**This is an old revision of the document!**

# How to correct by Intracranial Volume (ICV)

I'm going to suppose you did the pipeline thing over your MRI images and you already have the *study_mri.csv* file. The Freesurfer version I'm using makes an estimation of Intracraneal volume and the pipeline scripts put it as *EstimatedTotalIntraCranialVol_eTIV* into the results file. First do this for a real CSV file:

$ sed 's/;/,/g' ab255_mri.csv > ab255_mri_rc.csv

Let's say we want to get the hippocampus volume (HV) corrected by ICV. Then we must get Left and Right HV and calculate its medium value. **HV = 0.5*(HVR+HVL)**

Now first step is to fit a straight line for HV *vs* ICV and the ICV mean value (<ICV>). The adjusted HV will be **aHV = HV - b*(ICV-<ICV>)**, with *b* as the regression coefficient of HV *vs* ICV.

Now we need to get the data. Let's try it in R.

x <- read.csv("ab255_mri_rc.csv")
x$HV = 0.5*(x$"Right.Hippocampus"+x$"Left.Hippocampus")
a <- lm(x$HV~x$"EstimatedTotalIntraCranialVol_eTIV")
b=a$coefficients[[2]]
x$aHV = x$HV - b*(x$EstimatedTotalIntraCranialVol_eTIV - mean(x$EstimatedTotalIntraCranialVol_eTIV, na.rm=TRUE))
write.csv(x, file="ab255_mri_aHV.csv")

### For ADNIMERGE package

library("ADNIMERGE")
a <- lm(adnimerge$Hippocampus~adnimerge$ICV)
adnimerge$adj.Hippocampus = adnimerge$Hippocampus - a$coefficients[[2]]*(adnimerge$ICV - mean(adnimerge$ICV, na.rm=T))