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--- neuroimagen:byicv [2016/07/19 10:38]
osotolongo
+++ neuroimagen:byicv [2020/08/04 10:58]
@@ Line 1: / Line 1: @@
-====== How to correct by Intracranial Volume (ICV) ======
-{{ :neuroimagen:adjusted.png?nolink&300|}}
-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:
-<code bash>
-$ sed 's/;/,/g' ab255_mri.csv > ab255_mri_rc.csv
-</code>
-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.
-<code 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")
-</code>
-==== For ADNIMERGE package ====
-<code R>
-library("ADNIMERGE")
-a <- lm(adnimerge$Hippocampus~adnimerge$ICV)
-adnimerge$aHV = adnimerge$Hippocampus - a$coefficients[[2]]*(adnimerge$ICV - mean(adnimerge$ICV, na.rm=T))
-</code>

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