#!/bin/bash

data='fsga_data.csv'
tdf=$(mktemp)
echo "internal_id_fac,icv" > ${tdf}
for x in $(tail -n +2 ${data} | awk -F',' '{print $1}'); do
        icv=$(grep EstimatedTotalIntraCranialVol /old_nas/subjects/${x}/stats/aseg.stats | awk -F', ' '{print $4}')
        echo "${x},${icv}" >> ${tdf}
done

echo "read.csv('${tdf}') -> x" > convert.r
echo "x\$zICV <- (x\$icv - mean(x\$icv))/sd(x\$icv)" >> convert.r
echo "xw <- x[c(1,3)]" >> convert.r
echo "write.csv(xw, file='icvs.csv', row.names=FALSE, quote=FALSE)" >> convert.r

Rscript convert.r