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Copy pathCreatMatrix_dpabi2Func&Anat.R
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CreatMatrix_dpabi2Func&Anat.R
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################################
library(gifti)
library(freesurferformats)
###############################
data <- 'AnatSurfWThickness/'
FileName <- list.files(data)
FileAll <- lapply(FileName, function(x)
strsplit(x, '_')[[1]][1])
Files <- unique(unlist(FileAll))
for (i in Files) dir.create(i)
GiiFiles <- list.files(data, pattern = '.gii', full.names = T)
for (i in GiiFiles){
Files = unlist(strsplit(i, '//'))
Mid = strsplit(Files[2], '_')[[1]][1]
New = vector(); New[1] = Files[1]; New[2] = Mid; New[3] = Files[2]
NewFile = paste(New, collapse = '//')
file.rename(i, NewFile)
}
#############################################################################
Input.path <- 'FunSurfWIglobalCF/'; Output.path <- 'NetFun/'
Template.l5.annot <- 'fsaverage5/label/lh.aparc.a2009s.annot'
Template.r5.annot <- 'fsaverage5/label/rh.aparc.a2009s.annot'
Template.l5 <- read.fs.annot(Template.l5.annot)
Template.r5 <- read.fs.annot(Template.r5.annot)
Subs <- list.dirs(Input.path, full.names = F, recursive = F)
RoiList.l.all <- Template.l5$colortable_df$struct_name
# x[! x %in% c('A', 'D', 'E')]
RoiList.l <- RoiList.l.all[! RoiList.l.all %in% c('Unknown', 'Medial_wall')]
RoiList.r.all <- Template.r5$colortable_df$struct_name
RoiList.r <- RoiList.r.all[! RoiList.r.all %in% c('Unknown', 'Medial_wall')]
RoiOderKey <- data.frame(
Index = seq(1,148),
Hemi = c(rep('LH', 74), rep('RH', 74)),
RoiName = c(RoiList.l, RoiList.r)
)
write.csv(RoiOderKey, 'ROI_CenterOfMass.csv')
#############################################################################
## function prepare
for (i in Subs){
# files
Func.l.file = list.files(file.path(Input.path, i), pattern = 'L', full.names = T)
Func.r.file = list.files(file.path(Input.path, i), pattern = 'R', full.names = T)
Func.l = readgii(Func.l.file); Func.l = as.data.frame(Func.l$data)
Func.r = readgii(Func.r.file); Func.r = as.data.frame(Func.r$data)
TimeSeries <- dim(Func.l)[2]
df.r <- df.l <- matrix(NA, nrow = TimeSeries, ncol = length(RoiList.l))
# LH roi list
for (k in seq_along(RoiList.l)){
RoiMask <- Template.l5$label_names == RoiList.l[k]
df.l[,k] <- colMeans(Func.l[RoiMask, ])
}
# RH roi list
for (w in seq_along(RoiList.r)){
RoiMask <- Template.r5$label_names == RoiList.r[w]
df.r[,w] <- colMeans(Func.r[RoiMask, ])
}
# matrix
df <- cbind(df.l, df.r)
df.cor <- cor(df, method = 'pearson')
write.table(df.cor, paste0(Output.path, 'ROICorrelation_', i, '.txt'),
col.names = F, row.names = F)
}
#############################################################################
Input.path <- 'AnatSurfWThickness/'; Output.path <- 'NetAnat/'
Template.l5.annot <- 'fsaverage5/label/lh.aparc.a2009s.annot'
Template.r5.annot <- 'fsaverage5/label/rh.aparc.a2009s.annot'
Template.l5 <- read.fs.annot(Template.l5.annot)
Template.r5 <- read.fs.annot(Template.r5.annot)
Subs <- list.dirs(Input.path, full.names = F, recursive = F)
RoiList.l.all <- Template.l5$colortable_df$struct_name
# x[! x %in% c('A', 'D', 'E')]
RoiList.l <- RoiList.l.all[! RoiList.l.all %in% c('Unknown', 'Medial_wall')]
RoiList.r.all <- Template.r5$colortable_df$struct_name
RoiList.r <- RoiList.r.all[! RoiList.r.all %in% c('Unknown', 'Medial_wall')]
#############################################################################
## anat prepare
df <- matrix(nrow = length(Subs), ncol = 149)
for (i in seq_along(Subs)){
# files
Anat.l.file = list.files(file.path(Input.path, Subs[i]), pattern = 'L', full.names = T)
Anat.r.file = list.files(file.path(Input.path, Subs[i]), pattern = 'R', full.names = T)
Anat.l = readgii(Anat.l.file); Anat.l = as.vector(Anat.l$data$unknown)
Anat.r = readgii(Anat.r.file); Anat.r = as.vector(Anat.r$data$unknown)
df[i,1] = Subs[i]
# LH roi list
for (k in seq_along(RoiList.l)){
RoiMask <- Template.l5$label_names == RoiList.l[k]
df[i,k+1] <- round(mean(Anat.l[RoiMask]), 5)
}
# RH roi list
for (w in seq_along(RoiList.r)){
RoiMask <- Template.r5$label_names == RoiList.r[w]
df[i, w+75] <- round(mean(Anat.r[RoiMask]), 5)
}
}
colnames(df) <- c('SubId', paste0('lh_', RoiList.l), paste0('rh_', RoiList.r))
df <- as.data.frame(df)
write.csv(df, paste0(Output.path, 'aparc.a2009s_both_thickness.csv'), row.names = F)
## end