readMPMData: Read experimental Multi-Parameter Mapping (MPM) data.
In WIAS-BERLIN/qMRI: Methods for Quantitative Magnetic Resonance Imaging ('qMRI')

readMPMData

R Documentation

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 tabelow@wias-berlin.de
J\"org Polzehl polzehl@wias-berlin.de

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.

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)

WIAS-BERLIN/qMRI documentation built on March 28, 2024, 5:33 a.m.