R Under development (unstable) (2024-05-21 r86580 ucrt) -- "Unsuffered Consequences"
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Platform: x86_64-w64-mingw32/x64

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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(2, reprt = FALSE)
> modelMPMsp1 <- smoothESTATICS(modelMPM,
+                               kstar = 16,
+                               alpha = 0.004,
+                               patchsize=1,
+                               verbose = FALSE)
> #
> #  Compute quantitative maps (R1, R2star, PD, MT)
> #
> qMRIMaps <- calculateQI(modelMPM,
+                         b1File = B1File,
+                         TR2 = 3.4)
reading B1 correction file
calculating R1 ... Spoiling correction ... v3* 0.8mm R4 protocol
Spoiling correction ... v3* 0.8mm R4 protocol
done
calculating PD ... done
calculating MT ... done
> qMRISmoothedp1Maps <- calculateQI(modelMPMsp1,
+                                     b1File = B1File,
+                                     TR2 = 3.4)
reading B1 correction file
calculating R1 ... Spoiling correction ... v3* 0.8mm R4 protocol
Spoiling correction ... v3* 0.8mm R4 protocol
done
calculating PD ... done
calculating MT ... done
> #
> #   some statistics on differences between results
> #
> qm <- extract(qMRIMaps,c("R1","R2star","MT","PD"))
> qms <- extract(qMRISmoothedp1Maps,c("R1","R2star","MT","PD"))
> mask <- extract(mpm,"mask")
> cat("mean of estimated quantitative maps\n",
+     mean(qm$R1[mask]), mean(qm$R2star[mask]), mean(qm$MT[mask]), mean(qm$PD[mask]),"\n",
+     "mean of smoothed quantitative maps\n",
+     mean(qms$R1[mask]), mean(qms$R2star[mask]), mean(qms$MT[mask]), mean(qms$PD[mask]),"\n",
+     "Root mean squared difference between estimated and smoothed quantitative maps\n",
+     sqrt(mean((qm$R1-qms$R1)[mask]^2)), sqrt(mean((qm$R2star-qms$R2star)[mask]^2)),
+     sqrt(mean((qm$MT-qms$MT)[mask]^2)), sqrt(mean((qm$PD-qms$PD)[mask]^2)),"\n")
mean of estimated quantitative maps
 0.7799036 18.0383 0.891752 5740.898 
 mean of smoothed quantitative maps
 0.768893 17.87941 0.8579759 5682.832 
 Root mean squared difference between estimated and smoothed quantitative maps
 0.1163028 6.352211 0.2703803 564.6314 
> # set mask to y==11 only yo save time
> # reduce mask to save time, need also to adapt storage of data
> mask <- extract(mpm,"mask")
> mask[,c(1:10,12:21),] <- FALSE
> mpm <- qMRI:::setMPMmask(mpm, mask)
> # Alternatively using Quasi-Likelihood
> sigma <- 50
> modelMPMQL <- estimateESTATICS(mpm, method = "QL",
+                 sigma = array(sigma, mpm$sdim), L = 1, verbose=FALSE)
> qMRIMapsQL <- calculateQI(modelMPMQL,
+                 b1File = B1File,
+                 TR2 = 3.4)
reading B1 correction file
calculating R1 ... Spoiling correction ... v3* 0.8mm R4 protocol
Spoiling correction ... v3* 0.8mm R4 protocol
done
calculating PD ... done
calculating MT ... done
> mask <- extract(mpm,"mask")
> qmQL <- extract(qMRIMapsQL,c("R1","R2star","MT","PD"))
> cat("mean of estimated quantitative maps using QL\n",
+     mean(qmQL$R1[mask]), mean(qmQL$R2star[mask]), mean(qmQL$MT[mask]), mean(qmQL$PD[mask]),"\n")
mean of estimated quantitative maps using QL
 0.7726694 18.72987 0.9158866 5774.011 
> 
> proc.time()
   user  system elapsed 
  28.37    0.82   31.23