qMRI (version 1.2.7)

MREdisplacement: Calculate the motion induced signal phase for IR-MRE in biphasic material

Description

The function takes magnitude images and phase images (as NIfTI files) recordet with inversion IT1=Inf and a second inversion time IT2 that nulls the fluid signal. Tissue parameters (Relaxation rates) are extracted from an object of class "IRmixed" calculated from data of a related IRMRI experiment.

Usage

MREdisplacement(MagnFiles1, PhaseFiles1, MagnFiles2, PhaseFiles2, TI2 = 2400,
                IRmixobj, method = c("full", "approx"),rescale=FALSE,verbose=FALSE)

Value

A list of class "IRMREbiphasic" with components

phisolid

displacement solid

phifluid

displacement fluid

Arguments

MagnFiles1

Filenames of magnitude images recorded with inversion time IT=Inf .

PhaseFiles1

Filenames of phase images recorded with inversion time IT=Inf .

MagnFiles2

Filenames of magnitude images recorded with inversion time IT=IT2.

PhaseFiles2

Filenames of phase images recorded with inversion time IT=IT2 .

TI2

Inversion time used for MagnFiles2 and PhaseFiles2. IT2 should be selected to extinguish the signal intendity for fluid.

IRmixobj

Object of class "IRmixed" obtained from a related IRMRI experiment.

method

Either "full" or "approx"

rescale

Logical, do we need to rescale phase images ?

verbose

Report scale range of phase images

Author

Karsten Tabelow
J\"org Polzehl

Details

The first 4 arguments need to be vectors of filenames of identical length with files containing compatible 3D NIfTI images. Object IRmixobj needs to contain a components segm and Rx of compatible dimension that need to be registered to the MRE images.

See Also

estimateIRfluid, estimateIRsolid, estimateIRsolidfixed,smoothIRSolid

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (MagnFiles1, PhaseFiles1, MagnFiles2, PhaseFiles2, TI2 = 2400, 
    IRmixobj, method = c("full", "approx"), verbose = FALSE) 
{
    segm <- IRmixobj
    sdim <- dim(segm)
    nfiles <- length(MagnFiles1)
    if (length(PhaseFiles1) != nfiles || length(MagnFiles2) != 
        nfiles || length(PhaseFiles2) != nfiles) {
        stop("Incompatible lengths of filelists")
    }
    imgdim1 <- readNIfTI(MagnFiles1, read_data = FALSE)@dim_[2:4]
    imgdim2 <- readNIfTI(MagnFiles2, read_data = FALSE)@dim_[2:4]
    imgdim3 <- readNIfTI(PhaseFiles1, read_data = FALSE)@dim_[2:4]
    imgdim4 <- readNIfTI(PhaseFiles2, read_data = FALSE)@dim_[2:4]
    if (any(imgdim1 != sdim) || any(imgdim2 != sdim) || any(imgdim3 != 
        sdim) || any(imgdim4 != sdim)) {
        stop("Incompatible image dimensions")
    }
    Mimg1 <- Mimg2 <- phiimg1 <- phiimg2 <- array(0, c(sdim, 
        nfiles))
    for (i in 1:nfiles) {
        Mimg1[, , , i] <- readNIfTI(MagnFiles1, reorient = FALSE)@.Data
        phiimg1[, , , i] <- readNIfTI(PhaseFiles1, reorient = FALSE, 
            rescale = FALSE)@.Data
        Mimg2[, , , i] <- readNIfTI(MagnFiles2, reorient = FALSE)@.Data
        phiimg2[, , , i] <- readNIfTI(PhaseFiles2, reorient = FALSE, 
            rescale = FALSE)@.Data
        rngimg <- range(phiimg1, phiimg2)
        cat("range of phase images", rngimg, "\n")
        phiimg1 <- phiimg1/max(abs(rngimg)) * pi
        phiimg2 <- phiimg2/max(abs(rngimg)) * pi
    }
    Rf <- IRmixobj$Rf
    R1x <- IRmixobj$Rx
    masksolid <- segm > 1
    CCs <- array(1 - 2 * exp(-TI2 * R1x), dim(Mimg1))
    CCf <- array(1 - 2 * exp(-TI2 * Rf), dim(Mimg1))
    masks <- array(masksolid[, , 2:6], dim(Mimg1))
    if ("full" %in% method) {
        ss <- CCf * Mimg1 * sin(phiimg1) - Mimg2 * sin(phiimg2)
        cs <- CCf * Mimg1 * cos(phiimg1) - Mimg2 * cos(phiimg2)
    }
    else {
        ss <- -Mimg2 * sin(phiimg2)
        cs <- -Mimg2 * cos(phiimg2)
    }
    sf <- -CCs * Mimg1 * sin(phiimg1) + Mimg2 * sin(phiimg2)
    cf <- -CCs * Mimg1 * cos(phiimg1) + Mimg2 * cos(phiimg2)
    phis <- atan2(cs, ss)
    phif <- atan2(cf, sf)
    phis[!masks] <- 0
    phif[!masks] <- 0
  }