readMPMData {qMRI}

Read experimental Multi-Parameter Mapping (MPM) data.

Description

The function reads data generated in Multimodal Parameter Mapping (MPM) experiments.

Usage

readMPMData(t1Files = NULL, pdFiles = NULL, mtFiles = NULL, maskFile = NULL,
            TR = NULL, TE = NULL, FA = NULL, wghts = NULL, verbose = TRUE)

Arguments

t1Files

Vector of filenames corresponding to T1 weighted images (in Nifti-Format) with varying TE

pdFiles

Vector of filenames corresponding to PD weighted images (in Nifti-Format) with varying TE

mtFiles

optional Vector of filenames corresponding to MT weighted images (in Nifti-Format) with varying TE

maskFile

optional filename for mask (in Nifti-Format)

TR

optional numeric TR vector, if omitted information is extracted from .nii files if possible

TE

optional numeric TE vector, if omitted information is extracted from .nii files if possible

FA

optional numeric FA (flip-angle) vector, if omitted information is extracted from .nii files if possible

wghts

optional weights for MPM data volumes. Only needed is volumes have different data variance, e.g., in case of averages of multiple acquisitions.

verbose

logical - provide information on progress

Value

List with components

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

and class-attribute 'mpmData'

Author(s)

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

References

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 and K. Tabelow (2023), Magnetic Resonance Brain Imaging: Modeling and Data Analysis Using R, 2nd Edition, Chapter 6, Springer, Use R! Series. <doi:10.1007/978-3-031-38949-8_6>.

J. Polzehl and K. Tabelow (2023), Magnetic Resonance Brain Imaging - Modeling and Data Analysis Using R: Code and Data. <doi:10.20347/WIAS.DATA.6>.

See Also

estimateESTATICS, calculateQI, 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, "mask.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)