Coded By Stron

#Coded By Stron Stiglitz
#Subscrible :D
#fb.com/stron.msf

# INITIALIZATION
setwd("D:/Google Drive/Paper/ANALYSIS")

# Read in Data

THICK <- read.delim("THICK.txt", sep = ",",header=FALSE)
AREA <-
VOLUME <-


# Lobe Segmentation (AAL)
# Read in lobes_AAL Matrix
lobes_AAL <- read.delim("lobes_AAL.txt",sep = ",")

# AAL Mask Creation
ROIs = read.delim("roiMatrix_AAL_single.txt",sep=",")  # Manually created file
ROI_Mask = matrix()
outROIMatrix = matrix()

for (j in 1 :ncol(ROIs)) { # outROIMatrix created
    for (i in 1:ncol(lobes_AAL)) {
        if (lobes_AAL[i] == ROIs[j,1]) {
            ROI_Mask[i] = 1
        } else
            ROI_Mask[i] = 0
    }
    outROIMatrix[j,] = as.integer(as.logical((ROI_Mask)))
}


# LOBAR MEANS (for tickness, area, volume)

# Preload *Matrices
    ROI_THICKmasks = matrix()
    ROI_AREAmasks = matrix()
    ROI_VOLmasks = matrix()

    ROI_THICKmeans = matrix()
    ROI_AREAmeans = matrix()
    ROI_VOLmeans = matrix()

#(SubjectMeans,ROI) fot Thickness, Area, Volume

# THickness
for (j in 1:78) { #loop over ROIS
    for (i in 1:30) { #loop over subjects
        temp = THICK[i,]*outROIMatrix[j,]
        temp = tenp(find(outROIMatrix[j,]))
        ROI_THICKmeans[i,j] <- mean(temp)
    }
}

# AREA
for j=1:78 %loop over ROIS
    for i=1:30 %loop over subjects
        temp = AREA(i,)*outROIMatrix[j,]
        temp = temp(find(outROIMatrix[j,]))
        ROI_AREAmeans[i,j] = mean(temp)
    end
end

# VOLUME
for j =1:78 %loop over ROIS
    for i=1:30 %loop over subjects
        temp = VOLUME[i,]*outROIMatrix[,j]
        temp = temp(find(outROIMatrix[j,]))
        ROI_VOLmeans[i,j] = mean(temp)
    end
end

# Correlation Matrices (Thickness, Area, Volume)
ROI_THUCKcorr <- cor(ROI_THICKmeans)
write(ROI_THICKcorr, file = "ROI_THICKcorr.txt")

ROI_AREAcorr <- cor(ROI_AREAmeans);
write(ROI_AREAcorr, file = "ROI_AREAcorr.txt")

ROI_VOLcorr <- cor(ROI_VOLmeans);
write(ROI_VOLcorr, file = "ROI_VOLcorr.txt")


# Avarage Correlation?
THICKtriangle <- ROI_THICKcorr(find(~tril(ones(size(ROI_THICKcorr)))));
THICK_meancorr <- mean(THICKtriangle)  # 0.004654 Bonferroni

AREAtriangle <- RIU_AREAcorr(find(~tril(ones(size(ROI_AREAcorr)))));
AREA_meancorr <- mean(AREAtriangle)  # 0.0035473 Bonferroni

VOLtriangle <- ROI_VOLcorr(find(~tril(ones(size(ROI_VOLcorr)))));
VOL_meancorr <- mean(VOLtriangle)  # 0.003728 Bonferroni