readMPMData: Read experimental Multi-Parameter Mapping (MPM) data.

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

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, 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

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)

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