User Tools

Site Tools


neuroimagen:byicv

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

El paquete ADNIMERGE provee los valores de Hipoocampo (suma de ambos) e ICV. Puede corregirse directamente y dividirse entre 2 para obtener valores similares.

library("ADNIMERGE")
a <- lm(adnimerge$Hippocampus~adnimerge$ICV)
adnimerge$adj.Hippocampus = 0.5*(adnimerge$Hippocampus - a$coefficients[[2]]*(adnimerge$ICV - mean(adnimerge$ICV, na.rm=T)))
neuroimagen/byicv.1468925360.txt.gz · Last modified: 2020/08/04 10:46 (external edit)