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#%%%%% Fichier test 1.1 : loading NIFTI files and convert them to carto3D and MRIaggr object
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# setwd("V:/etude25/2891")
require(MRIaggr)
path <- system.file(file.path("nifti"), package = "MRIaggr")
#### A- conversion to Carto3D then to IRMaggr ####
#### 1- Import ####
#### manual ####
nifti.Pat1_MTT_t0 <- readMRI(file.path(path, "MTT_t0"), format = "nifti")
nifti.Pat1_TTP_t0 <- readMRI(file.path(path, "TTP_t0"), format = "nifti")
nifti.Pat1_MTT_t1 <- readMRI(paste(path, "MTT_t1", sep = "/"), format = "nifti")
nifti.Pat1_TTP_t1 <- readMRI(paste(path, "TTP_t1", sep = "/"), format = "nifti")
nifti.Pat1_DWI_t0 <- readMRI(paste(path, "DWI_t0", sep = "/"), format = "nifti")
nifti.Pat1_T1_t0 <- readMRI(paste(path, "T1_t0", sep = "/"), format = "nifti")
nifti.Pat1_T2_GRE_t0 <- readMRI(paste(path, "T2_GRE_t0", sep = "/"), format = "nifti")
nifti.Pat1_T2_FLAIR_t2 <- readMRI(paste(path, "T2_FLAIR_t2", sep = "/"), format = "nifti")
nifti.Pat1_MASK_DWI_t0 <- readMRI(paste(path, "MASK_DWI_t0", sep = "/"), format = "nifti")
nifti.Pat1_MASK_T2_FLAIR_t2 <- readMRI(paste(path, "MASK_T2_FLAIR_t2", sep = "/"), format = "nifti")
#### automatic ####
param_nifti <- unlist(strsplit(list.files(path), split = ".nii" , fixed = TRUE))
n.files <- length(param_nifti)
for(iter_file in 1:n.files){
assign(x = paste("nifti.Pat1_", param_nifti[iter_file], sep = ""),
value = readMRI(paste(path, param_nifti[iter_file], sep = "/"),
format = "nifti")
)
}
#### display ####
fields::image.plot(nifti.Pat1_DWI_t0[,,1,1])
#### 2- conversion from nifti to Carto3D ####
#### manual ####
ls.Carto3D.Pat1 <- list()
ls.Carto3D.Pat1$MTT_t0 <- constCarto3D(nifti.Pat1_MTT_t0,
identifier = "Pat1", param = "MTT_t0")
ls.Carto3D.Pat1$TTP_t0 <- constCarto3D(nifti.Pat1_TTP_t0,
identifier = "Pat1", param = "TTP_t0")
ls.Carto3D.Pat1$MTT_t1 <- constCarto3D(nifti.Pat1_MTT_t1,
identifier = "Pat1", param = "MTT_t1")
ls.Carto3D.Pat1$TTP_t1 <- constCarto3D(nifti.Pat1_TTP_t1,
identifier = "Pat1", param = "TTP_t1")
ls.Carto3D.Pat1$MASK_DWI_t0 <- constCarto3D(nifti.Pat1_MASK_DWI_t0,
identifier = "Pat1", param = "MASK_DWI_t0")
ls.Carto3D.Pat1$MASK_T2_FLAIR_t2 <- constCarto3D(nifti.Pat1_MASK_T2_FLAIR_t2,
identifier = "Pat1", param = "MASK_T2_FLAIR_t2")
ls.Carto3D.Pat1$T1.H0 <- constCarto3D(nifti.Pat1_T1_t0,
identifier = "Pat1", param = "T1_t0")
ls.Carto3D.Pat1$T2_GRE.H0 <- constCarto3D(nifti.Pat1_T2_GRE_t0,
identifier = "Pat1", param = "T2_GRE_t0")
multiplot(ls.Carto3D.Pat1$T1.H0)
#### automatic ####
ls.Carto3D.Pat1 <- list()
for(iter_file in 1:n.files){
eval(parse(text=paste(
"ls.Carto3D.Pat1[[iter_file]] <- constCarto3D(nifti.Pat1_", param_nifti[iter_file],",
identifier = \"Pat1\", param = param_nifti[iter_file])",
sep = "")))
}
names(ls.Carto3D.Pat1) <- param_nifti
#### display
multiplot(ls.Carto3D.Pat1[[1]], num = 1,
window = FALSE)
multiplot(ls.Carto3D.Pat1[[1]], num = 1:3,
window = FALSE)
multiplot(ls.Carto3D.Pat1[[1]], num = 1:3, axes = FALSE, legend = FALSE,
window = FALSE)
#### 3- conversion from Carto3D to MRIaggr ####
MRIaggr.Pat1 <- Carto3D2MRIaggr(ls.Carto3D = ls.Carto3D.Pat1,
rm.Carto3D = TRUE)
#### display
multiplot(MRIaggr.Pat1, num = 1:3, param = "DWI_t0",
window = FALSE)
multiplot(MRIaggr.Pat1, num = 1:3, param = "DWI_t0",
window = FALSE, axes = FALSE)
#### B- Direct conversion to MRIaggr ####
#### B1- import ####
param_nifti <- unlist(strsplit(list.files(path), split = ".nii", fixed = TRUE))
n.files <- length(param_nifti)
ls.array <- list()
for(iter_file in 1:n.files){
ls.array[[iter_file]] <- readMRI(paste(path, param_nifti[iter_file], sep = "/"),
format = "nifti")
}
#### display
fields::image.plot(ls.array[[1]][,,1,1])
#### B2- conversion to MRIaggr ####
MRIaggr.Pat1 <- constMRIaggr(ls.array = ls.array,
identifier = "Pat1", param = param_nifti,
default_value = NULL, pos_default_value = c(1,1,1),
rm.ls.array = TRUE)
#### display
multiplot(MRIaggr.Pat1, num = 1:3, param = "DWI_t0",
window = FALSE, legend = FALSE)
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