Once you have successfully segmented the tissue into gray matter, white matter, and CSF, you can use the atlases in iBEAT to label the cortical and subcortical regions of the brain. Open the “Brain Labeling” step from the tissue segmentation step or from the main iBEAT window and load in the tissue segmented data. Click “Label Brain” and after a few minutes, you will see a brain with different shades of gray representing different brain regions. Check that it looks about accurate, and then you have completed the brain labeling step.

I have never run into problems with this step as long as the tissue segmentation step runs correctly and the gray matter, white matter, and CSF segmentations look accurate.

This is the last step of the iBEAT process. However, you still don’t really have “results” that you can write up. From here, I am going to take the brain-labeled images and process them using FSL. Future versions of iBEAT may have additional steps that give you the output you ultimately want to write up (e.g., volume/cortical thickness/surface area of different regions).