estimateIR | R Documentation |
Parameter estimation ( intensity, relaxation rate, proportion of fluid) in Inversion Recovery MRI data.
estimateIR(IRdataobj, TEScale = 100, dataScale = 1000, method = c("NLR", "QL"),
varest = c("RSS","data"), fixed = TRUE, smoothMethod=c("PAWS","Depth"),
kstar = 24, alpha = .025, bysegment = TRUE, verbose = TRUE)
IRdataobj |
4D array of IRMRI signals. First dimension corresponds to Inversion times (InvTime). |
TEScale |
Internal scale factor for Echo Times. This influences parameter scales in numerical calculations. |
dataScale |
Internal scale factor for MR signals. This influences parameter scales in numerical calculations. |
method |
Either |
varest |
Method to, in case of |
fixed |
Should adaptive smoothing performed for Sx and Rx maps and fx maps reestimated afterwards ? |
smoothMethod |
Either "PAWS" or "Depth". the second option is not yet implemented. |
kstar |
number of steps used in PAWS |
alpha |
significance level for decisions in aws algorithm (suggestion: between 1e-5 and 0.025) |
bysegment |
|
verbose |
Logical. Provide some runtime diagnostics. |
This function implements the complete pipeline of IRMRI anlysis.
List of class "IRmixed"
with components
IRdata |
4D array containing the IRMRI data, first dimension refers to inversion times |
InvTimes |
vector of inversion times |
segm |
segmentation codes, 1 for CSF, 2 for GM, 3 for WM, 0 for out of brain |
sigma |
noise standard deviation, if not specified estimated fron CSF areas in image with largest inversion time |
L |
effective number of coils |
fx |
Array of fluid proportions |
Sx |
Array of maximal signals |
Rx |
Array of relaxation rates |
Sf |
Global estimate of maximal fluid signal |
Rf |
Global estimate of fluid relaxation rate |
ICovx |
Covariance matrix of estimates |
sigma |
Array of provided or estimated noise standard deviations |
Convx |
Array of convergence indicators |
rsdx |
Residual standard deviations |
The arrays contain entries for all voxel with segments%in%1:3
.
Karsten Tabelow tabelow@wias-berlin.de
J\"org Polzehl polzehl@wias-berlin.de
estimateIRfluid
, estimateIRsolid
, estimateIRsolidfixed
,smoothIRSolid
##---- 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 (IRdata, InvTimes, segments, fixed = TRUE, smoothMethod = c("Depth",
"PAWS"), bw = 5, TEScale = 100, dataScale = 1000, method = c("NLR",
"QL"), sigma = NULL, L = 1, maxR2star = 50, varest = c("RSS",
"data"), verbose = TRUE)
{
ergsFluid <- estimateIRfluid(IRdata, InvTimes, segments)
Sfluid <- median(ergsFluid$Sfluid)
Rfluid <- median(ergsFluid$Rfluid)
ergsBrain <- erstimateIRsolid(IRdata, InvTimes, segments,
Sfluid, Rfluid)
if (fixed) {
if (smmothMethod == "Depth") stop("not yet implemented")
# ergsSmooth <- SdepthSmooth(ergsBrain, segments)
if (smmothMethod == "PAWS")
ergsSmooth <- vpawscov2(ergsBrain, segments)
}
ergsSmooth
}
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