Create named means csv (all regions & striatal subset)

Symlink all individual means files to one directory

for i in `ls -d /data/joy/BBL/projects/beardt2star/output/*`; do 
  home=/data/joy/BBL/projects/beardt2star/
  bblid=`echo $i | cut -d "/" -f 8`

  if [ -e $home/output/$bblid/${bblid}_t2star_ROI.csv ]; then
    ln -s $home/output/$bblid/${bblid}_t2star_ROI.csv $home/means
  fi

done

Set up root directory

knitr::opts_knit$set(root.dir = '/data/joy/BBL')

Load in files

bblids <- read.csv("./projects/beardt2star/n1514_bblids.csv")
names <- read.csv("./studies/pnc/n1601_dataFreeze2016/neuroimaging/pncTemplate/jlf/OASIS30Labels.csv")

#this file was created using /home/arosen/adroseHelperScripts/bash/mergeCSV.sh
means <- read.csv("./projects/beardt2star/means/n1514_means_unnamed.csv")

Remove non-volume information

means_regions <- subset(means, select=-c(1:2))

Replace names with region names

colnames(means_regions) <- names$Label.Name

Subset for only striatal regions

means_striatum <- subset(means_regions, select = c("Right Pallidum","Left Pallidum","Right Accumbens Area","Left Accumbens Area","Right Caudate","Left Caudate","Right Putamen","Left Putamen"))

Merge with BBLID

means_final <-as.data.frame(cbind(bblids,means_striatum))

Write out csv for all means and for striatal means

write.csv(means_regions, "/data/joy/BBL/projects/beardt2star/means/n1514_means_named.csv",row.names=FALSE)
write.csv(means_final, "/data/joy/BBL/projects/beardt2star/means/n1514_striatalMeans.csv",row.names=FALSE)