calculateQI: Obtain quantitative maps from estimated ESTATICS parameters.

In neuroconductor-devel-releases/qMRI: Methods for Quantitative Magnetic Resonance Imaging ('qMRI')

Description

Quantitaive imaging parameters are calculated from the estimated parameters in the ESTATICS model. This involves a correction for magnetic field inhomogeneities if the information is provided in argument b1File and use of a second of a second recovery delay TR2 in case of Dual-Exitation FLASH measurements (Helms 2008).

Usage

calculateQI(mpmESTATICSModel, b1File = NULL, TR2 = 0, verbose = TRUE)

Arguments

mpmESTATICSModel	Object of class 'ESTATICSModel' as returned from function estimateESTATICS.
b1File	(optional) Name of a file containing a B1-field inhomogeneity map (.nii)
TR2	second recovery delay TR2 in case of Dual-Exitation FLASH measurements.
verbose	logical: Monitor process.

Value

List with components

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

and class-attribute 'qMaps' .

Author(s)

Karsten Tabelow [e-mail]
J\"org Polzehl [e-mail]

References

Helms, G.; Dathe, H.; Kallenberg, K. & Dechent, P. High-Resolution Maps of Magnetization Transfer with Inherent Correction for RF Inhomogeneity and T1 Relaxation Obtained from 3D FLASH MRI Magn. Res. Med., 2008, 60, 1396-1407

Weiskopf, N.; Suckling, J.; Williams, G.; Correia, M. M.; Inkster, B.; Tait, R.; Ooi, C.; Bullmore, E. T. & Lutti, A. Quantitative multi-parameter mapping of R1, PD(*), MT, and R2(*) at 3T: a multi-center validation. Front Neurosci, Wellcome Trust Centre for Neuroimaging, UCL Institute of Neurology, University College London, UK., 2013, 7, 95

J. Polzehl, K. Tabelow (2019). Magnetic Resonance Brain Imaging: Modeling and Data Analysis Using R. Springer, Use R! series. Doi:10.1007/978-3-030-29184-6.

See Also

readMPMData, estimateESTATICS, smoothESTATICS, writeESTATICS, awsLocalSigma

Examples

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)
#
# limit calculations to voxel in the central coronal slice
# to reduce execution time of the example
#
#
#  Estimate Parameters in the ESTATICS model
#
modelMPM <- estimateESTATICS(mpm, method = "NLR")
#
#  resulting ESTATICS parameter maps for central coronal slice
#
if(require(adimpro)){
rimage.options(zquantiles=c(.01,.99), ylab="z")
oldpar <- par(mfrow=c(2,2),mar=c(3,3,3,1),mgp=c(2,1,0))
pnames <- c("T1","MT","PD","R2star")
modelCoeff <- extract(modelMPM,"modelCoeff")
for(i in 1:4){
   rimage(modelCoeff[i,,11,])
   title(pnames[i])
   }
}
#
#  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(2,2),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)
}

neuroconductor-devel-releases/qMRI documentation built on May 6, 2020, 12:42 a.m.