extract-methods | R Documentation |
"MPMData"
,
"ESTATICSModel"
, "sESTATICSModel"
, "qMaps"
,
"IRdata"
, "IRfluid"
and "IRmixed"
.
The extract-methods extract and/or compute specified statistics from object of class
"MPMData"
, "ESTATICSModel"
, "sESTATICSModel"
, "qMaps"
,
"IRdata"
, "IRfluid"
and "IRmixed"
.
The [-methods can be used to reduce objects of class
"MPMData"
, "ESTATICSModel"
, "sESTATICSModel"
, "qMaps"
,
"IRdata"
, "IRfluid"
and "IRmixed"
such that they contain a subcube of data and results.
## S3 method for class 'MPMData'
extract(x, what, ...)
## S3 method for class 'ESTATICSModel'
extract(x, what, ...)
## S3 method for class 'sESTATICSModel'
extract(x, what, ...)
## S3 method for class 'qMaps'
extract(x, what, ...)
## S3 method for class 'IRdata'
extract(x, what, ...)
## S3 method for class 'IRfluid'
extract(x, what, ...)
## S3 method for class 'IRmixed'
extract(x, what, ...)
## S3 method for class 'MPMData'
x[i, j, k, ...]
## S3 method for class 'ESTATICSModel'
x[i, j, k, ...]
## S3 method for class 'sESTATICSModel'
x[i, j, k, ...]
## S3 method for class 'qMaps'
x[i, j, k, ...]
## S3 method for class 'IRdata'
x[i, j, k, tind, ...]
## S3 method for class 'IRfluid'
x[i, j, k, ...]
## S3 method for class 'IRmixed'
x[i, j, k, ...]
x |
object of class |
what |
Character vector of of names of statistics to extract. See Methods Section for details. |
i |
index vector for first spatial dimension |
j |
index vector for second spatial dimension |
k |
index vector for third spatial dimension |
tind |
index vector for inversion times |
... |
additional parameters, currently unused. |
A list with components carrying the names of the options specified in
argument what
.
Returns a warning for extract
Depending the occurence of names in what
a list with the specified components
is returned
ddata: mpm data
sdim: dimension of image cube
nFiles: number of images / image files
t1Files: character - filenames of t1Files
pdFiles: character - filenames of pdFiles
mtFiles: character - filenames of mtFiles
model: Number of the ESTATICS model that can be used
maskFile: character - filenames of maskFile
mask: mask
TR: vector of TR values
TE: vector of TE values
FA: vector of FA values
Depending the occurence of names in what
a list with the specified components
is returned
modelCoeff: Estimated parameter maps
invCov: map of inverse covariance matrices
rsigma: map of residual standard deviations
isConv: convergence indicator map
isThresh: logical map indicating where R2star==maxR2star
sdim: image dimension
nFiles: number of images
t1Files: vector of T1 filenames
pdFiles: vector of PD filenames
mtFiles: vector of MT filenames
model: model used (depends on specification of MT files)
maskFile: filename of brain mask
mask: brain mask
sigma: standard deviation sigma
L: effective number of receiver coils L
TR: TR values
TE: TE values
FA: Flip angles (FA)
TEScale: TEScale
dataScale: dataScale
Depending the occurence of names in what
a list with the specified components
is returned
modelCoeff: Estimated parameter maps
invCov: map of inverse covariance matrices
rsigma: map of residual standard deviations
isConv: convergence indicator map
bi: Sum of weights map from AWS/PAWS
smoothPar: smooting parameters used in AWS/PAWS
smoothedData: smoothed mpmData
isThresh: logical map indicating where R2star==maxR2star
sdim: image dimension
nFiles: number of images
t1Files: vector of T1 filenames
pdFiles: vector of PD filenames
mtFiles: vector of MT filenames
model: model used (depends on specification of MT files)
maskFile: filename of brain mask
mask: brain mask
sigma: sigma
L: effective number of receiver coils L
TR: TR values
TE: TE values
FA: Flip angles (FA)
TEScale: TEScale
dataScale: dataScale
Depending the occurence of names in what
a list with the specified components
is returned
b1Map: b1Map
R1: Estimated map of R1
R2star: Estimated map of R2star
PD: Estimated map of PD
MT: Estimated map of delta (if MT-series was used)
model: Type of ESTATICS model used
t1Files: filenames T1
mtFiles: filenames MT
pdFiles: filenames PD
mask: brainmask
Karsten Tabelow tabelow@wias-berlin.de
J\"org Polzehl polzehl@wias-berlin.de
dataDir <- system.file("extdata",package="qMRI")
#
# set file names for T1w, MTw and PDw images
#
t1Names <- paste0("t1w_",1:8,".nii.gz")
mtNames <- paste0("mtw_",1:6,".nii.gz")
pdNames <- paste0("pdw_",1:8,".nii.gz")
t1Files <- file.path(dataDir, t1Names)
mtFiles <- file.path(dataDir, mtNames)
pdFiles <- file.path(dataDir, pdNames)
#
# file names of mask and B1 field map
#
B1File <- file.path(dataDir, "B1map.nii.gz")
maskFile <- file.path(dataDir, "mask0.nii.gz")
#
# Acquisition parameters (TE, TR, Flip Angle) for T1w, MTw and PDw images
#
TE <- c(2.3, 4.6, 6.9, 9.2, 11.5, 13.8, 16.1, 18.4,
2.3, 4.6, 6.9, 9.2, 11.5, 13.8,
2.3, 4.6, 6.9, 9.2, 11.5, 13.8, 16.1, 18.4)
TR <- rep(25, 22)
FA <- c(rep(21, 8), rep(6, 6), rep(6, 8))
#
# read MPM example data
#
library(qMRI)
mpm <- readMPMData(t1Files, pdFiles, mtFiles,
maskFile, TR = TR, TE = TE,
FA = FA, verbose = FALSE)
#
# display some data
#
data <- extract(mpm,"ddata")
if(require(adimpro)){
rimage.options(ylab = "z")
oldpar <- par(mfrow=c(1,3),mar=c(3,3,3,1),mgp=c(2,1,0))
on.exit(par(oldpar))
rimage(data[1,,11,], main="first T1w image")
rimage(data[9,,11,], main="first MTw image")
rimage(data[15,,11,], main="first PDw image")
}
#
# Estimate Parameters in the ESTATICS model
#
modelMPM <- estimateESTATICS(mpm, method = "NLR")
#
# Parameter maps and residual standard deviation
#
z <- extract(modelMPM,c("rsigma","modelCoeff"))
if(require(adimpro)){
rimage.options(ylab = "z")
par(mfrow=c(1,5),mar=c(3,3,3,1),mgp=c(2,1,0))
rimage(z$modelCoeff[1,,11,], main="S_T1")
rimage(z$modelCoeff[2,,11,], main="S_MT")
rimage(z$modelCoeff[3,,11,], main="S_PD")
rimage(z$modelCoeff[4,,11,], main="R2star")
rimage(z$rsigma[,11,], main="Residual sd")
}
#
# Compute quantitative maps (R1, R2star, PD, MT)
#
qMRIMaps <- calculateQI(modelMPM,
b1File = B1File,
TR2 = 3.4)
#
# resulting quantitative maps for central coronal slice
#
if(require(adimpro)){
rimage.options(zquantiles=c(.01,.99), ylab="z")
par(mfrow=c(2,4),mar=c(3,3,3,1),mgp=c(2,1,0))
nmaps <- c("R1","R2star","PD","MT")
qmap <- extract(qMRIMaps,nmaps)
for (i in 1:4) rimage(qmap[[i]][,11,],main=nmaps[i])
}
par(oldpar)
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