R Under development (unstable) (2024-12-03 r87418 ucrt) -- "Unsuffered Consequences"
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> old <- options(warn=1)
> on.exit(options(old))
> suppressMessages(library(qMRI))
> 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
> #
> mpm <- readMPMData(t1Files, pdFiles, mtFiles,
+                    maskFile, TR = TR, TE = TE,
+                    FA = FA, verbose = FALSE)
> #
> #  Estimate Parameters in the ESTATICS model
> #
> modelMPM <- estimateESTATICS(mpm, method = "NLR", verbose=FALSE)
> #
> #  smooth maps of ESTATICS Parameters
> #
> setCores(1, reprt = FALSE)
> modelMPMsp1 <- smoothESTATICS(modelMPM,
+                               kstar = 16,
+                               alpha = 0.004,
+                               patchsize=1,
+                               verbose = FALSE)