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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