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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)
List with components
mpm data
dimension of image cube
number of images / image files
character - filenames of t1Files
character - filenames of pdFiles
character - filenames of mtFiles
Number of the ESTATICS model that can be used
character - filenames of maskFile
mask
vector of TR values
vector of TE values
vector of FA values
and class-attribute 'mpmData'
Vector of filenames corresponding to T1 weighted images (in Nifti-Format) with varying TE
Vector of filenames corresponding to PD weighted images (in Nifti-Format) with varying TE
optional Vector of filenames corresponding to MT weighted images (in Nifti-Format) with varying TE
optional filename for mask (in Nifti-Format)
optional numeric TR vector, if omitted information is extracted from .nii files if possible
optional numeric TE vector, if omitted information is extracted from .nii files if possible
optional numeric FA (flip-angle) vector, if omitted information is extracted from .nii files if possible
optional weights for MPM data volumes. Only needed is volumes have different data variance, e.g., in case of averages of multiple acquisitions.
logical - provide information on progress
Karsten Tabelow tabelow@wias-berlin.de
J\"org Polzehl polzehl@wias-berlin.de
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.
estimateESTATICS
, calculateQI
,
smoothESTATICS
, writeESTATICS
,
awsLocalSigma
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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