1. Localization & Normalization
fMRI: Theory and Practice
Spring 2010

2. 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

3. How can we define regions?
Talairach coordinates
Anatomical localization
Functional localization
Region of interest (ROI) analyses
already covered in Design lectures so will not be reconsidered here

4. Talairach Coordinate System
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
Note: That’s TalAIRach, not TAILarach!
Source: Brain Voyager course slides

5. Rotate brain into ACPC plane
Find anterior commisure (AC)
Corpus Callosum
Fornix
Find posterior commisure (PC)
ACPC line
= horizontal axis
Pineal Body
“bent asparagus”
Note: official Tal sez use top of AC and bottom of PC
Source: Duvernoy, 1999

6. Deform brain into Talairach space
Mark 8 points in the brain:
anterior commisure
posterior commisure
front
back
top
bottom (of temporal lobe)
left
right
Squish or stretch brain to fit in “shoebox” of Tal system
ACPC=0
y>0
y<0 z y
AC=0
y>0
y<0 x
Extract 3 coordinates

7. Left is what?!!! L R R L Neurologic (i.e. sensible) convention
left is left, right is right L R
x = 0 - +
Note: Make sure you know what your magnet and software are doing before publishing left/right info!
Radiologic (i.e. stupid) convention
left is right, right is left R L
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.

8. How to Talairach For each subject: For the group:
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:
Either
Average all of the functionals together and perform stats on that
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

9. Talairach Atlas

10. 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

11. 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:

12. Brodmann’s Areas Brodmann (1905):
Based on cytoarchitectonics: study of differences in cortical layers between areas
Most common delineation of cortical areas
More recent schemes subdivide Brodmann’s areas into many smaller regions
Monkey and human Brodmann’s areas not necessarily homologous

13. Anatomical Localization Sulci and Gyri
gray matter
(dendrites & synapses)
white matter
(axons)
FUNDUS
BANK
GYRUS
SULCUS
pial surface
gray/white border
SULCUS
FISSURE
GYRUS
Source: Ludwig & Klingler, 1956 in Tamraz & Comair, 2000

14. Variability of Sulci
Source: Szikla et al., 1977 in Tamraz & Comair, 2000

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

16. Cortical Surfaces Advantages surfaces are topologically more accurate
segment gray-white
matter boundary
render cortical surface
inflate cortical surface
sulci = concave = dark gray
gyri = convex = light gray
Advantages
surfaces are topologically more accurate
alignment across sessions and experiments allows task comparisons
Source: Jody Culham

17. Cortical Flattening 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
4) correct for the distortions so that the true cortical distances are preseved
3) unfold the medial surface so the cortical surface lies flat
Source: Brain Voyager Getting Started Guide

18. Spherical Averaging
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.mpeg
Source: Marty Sereno’s web page
Source: Fischl et al., 1999

19. 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