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--- neuroimagen:byicv [2015/01/28 10:02]
osotolongo
+++ neuroimagen:byicv [2020/08/04 10:58] (current)
@@ Line 1: / Line 1: @@
-====== How to correct by Intracraneal Volume (ICV) ======
+====== 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.
+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) correct by ICV. Then we must get Left and Right HV and calculate its medium value. **HV = 0.5*(HVR+HVL)**
+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 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 ====
+{{ :neuroimagen:adni_hippocampus_correction.png?300|}}
+El paquete ADNIMERGE provee los valores de Hipoocampo (suma de ambos) e ICV. Puede corregirse directamente y dividirse entre 2 para obtener valores similares.
+<code R>
+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)))
+</code>
+Este procedimiento se debera aplicar para realizar la replica de cualquier estudio donde se utilize la semisuma corregida de ambos hipocampos.

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