srtm2: Simplified Reference Tissue Model 2

In mathesong/kinfitr: Kinetic Modelling of PET Time Activity Curves

Simplified Reference Tissue Model 2

Description

Function to fit the SRTM2 model of Wu and Carson (2002) to data. Note that without setting the k2prime, the model is effectively equivalent to a conventional SRTM model. This configuration is allowed for estimating an appropriate k2prime value, but without re-fitting with a specified k2prime value, the model is not really SRTM2.

Usage

srtm2(
  t_tac,
  reftac,
  roitac,
  k2prime = NULL,
  weights = NULL,
  frameStartEnd = NULL,
  R1.start = 1,
  R1.lower = 0,
  R1.upper = 10,
  k2prime.start = 0.1,
  k2prime.lower = 0.001,
  k2prime.upper = 1,
  bp.start = 1.5,
  bp.lower = 0,
  bp.upper = 15,
  multstart_iter = 1,
  multstart_lower = NULL,
  multstart_upper = NULL,
  printvals = F
)

Arguments

t_tac	Numeric vector of times for each frame in minutes. We use the time halfway through the frame as well as a zero. If a time zero frame is not included, it will be added.
reftac	Numeric vector of radioactivity concentrations in the reference tissue for each frame. We include zero at time zero: if not included, it is added.
roitac	Numeric vector of radioactivity concentrations in the target tissue for each frame. We include zero at time zero: if not included, it is added.
k2prime	Optional. If empty, then the model will fit a value of k2prime. If specified, the model will be fitted with this parameter set (i.e. as a 2 parameter model).
weights	Optional. Numeric vector of the weights assigned to each frame in the fitting. We include zero at time zero: if not included, it is added. If not specified, uniform weights will be used.
frameStartEnd	Optional. This allows one to specify the beginning and final frame to use for modelling, e.g. c(1,20). This is to assess time stability.
R1.start	Optional. Starting parameter for fitting of R1. Default is 1.
R1.lower	Optional. Lower bound for the fitting of R1. Default is 0.
R1.upper	Optional. Upper bound for the fitting of R1. Default is 10.
k2prime.start	Optional. Starting parameter for fitting of k2prime. Default is 0.1.
k2prime.lower	Optional. Lower bound for the fitting of k2prime. Default is 0.001.
k2prime.upper	Optional. Upper bound for the fitting of k2prime. Default is 1.
bp.start	Optional. Starting parameter for fitting of bp. Default is 1.5.
bp.lower	Optional. Lower bound for the fitting of bp. Default is -10.
bp.upper	Optional. Upper bound for the fitting of bp. Default is 15.
multstart_iter	Number of iterations for starting parameters. Default is 1. For more information, see nls_multstart. If specified as 1 for any parameters, the original starting value will be used, and the multstart_lower and multstart_upper values ignored.
multstart_lower	Optional. Lower bounds for starting parameters. Defaults to the lower bounds. Named list of whichever parameters' starting bounds should be altered.
multstart_upper	Optional. Upper bounds for starting parameters. Defaults to the upper bounds. Named list of whichever parameters' starting bounds should be altered.
printvals	Optional. This displays the parameter values for each iteration of the model. This is useful for debugging and changing starting values and upper and lower bounds for parameters.

Value

A list with a data frame of the fitted parameters out$par, their percentage standard errors (scaled so that 1 represents 100%) out$par.se, the model fit object out$fit, the model weights out$weights, and a dataframe containing the TACs both of the data and the fitted values out$tacs.

Author(s)

Granville J Matheson, [e-mail]

References

Wu Y, Carson RE. Noise reduction in the simplified reference tissue model for neuroreceptor functional imaging. J Cereb Blood Flow Metab. 2002;22:1440-1452.

Examples

data(simref)

t_tac <- simref$tacs[[2]]$Times
reftac <- simref$tacs[[2]]$Reference
roitac <- simref$tacs[[2]]$ROI1
weights <- simref$tacs[[2]]$Weights

fit_setk2prime <- srtm2(t_tac, reftac, roitac, k2prime=0.1)

# Note: this is not really SRTM2 because the k2prime is not specified
fitk2prime <- srtm2(t_tac, reftac, roitac)

mathesong/kinfitr documentation built on Nov. 27, 2024, 1:38 a.m.