readMPMData function

Read experimental Multi-Parameter Mapping (MPM) data.

Read experimental Multi-Parameter Mapping (MPM) data.

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

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

Returns

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'

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.

Author(s)

Karsten Tabelow tabelow@wias-berlin.de

J"org Polzehl polzehl@wias-berlin.de

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)
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