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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: - - $sed 's/;/,/g' ab255_mri.csv > ab255_mri_rc.csv - - - Let's say we want to get the hippocampus volume (HV) corrected by ICV. Then we must get Left and Right HV and calculate its medium value. **HV = 0.5*(HVR+HVL)** - - Now first step is to fit a straight line for HV //vs// ICV and the ICV mean value (). The adjusted HV will be **aHV = HV - b*(ICV-)**, with //b// as the regression coefficient of HV //vs// ICV. - - Now we need to get the data. Let's try it in R. - - x <- read.csv("ab255_mri_rc.csv") - x$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$ICV) - adnimerge$aHV = adnimerge$Hippocampus - a$coefficients[[2]]*(adnimerge$ICV - mean(adnimerge$ICV, na.rm=T)) -