Transcript Variability of HRF

Localization & Normalization
fMRI: Theory and Practice
Spring 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
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
Rotate brain into ACPC plane
Corpus Callosum
Fornix
Find anterior commisure (AC)
Find posterior commisure (PC)
ACPC line
= horizontal axis
Note: official Tal sez use top of
AC and bottom of PC
Pineal Body
“bent asparagus”
Source: Duvernoy, 1999
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
y<0
AC=0
y
y>0
z
y>0
ACPC=0
y<0
x
Extract 3 coordinates
Left is what?!!!
Neurologic (i.e. sensible) convention
• left is left, right is right
L
R
-
Note: Make sure you know what your magnet
and software are doing before publishing
left/right info!
+
x=0
Radiologic (i.e. stupid) convention
• left is right, right is left
R
L
+
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 Talairach
For 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:
Either
a)
Average all of the functionals together and perform stats on that
b)
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 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
Anatomical Localization
Sulci and Gyri
gray matter
(dendrites & synapses)
BANK
white matter
(axons)
FISSURE
FUNDUS
Source: Ludwig & Klingler, 1956 in Tamraz & Comair, 2000
Variability of Sulci
Source: Szikla et al., 1977 in Tamraz & Comair, 2000
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
Cortical Surfaces
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
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
3) unfold the medial
surface so the
cortical surface lies
flat
Source: Brain Voyager Getting Started Guide
4) correct for the
distortions so that the
true cortical distances
are preseved
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
http://cogsci.ucsd.edu/~sereno/coord1.mpg
Source: Marty Sereno’s web page
Source: Fischl et al., 1999
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