Viewslices.R

#!/usr/bin/Rscript

#dti_FA image is in dti.dti directory
#Note: in flsview the slice number is one less than R. If x = 45, then in fslview x = 44 
#Note: masks and FA images must be saved in the directory where R started. Use bash script "~/selectracts"
#subject 775353 IFL_R z 26, best(continous), x (non of them are continous)
#y slice sometimes looks a little zquich - size/location of each plot
#the dark color makes it a little slow

library(Rniftilib)
library(tcltk)
library(base)
library(Matrix)
library(lattice)
library(base)
#require(grDevices) 

#prints the header for comments text file
	write(sprintf("IDNUM POSITION SIDE COMMENTS"), file="comments.txt", append = TRUE)

#array of all the subject	
IDNUMS<-c(775511, 775353)

#loop into one subject at a time
for (id in 1:2) {
	ID<-print(IDNUMS[id])

	FA_Map <- nifti.image.read(file=sprintf("%s_dti_FA.nii.gz", ID), read_data=1)
	iLF_l <- nifti.image.read(file=sprintf("%s_ILF_L_fdt_thr.nii.gz", ID), read_data=1)
	iLF_r <- nifti.image.read(file=sprintf("%s_ILF_R_fdt_thr.nii.gz", ID), read_data=1)
	sLF_l <- nifti.image.read(file=sprintf("%s_SLF_L_fdt_thr.nii.gz", ID), read_data=1)
	sLF_r <- nifti.image.read(file=sprintf("%s_SLF_R_fdt_thr.nii.gz", ID), read_data=1)

	#prints track position: 19 is for s(superior), 9 is for i(inferior)
	for (p in c(9, 19)) {
	#print track side: 18 is for r (right side), 12 is for l (left side)
		for (s in c(12, 18)) {
		#prints superior first then inferior

		zhighest=0
		xhighest=0
		yhighest=0

		zv=0
		x=0
		y=0
		#the width and height of a single image
		x11(12,20)
		par(mfrow=c(1,3), ps = 30 )
			for (i in 1:64) {
			#prints z slice
				output<-nnzero(eval(parse(text = sprintf("%sLF_%s[,,i,1]", paste(letters[p]), paste(letters[s]) ))))
				if(output > zhighest) {
					zhighest=output
					zv=i
				}
			}
			image(z=FA_Map[,,zv,1], col=grey((0:32)/32), axes=FALSE, xlab = sprintf("z = %s", zv) )
			par(new=TRUE)
			image(eval(parse(text = sprintf("z=%sLF_%s[,,zv,1]", paste(letters[p]), paste(letters[s]) ))), col=topo.colors(7, alpha = 0.2), axes=FALSE)
			

			#prints the x slice
			for (i in 1:127) {
				output<-nnzero(eval(parse(text = sprintf("%sLF_%s[i,,,1]", paste(letters[p]), paste(letters[s])  ))))
				if(output > xhighest) {
					xhighest=output
					x=i
				}
			}
			image(z=FA_Map[x,,,1], col=grey((0:32)/32), axes=FALSE, xlab = sprintf("x = %s", x) )
			par(new=TRUE)
			image(eval(parse(text = sprintf("z=%sLF_%s[x,,,1]", paste(letters[p]), paste(letters[s]) ))), col=topo.colors(7, alpha = 0.2), axes=FALSE)
			par(new=FALSE)
			title(main = sprintf("%s  %sLF_%s",ID, toupper(paste(letters[p])), toupper(paste(letters[s]))), font.main = 2)

			#prints y slice
			for (i in 1:127) {
				output<-nnzero(eval(parse(text = sprintf("%sLF_%s[,i,,1]", paste(letters[p]), paste(letters[s]) ))))
				if(output > yhighest) {
					yhighest=output
					y=i
				}
			}
			image(z=FA_Map[,y,,1], col=grey((0:32)/32), axes=FALSE, xlab = sprintf("y = %s", y) )
			par(new=TRUE)
			image(eval(parse(text = sprintf("z=%sLF_%s[,y,,1]", paste(letters[p]), paste(letters[s]) ))), col=topo.colors(7, alpha = 0.2), axes=FALSE)
			par(new=FALSE)
			
	
		#gets user's input (Note: removing the question saves time, and lets the user see which slice they are viewing)
		  	#ans <- readline("Are these images acceptable? (y/n)")
			#if (ans=="n") {
			#com<-readline(sprintf("%s, %s position, %s side:", ID, toupper(paste(letters[p])), toupper(paste(letters[s])) ))
			#add brake to allow the user to answer the question before showing the next image
			# adds to a file located where R was started
	
			#maybe adding all SL, SR, IL, IR in one line ...
			#write(sprintf("%s   %s      %s    %s", ID, toupper(paste(letters[p])), toupper(paste(letters[s])), com), file="comments.txt", append = TRUE)
			#}
		
		}
	}
}

#notes:
#maybe if n is set to something, then close images - command
  #n <- ifelse(grepl("\\D",n),-1,as.integer(n))
  #if(is.na(n)){break}  # breaks when hit enter
#par new true is the opposite due to the lattice library requested