Localization & Normalization

fMRI: Theory and PracticeSpring 2012

Brain Localization and Anatomy - with emphasis on cortical areas

Why so corticocentric?•cortex forms the bulk of the brain•subcortical structures are hard to image (more vulnerable to motion artifacts) and resolve with fMRI•cortex is relevant to many cognitive processes•neuroanatomy texts typically devote very little information to cortex

Caveats of corticocentrism:•other structures like the cerebellum are undoubtedly very important (contrary to popular belief it not only helps you “walk and chew gum at the same time” but also has many cognitive functions) but unfortunately are poorly understood as yet•need to remember there may be lots of subcortical regions we’re neglecting

How can we define regions?1. Talairach coordinates

2. Anatomical localization

3. Functional localization• Region of interest (ROI) analyses• already covered in Design lectures so will not be reconsidered here

Talairach Coordinate System

Source: Brain Voyager course slidesNote: That’s TalAIRach, not TAILarach!

Individual brains are different shapes and sizes… How can we compare or average brains?

Talairach & Tournoux, 1988• squish or stretch brain into “shoe box”• extract 3D coordinate (x, y, z) for each activation focus

Rotate brain into ACPC plane

Find posterior commisure (PC)

Find anterior commisure (AC)

ACPC line= horizontal axis

Corpus Callosum

Fornix

Pineal Body“bent asparagus”

Note: official Tal sez use top of AC and bottom of PC

Source: Duvernoy, 1999

Squish or stretch brain to fit in “shoebox” of Tal system

Deform brain into Talairach space

yAC=0 y>0y<0

ACPC=0

y>0

y<0

z

x

Extract 3 coordinates

Mark 8 points in the brain:• anterior commisure• posterior commisure• front• back• top• bottom (of temporal lobe)• left• right

Left is what?!!!

Neurologic (i.e. sensible) convention• left is left, right is right

L R

Radiologic (i.e. stupid) convention• left is right, right is left

R L

Note: Make sure you know what your magnet and software are doing before publishing left/right info!

x = 0-+

x = 0

+-

Note: If you’re really unsure which side is which, tape a vitamin E capsule to the one side of the subject’s head. It will show up on the anatomical image.

How to TalairachFor each subject:

• Rotate the brain to the ACPC Plane (anatomical)• Deform the brain into the shoebox (anatomical)• Perform the same transformations on the functional data

For the group:Eithera) Average all of the functionals together and perform stats on thatb) Perform the stats on all of the data (GLM) and superimpose the statmaps on an averaged

anatomical (or for SPM, a reference brain)

Averaged anatomical for 6 subjects Averaged functional for 7 subjects

Talairach Atlas

Talairach Pros and Cons

Advantages• widespread system• allows averaging of fMRI data between subjects• allows researchers to compare activation foci• easy to use

Disadvantages• based on the squished brain of an elderly alcoholic woman (how representative is that?!)• not appropriate for all brains (e.g., Japanese brains don’t fit well)• activation foci can vary considerably – other landmarks like sulci may be more reliable

MNI Space• There are several reasons the Talairach brain is suboptimal (the brain was from an

alcoholic older woman and became somewhat deformed sitting around)• Researchers at the Montreal Neurological Institute created a better template based on

a morphed average of hundreds of brains (not just one brain like Talairach)• The MNI brain is more representative of average brain shape; however, it does not

provide Brodmann areas• The MNI alignment is more complex than Talairach: SPM uses it but many software

packages still use Talairach• CAVEAT: The MNI and Talairach coordinate are similar but not identical -- careful

comparison requires a transformation

Source: http://www.mrc-cbu.cam.ac.uk/personal/matthew.brett/abstracts/MNITal/mniposter.pdf

Brodmann’s Areas

Brodmann (1905):Based on cytoarchitectonics: study of differences in cortical layers between areasMost common delineation of cortical areasMore recent schemes subdivide Brodmann’s areas into many smaller regionsMonkey and human Brodmann’s areas not necessarily homologous

Anatomical LocalizationSulci and Gyri

gray matter (dendrites & synapses)

white matter (axons)

FUNDUS

BA

NK

SULCUS

GY

RU

SS

ULC

US

gray

/whi

te b

orde

r

pial

sur

face

FISSURE

Source: Ludwig & Klingler, 1956 in Tamraz & Comair, 2000

Variability of Sulci

Source: Szikla et al., 1977 in Tamraz & Comair, 2000

Variability of Functional Areas

Source: Watson et al. 1995

Watson et al., 1995-functional areas (e.g., MT) vary between subjects in their Talairach locations-the location relative to sulci is more consistent

Cortical Surfaces

segment gray-whitematter boundary

inflate cortical surface

sulci = concave = dark graygyri = convex = light gray

render cortical surface

Advantages

• surfaces are topologically more accurate

• alignment across sessions and experiments allows task comparisonsSource: Jody Culham

Cortical Flattening

Source: Brain Voyager Getting Started Guide

2) make cuts along the medial surface

(Note, one cut typically goes along the fundus of the calcarine sulcus though in this example the cut was placed below)

1) inflate the brain

3) unfold the medial surface so the cortical surface lies flat

4) correct for the distortions so that the true cortical distances are preseved

Spherical Averaging

Source: Fischl et al., 1999

Future directions of fMRI: Use cortical surface mapping coordinates

Inflate the brain into a sphere

Use sulci and/or functional areas to match subject’s data to template

Cite “latitude” & “longitude” of spherical coordinates

Movie: brain2ellipse.mpeghttp://cogsci.ucsd.edu/~sereno/coord1.mpg

Source: Marty Sereno’s web page

How can we define regions?Talairach coordinates• Example: The FFA is at x = 40, y

= -55, z = -10

Anatomical localization• Example: The FFA is in the right fusiform

gyrus at the level of the occipitotemporal junction

Functional localization• Example: The FFA includes all voxels around

the fusiform gyrus that are activated by the comparison between faces and objects

Kanwisher, McDermott & Chun, 1997, J Neurosci