Here we’ll just briefly go over how MNI coordinates relate to different brain regions on templates. You’ll often see in papers that brain results (e.g., significant fMRI clusters) are reported with MNI (Montreal Neurologic Institute) coordinates. This is just specifying the location of the result on a certain brain template. Your SPM statistics will also return the MNI coordinates of the significant clusters. For instance, here we see that -33, -34, 44 corresponds with the MNI location of the first significant result. If we then plug in these coordinates to an MNI space atlas, we can name this region; for instance, according to the Neuromorphometerics atlas, -33, -34, 44 corresponds to the left postcentral gyrus.
Now let’s just create a cheat sheet to orient ourselves to how these coordinates work. First, let’s open the CAT12 MNI-space template called Template_T1_IXI555_MNI152_GS.nii in MRIcron. In MRIcron, we can then go to View > MNI coordinates to open a panel that allows us to enter and scroll through different MNI coordinates.
NOTE: this is not the case for all imaging viewers, but please note that in MRIcron the upper left hand corner of the screen does NOT show MNI coordinates. These are instead coordinates based on the image you’ve opened. They still allow you to scroll through the image in the X, Y, and Z directions, but they are not the same as MNI coordinates. You need to go to View > MNI coordinates to see MNI coordinates in MRIcron.
Names for the planes of the brain
Just briefly, we’ll list the common names of the different planes of the brain. I’m including this because folks often use different names (e.g., coronal vs. frontal) to mean the same thing:
- Coronal = frontal
- Horizontal = axial = transverse
- Sagittal = longitudinal
MNI = 0, 0, 0
Now, let’s start looking at how MNI coordinates map onto the brain template. Here, we can see what MNI = 0, 0, 0 looks like. It’s essentially in the middle of the brain. This makes sense — that X = 0, Y = 0, and Z = 0 would put you somewhere in the middle. Now, let’s look at where we get when we scroll through the X, Y, and Z planes.
X Direction = Left / Right
The X direction scrolls through the sagittal or left-right plane of the brain. If you scroll to the right side (hemisphere) of the brain, the MNI coordinates are positive. If you scroll to the left side (hemisphere) of the brain, the MNI coordinates are negative.
- Sagittal (left-right) plane
- Positive (+) coordinates = right hemisphere
- Negative (-) coordinates = left hemisphere
Y Direction = Front / Back
The Y direction scrolls through the coronal or front-back plane of the brain. If you scroll to the front of the brain, the MNI coordinates are positive. If you scroll to the back of the brain, the MNI coordinates are negative.
- Coronal (front-back) plane
- Positive (+) coordinates = front of brain
- Negative (-) coordinates = back of brain
Z Direction = Top / Bottom
The Z direction scrolls through the transverse or top-bottom plane of the brain. If you scroll to the top of the brain, the MNI coordinates are positive. If you scroll to the bottom of the brain, the MNI coordinates are negative.
- Transverse (up-down) plane
- Positive (+) coordinates = top of brain
- Negative (-) coordinates = bottom of brain
That’s all! I just wanted to review this and provide a cheatsheet because this is easy to get tripped up on (e.g., with different names for the different planes of the brain) — and important (e.g., if your X coordinate is negative but you’ve labeled it as a right sided structure, you know you’ve made a typo)!