How to diagram an anatomical region of interest (ROI) on a brain

You might need to eventually create an anatomical illustration highlighting a particular brain region. This figure on the right is from my chapter on Transcortical Sensory Aphasia in the Oxford Handbook of Aphasia. This illustrates specific regions on a cutout using semi-transparent colors with gyri and sulci labeled. I created this figure to highlight the anatomy of the temporoparietal junction (TPJ), a nexus point where many gyri converge. Tbh I always forget where the supramarginal and angular gyri are. For this particular figure, I used the Ch2Better.nii brain template from MRIcron as the base. These illustrations are not too challenging to create. I find them helpful, and they are often quite beautiful. Let’s give this a whirl, shall we?

Before you start, isolate the target structure and determine the best plane to illustrate it in. Let’s say you want to highlight the left inferior frontal gyrus. You might do this on a saggital slice or 3d surface map. In contrast, if you wanted to highlight the hippocampi, you might choose a coronal slice. This tracing technique is best for highlighting coarse macrostructure (e.g., a gyrus). Co-reference a brain atlas when you do the manual tracing. Here are some links to human brain atlases. We will explore two tracing methods. Method 1 will involve manually tracing ROIs on a template brain using Adobe Photoshop. Method 2 will involve highlighting structures using a segmented human brain atlas from Neuromorphemetrics Inc.

Method I: manual tracing on a template brain

ch2better (MRIcron)

freesurfer inflated oren-neyer Surfice

Brain mesh2 w/ cerebellum (Surfice)

Brain Mesh ICBM152 L (Surfice)

step 1: choose a base brain for diagramming

Select a template brain you plan to diagram on. You have many options nested within some of the most popular imaging analysis programs (MRIcron, SPM12, Freesurfer, AFNI, Surfice). Take a look at just a few choices on the figure to the right. When you find a template you like, navigate to the 3d template brain within the program you are working in, then export the slice you are interested in as a 2d flat image. Higher resolution is best (.png lossless if possible, jpeg if not). The images in the slideshow reflect 2d views exported from several different 3d templates all within Professor Chris Rorden’s Surfice software. I changed the background to white. It’s a personal preference whether you want to illustrate an inflated brain or something that looks more lifelike.

1. Crop the brain square

Open your image in Adobe Photoshop. Hold the shift key down and select the brain. This will get you a perfect square. Crop it.

2. Zoom

Zoom in on the brain to somewhere between 150 and 200%. Look at the bottom left corner of your window for the zoom adjustment

3. Create a separate layer for each area

Here we will do one layer for MTG and another for M1. I just rename the layer MTG to keep track of it.

4. adjust color

Let’s just try an indigo first

5. adjust color opacity

This takes some fiddling around with. We will try 50% transparent first

6. click the add anchorpoint tool

You will then start dropping anchorpoints to outline the shape you hope to fill. The more anchorpoints, the more granularity you have in your shape contours

7. continue dropping anchorpoints

It will look strange, but keep going. Trust the process. Hide the fill if it obstructs your view

8. Adjust anchorpoints

Use the direct selectin tool to drag individual anchropoints.

Create a new layer for motor cortex

I’ll just call it M1

10. select the new layer

In the layers panel — this will get you editing the new ROI

Step 11. Find an Orange

This looks a little bla but whatevs

Step 12: Drop anchor!

Same as before

Feather the edges

Using the slider in the properties panel. This will smooth out all the hard edges on your tracing.

Step 15. Export it!

As png — You can pipe this into Illustrator if you want a multipanel figure. It’s pretty!

Steps 2-15: follow this sequence

Let’s say we have settled on a left lateral view of BrainMeshICBM152 as our base brain.

Maybe we want to highlight the precentral gyrus and the middle temporal gyrus. This is getting exciting! You’ll open the brain png file in Adobe Photoshop first. I usually crop the brain square to a 1:1 aspect ratio first (a perfect square). You don’t have to do this step, but squares seem to render pretty well on websites and in presentations. Zoom in on the brain (200%). It is much easier to see gryal/sulcal boundaries when you do this. Our aim is to shade in the MTG and M1. Check an atlas to make sure that you know where these are. I’m going to skip this step and go right into tracing out the two areas. We will go with violet and orange at 60% opacity. A semi-transparent mask allows you to see some tissue underneath the tracing. Drop anchorpoints around the boundaries you want to highlight, and there you have it.

step 3: sit back and revel in your figure

If you need to label this, the best thing to do is port it over to Illustrator.

method ii: automating the labelling process