Nothing
##
##
## Copyright (c) 2009, Brandon Whitcher and Volker Schmid
## All rights reserved.
##
## Redistribution and use in source and binary forms, with or without
## modification, are permitted provided that the following conditions are
## met:
##
## * Redistributions of source code must retain the above copyright
## notice, this list of conditions and the following disclaimer.
## * Redistributions in binary form must reproduce the above
## copyright notice, this list of conditions and the following
## disclaimer in the documentation and/or other materials provided
## with the distribution.
## * The names of the authors may not be used to endorse or promote
## products derived from this software without specific prior
## written permission.
##
## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
## "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
## LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
## A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
## HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
## SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
## LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
## DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
## THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
## (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
## OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
##
##
adc.lm <- function(signal, b, guess, nprint=0) {
func <- function(x, y) {
S0 <- x[1]
D <- x[2]
signal <- y[[1]]
b <- y[[2]]
signal - S0 * exp(-b*D)
}
require("minpack.lm") # Levenberg-Marquart fitting
out <- nls.lm(par=guess, fn=func, control=list(nprint=nprint),
y=list(signal, b))
list(S0=out$par[1], D=out$par[2], info=out$info, message=out$message)
}
ADC.fast <- function(dwi, bvalues, dwi.mask, verbose=FALSE) {
if (length(dim(dwi)) != 4) # Check dwi is a 4D array
stop("Diffusion-weighted data must be a 4D array.")
if (!is.logical(dwi.mask)) # Check dyn.mask is logical
stop("Mask must be logical.")
nvalues <- length(bvalues)
nvoxels <- sum(dwi.mask)
if (verbose)
cat(" Deconstructing data...", fill=TRUE)
dwi.mat <- matrix(dwi[dwi.mask], nvoxels)
S0 <- D <- numeric(nvoxels)
if (verbose)
cat(" Calculating S0 and D...", fill=TRUE)
for(i in 1:nvoxels) {
fit <- adc.lm(dwi.mat[i,], bvalues, guess=c(0.75*dwi.mat[i,1], 0.05))
if(fit$info < 4) {
S0[i] <- fit$S0 ; D[i] <- fit$D
} else {
S0[i] <- D[i] <- NA
}
}
if (verbose)
cat(" Reconstructing results...", fill=TRUE)
S0.array <- D.array <- array(NA, dim(dwi)[1:3])
S0.array[dwi.mask] <- S0
D.array[dwi.mask] <- D
list(S0 = S0.array, D = D.array)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.