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berkeley.lyx
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#LyX 1.6.4 created this file. For more info see http://www.lyx.org/
\lyxformat 345
\begin_document
\begin_header
\textclass beamer
\begin_preamble
\usetheme{Warsaw}
% or ...
\setbeamercovered{transparent}
% or whatever (possibly just delete it)
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\papercolumns 1
\papersides 1
\paperpagestyle default
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\author ""
\author ""
\end_header
\begin_body
\begin_layout Title
Exploring the Land of Tracks
\end_layout
\begin_layout Subtitle
...
riding a Python
\end_layout
\begin_layout Author
Eleftherios
\begin_inset space ~
\end_inset
Garyfallidis
\begin_inset Flex InstituteMark
status open
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1,2
\end_layout
\end_inset
\begin_inset ERT
status collapsed
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\backslash
and
\end_layout
\end_inset
Ian
\begin_inset space ~
\end_inset
Nimmo-Smith
\begin_inset Flex InstituteMark
status collapsed
\begin_layout Plain Layout
2
\end_layout
\end_inset
\begin_inset Note Note
status collapsed
\begin_layout Plain Layout
- Give the names in the same order as the appear in the paper.
\end_layout
\begin_layout Plain Layout
- Use the
\backslash
inst{?} command only if the authors have different affiliations.
\end_layout
\end_inset
\end_layout
\begin_layout Institute
\begin_inset Flex InstituteMark
status collapsed
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1
\end_layout
\end_inset
University of Cambridge, UK,
\begin_inset Flex InstituteMark
status collapsed
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2
\end_layout
\end_inset
MRC Cognition and Brain Sciences Unit, UK.
\end_layout
\begin_layout Date
Berkeley, March, 2010
\begin_inset Note Note
status collapsed
\begin_layout Plain Layout
- Either use conference name or its abbreviation.
\end_layout
\begin_layout Plain Layout
- Not really informative to the audience, more for people (including yourself)
who are reading the slides online
\end_layout
\end_inset
\begin_inset OptArg
status collapsed
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CFP 2003
\end_layout
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\begin_inset Note Note
status open
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optional, should be abbreviation of conference name
\end_layout
\end_inset
\end_layout
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\begin_layout Standard
\begin_inset Note Note
status collapsed
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If you have a file called "institution-logo-filename.xxx", where xxx is a
graphic format that can be processed by latex or pdflatex, resp., then you
can add a logo by uncommenting the following:
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%
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pgfdeclareimage[height=1.5cm]{institution-logo}{./Black-RGB-CBSU.jpg}
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%
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logo{
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pgfuseimage{institution-logo}}
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\begin_layout Standard
\begin_inset Note Note
status collapsed
\begin_layout Plain Layout
The following causes the table of contents to be shown at the beginning
of every subsection.
Delete this, if you do not want it.
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\begin_layout Standard
\begin_inset ERT
status open
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%
\backslash
AtBeginSubsection[]{
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%
\backslash
frame<beamer>{
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\begin_layout Plain Layout
%
\backslash
frametitle{Outline}
\end_layout
\begin_layout Plain Layout
\end_layout
\begin_layout Plain Layout
%
\backslash
tableofcontents[currentsection,currentsubsection]
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\end_layout
\begin_layout Plain Layout
% }
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\end_layout
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%}
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\begin_inset Note Note
status collapsed
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If you wish to uncover everything in a step-wise fashion, uncomment the
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%
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beamerdefaultoverlayspecification{<+->}
\end_layout
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\end_layout
\begin_layout Standard
\begin_inset Note Note
status collapsed
\begin_layout Plain Layout
Structuring a talk is a difficult task and the following structure may not
be suitable.
Here are some rules that apply for this solution:
\end_layout
\begin_layout Plain Layout
- Exactly two or three sections (other than the summary).
\end_layout
\begin_layout Plain Layout
- At *most* three subsections per section.
\end_layout
\begin_layout Plain Layout
- Talk about 30s to 2min per frame.
So there should be between about 15 and 30 frames, all told.
\end_layout
\begin_layout Plain Layout
- A conference audience is likely to know very little of what you are going
to talk about.
So *simplify*!
\end_layout
\begin_layout Plain Layout
- In a 20min talk, getting the main ideas across is hard enough.
Leave out details, even if it means being less precise than you think necessary.
\end_layout
\begin_layout Plain Layout
- If you omit details that are vital to the proof/implementation, just say
so once.
Everybody will be happy with that.
\end_layout
\end_inset
\end_layout
\begin_layout Section
Motivation
\end_layout
\begin_layout BeginFrame
Brain & White Matter
\end_layout
\begin_layout Standard
\begin_inset Float figure
wide false
sideways false
status open
\begin_layout Plain Layout
\begin_inset Graphics
filename white_matter.jpg
scale 50
rotateOrigin center
\end_inset
\end_layout
\begin_layout Plain Layout
Undifferentiated white matter (ignore labels) from Wikipedia.
\end_layout
\begin_layout Plain Layout
\end_layout
\end_inset
\end_layout
\begin_layout BeginFrame
Labeled Bundles
\end_layout
\begin_layout Standard
\begin_inset Float figure
wide false
sideways false
status open
\begin_layout Plain Layout
\begin_inset Graphics
filename pbc_figures/white_brain.png
scale 20
rotateOrigin center
\end_inset
\end_layout
\begin_layout Plain Layout
White matter tractography with labeled bundles.
\end_layout
\end_inset
\end_layout
\begin_layout BeginFrame
Connecting cortical areas
\end_layout
\begin_layout Standard
\begin_inset Float figure
wide false
sideways false
status open
\begin_layout Plain Layout
\begin_inset Graphics
filename figures/Screenshot-Lights-4.png
scale 20
rotateOrigin center
\end_inset
\end_layout
\begin_layout Plain Layout
Produced by Freesurfer and visualized with Fos.
\end_layout
\end_inset
\end_layout
\begin_layout BeginFrame
What do we need?
\end_layout
\begin_layout Itemize
\series bold
Diffusion MRI
\series default
to find local directions
\end_layout
\begin_layout Itemize
\series bold
Tractography
\series default
by integration along directions
\end_layout
\begin_layout Itemize
Metric
\series bold
clustering methods
\series default
identify bundles in one brain
\end_layout
\begin_layout Itemize
\series bold
Metrics
\series default
can find correspondence between tracks and track bundles in multiple brains
\end_layout
\begin_layout Itemize
\series bold
Software
\series default
to achieve these goals
\end_layout
\begin_layout Itemize
Advanced
\series bold
visualisation tools
\series default
to understand the solutions
\end_layout
\begin_layout Subsection
dMRI signal & modeling
\end_layout
\begin_layout BeginFrame
dMRI
\end_layout
\begin_layout Standard
\begin_inset Float figure
wide false
sideways false
status open
\begin_layout Plain Layout
\begin_inset Graphics
filename voxel_modeling.png
scale 70
rotateOrigin center
\end_inset
\end_layout
\begin_layout Plain Layout
Figure from the Diffusion MRI Book Chapter 4
\begin_inset CommandInset citation
LatexCommand cite
key "DiffMRIBook"
\end_inset
.
\end_layout
\end_inset
\end_layout
\begin_layout BeginFrame
ODF
\end_layout
\begin_layout Standard
\begin_inset Float figure
wide false
sideways false
status open
\begin_layout Plain Layout
\begin_inset Graphics
filename dODF.png
rotateOrigin center
\end_inset
\end_layout
\begin_layout Plain Layout
From the Diffusion MRI Book Ch.
4
\begin_inset CommandInset citation
LatexCommand cite
key "DiffMRIBook"
\end_inset
\end_layout
\end_inset
\end_layout
\begin_layout Subsection
What is tractography?
\end_layout
\begin_layout BeginFrame
Definitions
\end_layout
\begin_layout Itemize
\emph on
\color red
dMRI tractography
\emph default
\color inherit
is a family of methods for identifying fiber tracts in the brain or other
tissue.
\end_layout
\begin_layout Itemize
3 categories -
\emph on
deterministic
\emph default
,
\emph on
probabilistic
\emph default
,
\emph on
global
\emph default
.
\end_layout
\begin_layout Itemize
\emph on
\color red
streamline tractography
\emph default
\color inherit
is the process of integrating voxel-wise fiber orientations into a pathway
that connects remote brain regions.
\end_layout
\begin_layout Itemize
a
\emph on
\color red
track
\emph default
\color inherit
is simulating thousands of neuronal axons and is represented by a series
of line segments i.e.
discretized curves.
\begin_inset Float figure
wide false
sideways false
status open
\begin_layout Plain Layout
\begin_inset Graphics
filename streamline.svg
scale 30
rotateOrigin center
\end_inset
\end_layout
\end_inset
\end_layout
\begin_layout BeginFrame
Tractography
\end_layout
\begin_layout Standard
\lang british
\begin_inset Float figure
wide false
sideways false
status open
\begin_layout Plain Layout
\noindent
\align center
\lang british
\begin_inset Graphics
filename figures/DTI_FACT_low26mm_SIDE.png
lyxscale 40
scale 25
rotateOrigin center
\end_inset
\end_layout
\begin_layout Plain Layout
DTK with FACT propagation - color distinguishes track orientation
\begin_inset CommandInset citation
LatexCommand cite
key "WWS+08"
\end_inset
.
\end_layout
\end_inset
\end_layout
\begin_layout BeginFrame
Tractography
\end_layout
\begin_layout Standard
\noindent
\align center
\lang british
\begin_inset Float figure
wide false
sideways false
status open
\begin_layout Plain Layout
\noindent
\align center
\lang british
\begin_inset Graphics
filename figures/DTI_RK2_low26mm_SIDE.png
lyxscale 40
scale 25
\end_inset
\end_layout
\begin_layout Plain Layout
DTK Runge-Kutta
\begin_inset CommandInset citation
LatexCommand cite
key "WWS+08"
\end_inset
.
More on tractography of crossings in
\begin_inset CommandInset citation
LatexCommand cite
key "descoteaux2009deterministic"
\end_inset
.
\end_layout
\end_inset
\end_layout
\begin_layout BeginFrame
Track distances
\end_layout
\begin_layout Itemize
More than 20 different distance metrics to compare tracks used in the literature
\begin_inset CommandInset citation
LatexCommand cite
key "maddah_phdthesis2008"
\end_inset
.
\end_layout
\begin_layout Itemize
However it would be useful to use a
\emph on
metric distance
\emph default
.
\end_layout
\begin_layout Itemize
A
\emph on
metric distance
\emph default
has the following properties:
\end_layout
\begin_deeper
\begin_layout Itemize
\begin_inset Formula $d(a,b)\geq0$
\end_inset
,
\end_layout
\begin_layout Itemize
\begin_inset Formula $d(a,b)=0$
\end_inset
iff
\begin_inset Formula $a=b$
\end_inset
,
\end_layout
\begin_layout Itemize
\begin_inset Formula $d(a,b)=d(b,a)$
\end_inset
,
\end_layout
\begin_layout Itemize
\begin_inset Formula $d(a,c)\leq d(a,b)+d(b,c)$
\end_inset
where
\begin_inset Formula $a,b,c$
\end_inset
are tracks and
\begin_inset Formula $d$
\end_inset
is the distance function.
\end_layout
\end_deeper
\begin_layout Itemize
Average minimum distance has been also used successfully by others.
\begin_inset CommandInset citation
LatexCommand cite
key "corouge2004towards,zhang2008identifying"
\end_inset
\begin_inset Newline newline
\end_inset
\end_layout
\begin_layout BeginFrame
Average Minimum Distances
\end_layout
\begin_layout Standard
\begin_inset Float figure
wide false
sideways false
status open
\begin_layout Plain Layout
\begin_inset Graphics
filename avg_min.png
scale 80
rotateOrigin center
\end_inset
\end_layout
\end_inset
\end_layout
\begin_layout Section
Contribution
\end_layout
\begin_layout Subsection
Main Results
\end_layout
\begin_layout BeginFrame
Distances - Avg.
Min.
\end_layout
\begin_layout Standard
\begin_inset Float figure
wide false
sideways false
status open
\begin_layout Plain Layout
\begin_inset Graphics
filename arcuate_zhang2.png
scale 20
rotateOrigin center
\end_inset
\end_layout
\begin_layout Plain Layout
Arcuate Fasciculus - Reference track is coloured in yellow.
\end_layout
\begin_layout Plain Layout
Red means very similar with the reference track.
\end_layout
\begin_layout Plain Layout
Blue means not very similar with the reference track.
\end_layout
\end_inset
\end_layout
\begin_layout BeginFrame
Detecting Individual Tracks
\end_layout
\begin_layout Standard
\begin_inset Float figure
wide false
sideways false
status open
\begin_layout Plain Layout
\begin_inset Graphics
filename pbc_figures/three_brains_golden.png
scale 20
rotateOrigin center
\end_inset
\end_layout
\begin_layout Plain Layout
Red: Initially selected tracks, Cyan & Blue corresponding tracks.
CBU datasets.
\end_layout
\end_inset
\end_layout
\begin_layout BeginFrame
Detecting Individual Tracks (cont.)
\end_layout
\begin_layout Standard
\begin_inset Float figure
wide false
sideways false
status open