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neuroimagen:byicv [2015/01/28 10:07]
osotolongo
neuroimagen:byicv [2020/08/04 10:58] (current)
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-====== 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. First do this for a real CSV 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:
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 </code> </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.
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 x <- read.csv("ab255_mri_rc.csv") x <- read.csv("ab255_mri_rc.csv")
 x$HV = 0.5*(x$"Right.Hippocampus"+x$"Left.Hippocampus") x$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$EstimatedTotalIntraCranialVol_eTIV, na.rm=TRUE))
 +write.csv(x, file="ab255_mri_aHV.csv")
 </code> </code>
 +
 +==== For ADNIMERGE package ====
 +
 +{{ :neuroimagen:adni_hippocampus_correction.png?300|}}
 +
 +El paquete ADNIMERGE provee los valores de Hipoocampo (suma de ambos) e ICV. Puede corregirse directamente y dividirse entre 2 para obtener valores similares.
 +
 +<code R>
 +library("ADNIMERGE")
 +a <- lm(adnimerge$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.
neuroimagen/byicv.1422439678.txt.gz · Last modified: 2020/08/04 10:47 (external edit)