Extract Shen 278 ROIs

Zikai Lin
04/25/2019

Idea - Why This Application?

One of the most commonly used functional brain atlas is [Shen et al Neuroimage 2013] https://www.sciencedirect.com/science/article/pii/S1053811913005818?via%3Dihub.

However,

  • Contain 278 brain functional region of interests (ROI)
  • Related materials (nii files) can be downloaded https://www.nitrc.org/frs/?group_id=51
  • Not designed in R environment.
  • Need Matlab, AFNI or FSL to extract the information.

Therefore, I designed this application to make this parcellation usable in R, or users that is not familiar with R.

Required libraries

require(oro.dicom)
require(oro.nifti)
require(mritc)
library(scales)
library(RNifti)
library(neurobase)

These are required R packages for hacking neuroimage in R.

Sample Brain Parcellation Plot

load(file = "../Shen_MNI152_ORG.RData")
oro.nifti::orthographic(shen_MNI152_org)

plot of chunk unnamed-chunk-2

The parcellation can be visulized in this application, and it will automatically be updated once the user enter new coordinates.

Thank You!

You can view the source code in my github repo: https://github.com/proteuslinzk/locateShenROIs.