modelling using DCE-MRI, Physics in Medicine and Biology 53, 1225-1239.

Tofts, P.S., Brix, G, Buckley, D.L., Evelhoch, J.L., Henderson, E., Knopp, M.V., Larsson, H.B.W., Lee, T.-Y., Mayr, N.A., Parker, G.J.M., Port, R.E., Taylor, J. and Weiskoff, R. (1999) Estimating kinetic parameters from dynamic contrast-enhanced T_1-weighted MRI of a diffusable tracer: Standardized quantities and symbols, Journal of Magnetic Resonance, 10, 223-232.

Tofts, P.S. and Kermode, A.G. (1984) Measurement of the blood-brain barrier permeability and leakage space using dynamic MR imaging. 1. Fundamental concepts, Magnetic Resonance in Medicine, 17, 357-367.

Weinmann, H.J., Laniado, M. and Mutzel, W. (1984) Pharmacokinetics of Gd-DTPA/dimeglumine after intraveneous injection into healthy volunteers, Physiological Chemistry and Physics and Medical NMR, 16, 167-172.

dcemri.bayes, dcemri.map, dcemri.spline, nls.lm

data("buckley")

## Set up breast data for dcemri
xi <- seq(5, 300, by=5)
img <- array(t(breast$data)[,xi], c(13,1,1,60))
time <- buckley$time.min[xi]
aif <- buckley$input[xi]
mask <- array(TRUE, dim(img)[1:3])

## Generate AIF params using the orton.exp function from Buckley's AIF
aifparams <- orton.exp.lm(time, aif)
fit <- dcemri.lm(img, time, mask, model="orton.exp",
                 aif="user", user=aifparams)

## Scatterplot comparing true and estimated Ktrans values
plot(breast$ktrans, fit$ktrans, xlim=c(0,0.75), ylim=c(0,0.75),
     xlab=expression(paste("True ", K^{trans})),
     ylab=expression(paste("Estimated ", K^{trans})))
abline(0, 1, lwd=1.5, col="red")
cbind(breast$ktrans, fit$ktrans[,,1])