Brain Finder - Introduction

The Brain Finder tool can be used to isolate the brain on MRI head scans, and to calculate a simple index of brain atrophy - the Brain Parenchymal Fraction (BPF). The BPF is:

BPF=^{Parenchyma Volume}⁄_{(Parenchyma Volume + CSF Volume)}

Start the Brain Finder tool from the Toolkits menu:

The Brain Finder tool will now appear as shown below:

Note that the ROI Toolkit also pops up when you start the Brain Finder.

The procedure for calculating the Brain Parenchymal Fraction can be summarised as follows:

• Load an image containing an MRI head scan covering the whole brain into Jim's display. The image contrast should be such that the CSF appears dark in the image. This could be:
  • Multi-slice T₁-weighted.
  • Multi-slice FLAIR.
  • 3-dimensional acquisition T₁-weighted.
• Use the "Find Brain" function of the Brain Finder tool to automatically outline the brain in every slice of the image. Manually correct any errors that are apparent.
• Calculate the BPF either automatically, or by manually setting the intensity threshold that separates brain parenchyma from CSF.