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dMRI_day.lyx
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#LyX 1.6.4 created this file. For more info see http://www.lyx.org/
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\begin_document
\begin_header
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\begin_body
\begin_layout Title
Diffusion MRI Software
\end_layout
\begin_layout Subtitle
DiPy, TRN and Fos
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\begin_layout Author
Eleftherios
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Garyfallidis
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and
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Ian
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Nimmo-Smith
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1
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1
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MRC Cognition and Brain Sciences Unit
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dMRI Day, 4th December, 2009
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- Either use conference name or its abbreviation.
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- Not really informative to the audience, more for people (including yourself)
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CFP 2003
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Delete this, if you do not want it.
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\begin_layout BeginFrame
dMRI Software
\end_layout
\begin_layout Enumerate
Overview
\end_layout
\begin_layout Enumerate
Dtk + trackvis
\end_layout
\begin_layout Enumerate
Fsl/fdt
\end_layout
\begin_layout Enumerate
Dipy/trn
\end_layout
\begin_layout Enumerate
Fos
\end_layout
\begin_layout BeginFrame
A bit less than 30 tools
\end_layout
\begin_layout Itemize
AFNI (via a diffusion plug-in, C/C++)
\end_layout
\begin_layout Itemize
Camino (Java)
\end_layout
\begin_layout Itemize
GTract (C++)
\end_layout
\begin_layout Itemize
FSL/FDT(shell, C/C++)
\end_layout
\begin_layout Itemize
DTK/TrackVis( closed source)
\end_layout
\begin_layout Itemize
med- INRIA (currently closed source, C/C++)
\end_layout
\begin_layout Itemize
DTI-Query (C/C++)
\end_layout
\begin_layout Itemize
CINCH (closed source)
\end_layout
\begin_layout Itemize
mrDiffusion (Matlab with links to C/C++ code)
\end_layout
\begin_layout Itemize
ConTrack (C/C++)
\end_layout
\begin_layout Itemize
BioImage Suite (C/C++)
\end_layout
\begin_layout Itemize
DTI Studio (closed source, Windows only)
\end_layout
\begin_layout Itemize
3D Slicer (C/C++ with Python shell)
\end_layout
\begin_layout Itemize
BrainVISA (Python/C/C++, some closed source)
\end_layout
\begin_layout Itemize
Diffusion II (Matlab)
\end_layout
\begin_layout Itemize
DST (C/- Fortran)
\end_layout
\begin_layout BeginFrame
Wait there are some more
\end_layout
\begin_layout Itemize
BRAINS (closed source; C/C++/Python/Tcl/Tk/Bash)
\end_layout
\begin_layout Itemize
DSI Studio (closed source, Windows only)
\end_layout
\begin_layout Itemize
MRtrix (C++)
\end_layout
\begin_layout Itemize
Numerical Fibre Generator (C/C++)
\end_layout
\begin_layout Itemize
JDTI (Java; ImageJ plugin)
\end_layout
\begin_layout Itemize
fibertracker / fiberviewer (closed source)
\end_layout
\begin_layout Itemize
DTIChecker (closed source)
\end_layout
\begin_layout Itemize
ExploreDTI (Matlab, no source available at time of writing)
\end_layout
\begin_layout Itemize
CATNAP (Matlab; uses FSL, dtiproc)
\end_layout
\begin_layout Itemize
dtiproc (Java).
\end_layout
\begin_layout Itemize
TractoR (R).
\end_layout
\begin_layout BeginFrame
DTK + Trackvis
\end_layout
\begin_layout Itemize
Deterministic Tractography.
\end_layout
\begin_layout Itemize
Very fast.
\end_layout
\begin_layout Itemize
Many propagation models.
\end_layout
\begin_layout Itemize
Not enough documentation.
\end_layout
\begin_layout Itemize
No analysis between subjects.
\end_layout
\begin_layout Itemize
Show demo.
\end_layout
\begin_layout BeginFrame
FSL/FDT
\end_layout
\begin_layout Itemize
Dtifit
\end_layout
\begin_layout Itemize
BedpostX / Probabilistic tractography (slow...).
\end_layout
\begin_layout Itemize
TBSS
\end_layout
\begin_layout Itemize
Documentation / FSL List.
\end_layout
\begin_layout Itemize
Use practicals.
\end_layout
\begin_layout BeginFrame
WM Templates/Atlases
\end_layout
\begin_layout Itemize
Mori Atlas
\end_layout
\begin_layout Itemize
LONI ICBM DTI-81
\end_layout
\begin_layout Itemize
Fiber Pathways of the Brain by Schmahmann and Pandya
\end_layout
\begin_layout BeginFrame
DiPy / TRN
\end_layout
\begin_layout Itemize
DiPy (Diffusion Imaging in Python).
\end_layout
\begin_layout Itemize
Part of NiPy (Neuroimaging in Python).
\end_layout
\begin_layout Itemize
Using volumeimages i.e.
reading Nifti, Analyze files.
\end_layout
\begin_layout Itemize
Reads Trackvis *.trk files.
\end_layout
\begin_layout Itemize
Detects tracks.
\end_layout
\begin_layout Itemize
Detects bundles.
\end_layout
\begin_layout Itemize
Finds
\begin_inset Quotes eld
\end_inset
important
\begin_inset Quotes erd
\end_inset
tracks ('skeletal').
\end_layout
\begin_layout BeginFrame
Fos / Lights
\end_layout
\begin_layout Itemize
3d engine
\end_layout
\begin_layout Itemize
Using python-vtk
\end_layout
\begin_layout Itemize
Picking tracks.
\end_layout
\begin_layout Itemize
Visualizing volumes with tracks together.
\end_layout
\begin_layout Itemize
Visualizing multiple track brains simultaneously.
\end_layout
\begin_layout Itemize
Show demo.
\end_layout
\begin_layout Section*
\start_of_appendix
Appendix
\end_layout
\begin_layout Standard
\lang british
\begin_inset CommandInset bibtex
LatexCommand bibtex
bibfiles "diffusion"
options "plain"
\end_inset
\end_layout
\begin_layout EndFrame
\end_layout
\end_body
\end_document