NAMIC Wiki - User contributions [en]

2008 Winter Project Week:fmri eeg analysis

2008-01-11T18:39:54Z

Padma: /* References */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:padma_eeg.jpg|thumb|400px|Visualization of Electromagnetic Activity (Sleep, Epilepsy)]]
|}

__NOTOC__
===Key Investigators===
* BWH: Padma Sundaram, Darren Orbach

<div style="margin: 20px;">

<div style="width: 30%; float: left; padding-right: 3%;">
<h1>Objective</h1>
We are interested in visualizing electromagnetic activity in the brain using
MR imaging with concurrent EEG.
We are particularly interested in inspecting epileptic foci and sleeping individuals.

<h1>Approach, Plan </h1>
We would like to analyze the fMRI data within the slicer framework and also use SCIRun to analyze the EEG and visualize the bioelectric fields.
</div>

<div style="width: 60%; float: left;">

<h1>Progress</h1>
The SCIrun environment was compiled on our Ubuntu laptop. This will enable us to create
volume meshes, store eeg electrode locations and calculate electric field streamlines
in our brain data.

[[Image:scirunhead1.jpg|256px]]
[[Image:scirunhead2.jpg|256px]]
[[Image:scirunhead3.jpg|256px]]
[[Image:scirunhead4.jpg|256px]]
[[Image:scirunhead5.jpg|256px]]
</div>

<br style="clear: both;" />

</div>

===References===
* Direct detection of neuronal activity with MRI: fantasy, possibility, or reality?, Bandettini, N. Petridou and J. Bodurka, Appl. Magn. Reson. 29 (2005), pp. 65–88.
* Visual Analysis of Bioelectric Fields, Xavier Trioche, Rob MacLeod, Chris Johnson.

2008 Winter Project Week:fmri eeg analysis

2008-01-11T18:39:36Z

Padma:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:padma_eeg.jpg|thumb|400px|Visualization of Electromagnetic Activity (Sleep, Epilepsy)]]
|}

__NOTOC__
===Key Investigators===
* BWH: Padma Sundaram, Darren Orbach

<div style="margin: 20px;">

<div style="width: 30%; float: left; padding-right: 3%;">
<h1>Objective</h1>
We are interested in visualizing electromagnetic activity in the brain using
MR imaging with concurrent EEG.
We are particularly interested in inspecting epileptic foci and sleeping individuals.

<h1>Approach, Plan </h1>
We would like to analyze the fMRI data within the slicer framework and also use SCIRun to analyze the EEG and visualize the bioelectric fields.
</div>

<div style="width: 60%; float: left;">

<h1>Progress</h1>
The SCIrun environment was compiled on our Ubuntu laptop. This will enable us to create
volume meshes, store eeg electrode locations and calculate electric field streamlines
in our brain data.

[[Image:scirunhead1.jpg|256px]]

[[Image:scirunhead2.jpg|256px]]

[[Image:scirunhead3.jpg|256px]]

[[Image:scirunhead4.jpg|256px]]

[[Image:scirunhead5.jpg|256px]]
</div>

<br style="clear: both;" />

</div>

===References===
* Direct detection of neuronal activity with MRI: fantasy, possibility, or reality?, Bandettini, N. Petridou and J. Bodurka, Appl. Magn. Reson. 29 (2005), pp. 65–88.
* Visual Analysis of Bioelectric Fields, Xavier Trioche, Rob MacLeod, Chris Johnson.

2008 Winter Project Week:fmri eeg analysis

2008-01-11T18:38:31Z

Padma:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:padma_eeg.jpg|thumb|400px|Visualization of Electromagnetic Activity (Sleep, Epilepsy)]]
|}

__NOTOC__
===Key Investigators===
* BWH: Padma Sundaram, Darren Orbach

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
We are interested in visualizing electromagnetic activity in the brain using
MR imaging with concurrent EEG.
We are particularly interested in inspecting epileptic foci and sleeping individuals.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan </h1>
We would like to analyze the fMRI data within the slicer framework and also use SCIRun to analyze the EEG and visualize the bioelectric fields.
</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>
The SCIrun environment was compiled on our Ubuntu laptop. This will enable us to create
volume meshes, store eeg electrode locations and calculate electric field streamlines
in our brain data.

[[Image:scirunhead1.jpg|256px]]

[[Image:scirunhead2.jpg|256px]]

[[Image:scirunhead3.jpg|256px]]

[[Image:scirunhead4.jpg|256px]]

[[Image:scirunhead5.jpg|256px]]
</div>

<br style="clear: both;" />

</div>

===References===
* Direct detection of neuronal activity with MRI: fantasy, possibility, or reality?, Bandettini, N. Petridou and J. Bodurka, Appl. Magn. Reson. 29 (2005), pp. 65–88.
* Visual Analysis of Bioelectric Fields, Xavier Trioche, Rob MacLeod, Chris Johnson.

2008 Winter Project Week:fmri eeg analysis

2008-01-11T18:38:04Z

Padma:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:padma_eeg.jpg|thumb|400px|Visualization of Electromagnetic Activity (Sleep, Epilepsy)]]
|}

__NOTOC__
===Key Investigators===
* BWH: Padma Sundaram, Darren Orbach

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
We are interested in visualizing electromagnetic activity in the brain using
MR imaging with concurrent EEG.
We are particularly interested in inspecting epileptic foci and sleeping individuals.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan </h1>
We would like to analyze the fMRI data within the slicer framework and also use SCIRun to analyze the EEG and visualize the bioelectric fields.
</div>

<div style="width: 40%; float: left;">

<h1>Approach, Plan </h1>
We would like to analyze the fMRI data within the slicer framework and also use SCIRun to analyze the EEG and visualize the bioelectric fields.
</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>
The SCIrun environment was compiled on our Ubuntu laptop. This will enable us to create
volume meshes, store eeg electrode locations and calculate electric field streamlines
in our brain data.

[[Image:scirunhead1.jpg|256px]]

[[Image:scirunhead2.jpg|256px]]

[[Image:scirunhead3.jpg|256px]]

[[Image:scirunhead4.jpg|256px]]

[[Image:scirunhead5.jpg|256px]]
</div>

<br style="clear: both;" />

</div>

===References===
* Direct detection of neuronal activity with MRI: fantasy, possibility, or reality?, Bandettini, N. Petridou and J. Bodurka, Appl. Magn. Reson. 29 (2005), pp. 65–88.
* Visual Analysis of Bioelectric Fields, Xavier Trioche, Rob MacLeod, Chris Johnson.

File:Scirunhead5.jpg

2008-01-11T18:37:00Z

Padma:

File:Scirunhead4.jpg

2008-01-11T18:35:34Z

Padma:

2008 Winter Project Week:fmri eeg analysis

2008-01-11T18:33:34Z

Padma: /* References */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:padma_eeg.jpg|thumb|400px|Visualization of Electromagnetic Activity (Sleep, Epilepsy)]]
|}

__NOTOC__
===Key Investigators===
* BWH: Padma Sundaram, Darren Orbach

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
We are interested in visualizing electromagnetic activity in the brain using
MR imaging with concurrent EEG.
We are particularly interested in inspecting epileptic foci and sleeping individuals.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan </h1>
We would like to analyze the fMRI data within the slicer framework and also use SCIRun to analyze the EEG and visualize the bioelectric fields.
</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>
The SCIrun environment was compiled on our Ubuntu laptop. This will enable us to create
volume meshes, store eeg electrode locations and calculate electric field streamlines
in our brain data.

[[Image:scirunhead1.jpg|256px]]

[[Image:scirunhead2.jpg|256px]]

[[Image:scirunhead3.jpg|256px]]

[[Image:scirunhead4.jpg|256px]]

[[Image:scirunhead5.jpg|256px]]
</div>

<br style="clear: both;" />

</div>

===References===
* Direct detection of neuronal activity with MRI: fantasy, possibility, or reality?, Bandettini, N. Petridou and J. Bodurka, Appl. Magn. Reson. 29 (2005), pp. 65–88.
* Visual Analysis of Bioelectric Fields, Xavier Trioche, Rob MacLeod, Chris Johnson.

2008 Winter Project Week:fmri eeg analysis

2008-01-11T18:30:56Z

Padma: /* References */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:padma_eeg.jpg|thumb|400px|Visualization of Electromagnetic Activity (Sleep, Epilepsy)]]
|}

__NOTOC__
===Key Investigators===
* BWH: Padma Sundaram, Darren Orbach

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
We are interested in visualizing electromagnetic activity in the brain using
MR imaging with concurrent EEG.
We are particularly interested in inspecting epileptic foci and sleeping individuals.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan </h1>
We would like to analyze the fMRI data within the slicer framework and also use SCIRun to analyze the EEG and visualize the bioelectric fields.
</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>
The SCIrun environment was compiled on our Ubuntu laptop. This will enable us to create
volume meshes, store eeg electrode locations and calculate electric field streamlines
in our brain data.

[[Image:scirunhead1.jpg|256px]]
[[Image:scirunhead2.jpg|256px]]
[[Image:scirunhead3.jpg|256px]]

Data currently acquired:
* Rest-state fMRI and concurrent EEG (normal healthy volunteer)
* EEG of a sleeping individual (no MRI yet, but data covers 8 pm to 10 am and all sleep stages)

</div>

<br style="clear: both;" />

</div>

===References===
* Direct detection of neuronal activity with MRI: fantasy, possibility, or reality?, Bandettini, N. Petridou and J. Bodurka, Appl. Magn. Reson. 29 (2005), pp. 65–88.
* Visual Analysis of Bioelectric Fields, Xavier Trioche, Rob MacLeod, Chris Johnson.

File:Scirunhead3.jpg

2008-01-11T18:29:40Z

Padma:

2008 Winter Project Week:fmri eeg analysis

2008-01-11T18:22:14Z

Padma: /* References */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:padma_eeg.jpg|thumb|400px|Visualization of Electromagnetic Activity (Sleep, Epilepsy)]]
|}

__NOTOC__
===Key Investigators===
* BWH: Padma Sundaram, Darren Orbach

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
We are interested in visualizing electromagnetic activity in the brain using
MR imaging with concurrent EEG.
We are particularly interested in inspecting epileptic foci and sleeping individuals.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan </h1>
We would like to analyze the fMRI data within the slicer framework and also use SCIRun to analyze the EEG and visualize the bioelectric fields.
</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>
The SCIrun environment was compiled on our Ubuntu laptop.

[[Image:scirunhead1.jpg|256px]]
[[Image:scirunhead2.jpg|256px]]
[[Image:scirunhead3.jpg]]

Data currently acquired:
* Rest-state fMRI and concurrent EEG (normal healthy volunteer)
* EEG of a sleeping individual (no MRI yet, but data covers 8 pm to 10 am and all sleep stages)

</div>

<br style="clear: both;" />

</div>

===References===
* Direct detection of neuronal activity with MRI: fantasy, possibility, or reality?, Bandettini, N. Petridou and J. Bodurka, Appl. Magn. Reson. 29 (2005), pp. 65–88.
* Visual Analysis of Bioelectric Fields, Xavier Trioche, Rob MacLeod, Chris Johnson.

File:Scirunhead2.jpg

2008-01-11T18:21:49Z

Padma:

2008 Winter Project Week:fmri eeg analysis

2008-01-11T18:20:43Z

Padma: /* References */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:padma_eeg.jpg|thumb|400px|Visualization of Electromagnetic Activity (Sleep, Epilepsy)]]
|}

__NOTOC__
===Key Investigators===
* BWH: Padma Sundaram, Darren Orbach

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
We are interested in visualizing electromagnetic activity in the brain using
MR imaging with concurrent EEG.
We are particularly interested in inspecting epileptic foci and sleeping individuals.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan </h1>
We would like to analyze the fMRI data within the slicer framework and also use SCIRun to analyze the EEG and visualize the bioelectric fields.
</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>
The SCIrun environment was compiled on our Ubuntu laptop.

[[Image:scirunhead1.jpg|256px]]
[[Image:scirunhead2.jpg]]
[[Image:scirunhead3.jpg]]

Data currently acquired:
* Rest-state fMRI and concurrent EEG (normal healthy volunteer)
* EEG of a sleeping individual (no MRI yet, but data covers 8 pm to 10 am and all sleep stages)

</div>

<br style="clear: both;" />

</div>

===References===
* Direct detection of neuronal activity with MRI: fantasy, possibility, or reality?, Bandettini, N. Petridou and J. Bodurka, Appl. Magn. Reson. 29 (2005), pp. 65–88.
* Visual Analysis of Bioelectric Fields, Xavier Trioche, Rob MacLeod, Chris Johnson.

File:Scirunhead1.jpg

2008-01-11T18:19:49Z

Padma:

2008 Winter Project Week:fmri eeg analysis

2008-01-11T18:18:21Z

Padma: /* References */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:padma_eeg.jpg|thumb|400px|Visualization of Electromagnetic Activity (Sleep, Epilepsy)]]
|}

__NOTOC__
===Key Investigators===
* BWH: Padma Sundaram, Darren Orbach

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
We are interested in visualizing electromagnetic activity in the brain using
MR imaging with concurrent EEG.
We are particularly interested in inspecting epileptic foci and sleeping individuals.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan </h1>
We would like to analyze the fMRI data within the slicer framework and also use SCIRun to analyze the EEG and visualize the bioelectric fields.
</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>
The SCIrun environment was compiled on our Ubuntu laptop.

[[Image:scirunhead1.jpg]]
[[Image:scirunhead2.jpg]]
[[Image:scirunhead3.jpg]]

Data currently acquired:
* Rest-state fMRI and concurrent EEG (normal healthy volunteer)
* EEG of a sleeping individual (no MRI yet, but data covers 8 pm to 10 am and all sleep stages)

</div>

<br style="clear: both;" />

</div>

===References===
* Direct detection of neuronal activity with MRI: fantasy, possibility, or reality?, Bandettini, N. Petridou and J. Bodurka, Appl. Magn. Reson. 29 (2005), pp. 65–88.
* Visual Analysis of Bioelectric Fields, Xavier Trioche, Rob MacLeod, Chris Johnson.

2008 Winter Project Week:fmri eeg analysis

2008-01-11T18:16:59Z

Padma: /* References */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:padma_eeg.jpg|thumb|400px|Visualization of Electromagnetic Activity (Sleep, Epilepsy)]]
|}

__NOTOC__
===Key Investigators===
* BWH: Padma Sundaram, Darren Orbach

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
We are interested in visualizing electromagnetic activity in the brain using
MR imaging with concurrent EEG.
We are particularly interested in inspecting epileptic foci and sleeping individuals.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan </h1>
We would like to analyze the fMRI data within the slicer framework and also use SCIRun to analyze the EEG and visualize the bioelectric fields.
</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>
The SCIrun environment was compiled on our Ubuntu laptop.

[[Image:Example.jpg]]
[[Image:Example.jpg]]
[[Image:Example.jpg]]

Data currently acquired:
* Rest-state fMRI and concurrent EEG (normal healthy volunteer)
* EEG of a sleeping individual (no MRI yet, but data covers 8 pm to 10 am and all sleep stages)

</div>

<br style="clear: both;" />

</div>

===References===
* Direct detection of neuronal activity with MRI: fantasy, possibility, or reality?, Bandettini, N. Petridou and J. Bodurka, Appl. Magn. Reson. 29 (2005), pp. 65–88.
* Visual Analysis of Bioelectric Fields, Xavier Trioche, Rob MacLeod, Chris Johnson.

2008-SCI-tour

2008-01-09T09:56:43Z

Padma: /* List of Participants */

__NOTOC__

Back to [[AHM_2008]], [[Events]]

=Tour of the Scientific Computing and Imaging (SCI) Institute=

The SCI Institute (http://www.sci.utah.edu) recently moved into the new Warnock Engineering Building at the University of Utah.

Here is information about our new space:

http://www.sci.utah.edu/stories/2007/Warnock.html

http://www.sci.utah.edu/stories/2007/sci_moving.html

Please join us for a short tour of the SCI Institute.

=Logistics=
We have rented a van/bus that will hold 20 people and take people from the Marriott Hotel to the SCI Institute and then back again to the Hotel.

The van/bus will leave the Marriott Hotel at '''5:00 p.m. on Wednesday, January 9''' and return to the Hotel around 6:15 p.m.

The first 20 people to sign up will be able to ride on the van/bus. Others who would like to join us can car pool.

Here is a map and directions to the SCI Institute (Warnock Engineering Building). It is about a 10 minute drive from the Hotel to the SCI Institute.

http://www.sci.utah.edu/map.html

=List of Participants=
Please add your name to the bottom of the list, if you intend to participate in the tour.
#Ron Kikinis
#Zohara Cohen
#Curtis Lisle
#Martin Styner
#Vincent Magnotta
#Nicole Grosland
#Carl-Fredrik Westin
#Nikos Chrisochoides
#Marek Kubicki
#Sonia Pujol
#Csaba Csoma
#Steve Pieper
#Randy Gollub
#Terry Yoo
#Michael Halle
#Luis Ibanez
#Carlo Pierpaoli
#Sylvain Bouix
#Katie Hayes
#Douglas Alan
#Koen Van Leemput
#Padma Sundaram

2008 Winter Project Week Image Registration Update

2008-01-08T17:39:40Z

Padma: /* Attendees */

__NOTOC__
Back to [[AHM_2008]]

=Breakout session on "Registration methods in the NAMIC Toolkit"=

== Attendees ==

<em>Please add your name below, if your plan on attending.</em>

* Guido Gerig
* Jim Miller
* Stephen Aylward
* Ross Whitaker
* Luis Ibanez
* Alex hanfei Gouaillard
* Casey Goodlett
* Bill Lorensen
* Luca Antiga
* Clement Vachet
* Ron Kikinis
* Serdar Balci
* Daniel Blezek
* Li Shen
* Kilian Pohl
* Xiaodong Tao
* Marcel Prastawa
* Francois Budin
* Padma Sundaram

== Topics ==

<em>Please submit your ideas for topics to be discussed.</em>

* Demonstration of a registration module in Slicer (Stephen)
* Needs, Categorization (Guido)
* What is available (Guido)
* Use in a pipeline (Guido)
* Choice of appropriate/optimal algorithm, Validation (Guido)
* Testing (Luis)
* Heuristics for selecting components(Luis)

== Presentations ==

<em>If you would like to give a short (5-10 minute) presentation, please describe it below.</em>

* Opening remarks (Guido)
* Demonstration of a registration module in Slicer (Stephen, Matt Turek, and Luis Ibanez)
** [http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization#Performance_Testing_Results Preliminiary ITK Multi-threaded performance results] (Matt Turek)
* Discussion of directions for future work (assign priorities and responsibilities)
** Passing and tracking transforms in Slicer (Jim)
** Regularization of BSplines (Stephen)
** Adding "don't process" zones in BSplines (Stephen)
** Objects as masks: mrml -=> SpatialObject conversion (Stephen)
** Reducing BSpline memory requirements (Brad)
** Specializing particular metric/transform combinations (Luis)
** Batch processing registration
*** Atlas formation
*** Atlas application
** Validation
*** STAPLE

== Related Links ==

<em>Add papers, presentations, wiki pages, etc.</em>

* [http://www.vtk.org/Wiki/Proposals:GridComputing Grid Computing in ITK]
* [http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization ITK Multi-threaded registration]
** [http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization#Performance_Testing_Results Preliminiary ITK Multi-threaded performance results]
* [http://www.vtk.org/Wiki/ITK_Roadmap_2007_2008 ITK Roadmap for 2008]

2008 Winter Project Week Geometry and Topology processing of Meshes

2008-01-08T17:38:52Z

Padma: /* Attendees */

Breakout session on "Geometry and Topology processing of Meshes"
Owner: Alex Gouaillard, Caltech

== Presentations ==

*45 mn Prof. David Gu - Discrete Algorithms for Surface mesh processing
*45 mn Alex Gouaillard - Current and future ITK Implementations (QuadEdge, ...) - Parameterization code in ITK, Decimation/smoothing and more in progress.
*20 mn Luca Antiga - Current and potential uses for vascular modelling applications
*15 mn Interactions

== Attendees ==

<em>Please add your name below, if your plan on attending.</em>

* David xianfeng Gu (?)
* Alex hanfei Gouaillard
* Luca Antiga
* Bill Lorensen
* Sean Megason
* Xiaodong Tao
* william schroeder
* Bob O'Bara
* Jim Miller
* Li Shen
* Kishore Mosaliganti
* Okan Irfanoglu
* Firdaus Janoos
* Padma Sundaram

== Presenters ==

=== Professor David Xianfeng GU and/or students (http://www.cs.sunysb.edu/~gu/) ===

Prof. GU will be in China mid-december. Depending on the rapidity of the US embassy in China to give him a visa to go back, he will be able to attend the meeting or not. In the unfortunate case he wouldn't be able to attend, one or two of his postdoc students would be there in replacement.

Ricci flow is a powerful geometric analytic tool, which has been applied to prove Poincare conjecture. Ricci flow is a parabolic system of partial differential equations which acts like the heat equation to spread the curvature of a Riemannian metric evenly over the surface to produce a metric of constant curvature. Computational Ricci flow has been invented and applied for computing hyperbolic structures and conformal surface parameterizations, it is expected to play important roles in both mathematics and engineering fields.

Algorithms for computing conformal structure can be summarized as
*For genus zero surface in the first column, the mapping can be computed using spherical harmonic maps, in paper "Genus Zero Surface Conformal Mapping and Its Application to Brain Surface Mapping". Spherical geometry can be defined on the surface.
*For genus one surface in the second column, the mapping can be computed using holomorphic one forms, in paper "Global Conformal Surface Parameterization". Another algorithm is to use Euclidean Ricci flow, in paper "Conformal Surface Parameterization Using Euclidean Ricci Flow". Euclidean geometry can be defined on the surface.
*For higher genus surfaces in the third column, the mapping can be computed using hyperbolic Ricci flow, in paper "Computing Surface Hyperbolic Structure and Real Projective Structure". Hyperbolic geometry can be defined on the surface.

Applications of conformal geometry in engineering fields are innumerous, the followings are the most directly related ones,
*Graphics: surface global conformal parameterization.
*Medical Imaging: conformal brain mapping and colon flattening.
*Geometric Modeling: manifold splines.
*Vision: Surface matching and recognition.

=== Alex. Hanfei Gouaillard (http://www.itk.org/Wiki/User:Agouaillard) and Arnaud Gelas (http://www.creatis.insa-lyon.fr/~gelas) ===

For the past 5 years, both A.G. have been working on applying gometry and topology processing to medical / biological image processing problems, some of them in collaboration for some with Prof. David GU.

They identified very early that surface processing could only be done rigorously using at least an Half-Edge Structure, and even better in the case of image procesing, a Quad-Edge datastructure. They also concluded from their experiment that, even though C-GAL was the best tool out there to do geometry and topology processing, its license, its complexity, the lack of support of several key platform, and the lack of support for Images was ruling it out for Image processing oriented applications. They decided to go for ITK, and to re-implement whatever would be necessary. It was a long term project, done on spare time, which started around 2002.

Nowadays, the data structure is available under the name itkQuadEdgeMesh and is fairly stable and compliant with existing itkMesh API. The original submission can be read here: http://hdl.handle.net/1926/306. The code is available in ITK since 3.2, if compiled with the USE_REVIEW option. Most of the surface processing algorithms can be more easily implemented on top of Euler operators. Their second work has been to implement those on top of itkQuadEdgeMesh to ease further implementations. The code is available in ITK since 3.4, still with the compilation condition. There is still a lot of algorithms waiting to be transfered in ITK, of which the recent submission of the parameterization code (http://hdl.handle.net/1926/1315) is but a small example.

During this presentation, they will list the features they already have a prototype for and try to give a release timeline. We can expect most of the processing features of VTK to be transfered very soon in ITK, and then some more advanced features to come in. They hope to provide ITK with a complete geometrical and topological toolkit. They dream, in a distant future, to be able to implement an exact kernel in ITK to be able to compute in a robust manner Voronoi tesselations and their duals, Delaunay triangulations.
http://iorich.caltech.edu/guithoughts/wiki/itkQuadEdgeMesh

[[Image:TopologicalArtifact.jpg]]

*A. GOUAILLARD, C. Odet, X. GU, “Computing Shortest Cycles on Discrete Surfaces for Acurate Topological Modifications of Medical Image Isosurfaces”, In Proceedings of IEEE EMBC’05, Shanghai, September 11th-14th 2005.
*A. GOUAILLARD, T. Kanai, C. Odet, X. GU, “Optimal Localization of Topological Artefacts on 3D Meshes”, The 11th Int. Conf. on Geometry and Graphics, 1-5 Aug., 2004, Guangzhou, China.

*A. GELAS, Olivier Bernard, Denis Friboulet, Rémy Prost. "Compactly Supported Radial Basis Functions Collocation Method for Image Segmentation". IEEE Transaction on Image Processing, vol. 16(7), pp.1873--1887 2007.
*A. GELAS, Yutaka Ohtake, Takashi Kanai, Rémy Prost. "Surface Reconstruction Using Radial Basis Functions With Support Adapted to the Medial Axis." Elsevier Computer & Graphics, 2006 (submitted).

[[Image:MultiresolutionRemeshing.jpg]]

*A.GELAS, Joel Schaerer, Olivier Bernard, Denis Friboulet, Patrick Clarysse, Isabelle Magnin, Rémy Prost. "Radial basis functions collocation methods for model based level-set segmentation". IEEE ICIP 2007 Proceedings, vol. 2, pp.237--240, San Antonio, Texa, USA, September 2007.
*A. GELAS, Yutaka Ohtake, Takashi Kanai, Rémy Prost. "Approximation of unorganized point set with composite implicit surface". IEEE ICIP 2006 Proceedings, pp.1217--1220, Atlanta, Georgia, USA, October 2006.
*A. GELAS, Rémy Prost. "Multi-resolution reconstruction of irregularly sampled signals with compactly supported radial basis functions". IEEE ICASSP 2006's Proceedings, vol. 3, pp.388--391, Toulouse, France, May 2006.
*A. GOUAILLARD, A. GELAS, S. Valette, E. Boix and R. Prost, “Curvature-based Adaptive Remeshing for Wavelet-Based Multiresolution 3D Meshes”. In Proc. of International Conference on Image Processing ICIP’05, Genova, September 11th-14th 2005. To appear.
*A. GOUAILLARD, A. GELAS, S. Valette, E. Boix, R. Prost, “Remeshing Algorithm for Multiresolution Prior Model in Segmentation. In Proc. of International Conference on Image Processing, ICIP‘04, Singapore, October 24~27 October 2003, pp. 2753-

=== Luca Antiga (http://villacamozzi.marionegri.it/~luca/) ===

Luca Antiga submitted several vessel detection filters to ITK, and is also in charge of the Vascular Modelling Toolkit (vmtk, http://vmtk.sourceforge.net), developed in collaboration with David Steinman, University of Toronto. In vmtk he is working on the detection and quantification of vessels, as well as on pre- and post-processing for computational fluid dynamics (CFD), aimed at population studies on the relationships between geometry, hemodynamics and physio-pathology of the cardiovascular system. Using vtk so far to represent and handle the vessel representation and further quantification, he will talk about the geometrical problems he is facing (medial axis detection, bifurcation detection, vessel reconstruction, and vessels / branch analysis) and how the tools discussed in this breakout session would solve current problems and allow further investigations on different medical problems.

Using Voronoi/Delaunay a lot, he also witnessed a great improvement in the robustness of the solutions when he changed to an exact kernel. Interested today in Ricci flows and other nice discrete algorithms introduced from abstract mathematics by Prof. GU, he is thinking about moving to itkQuadEdge and itkMesh to implement those algorithms. His dreams would be an exact kernel in ITK, 3-manifolds (volume meshes) / 2-manifolds (surface meshes) algorithms, and ultimately to have computational and differential geometry infrastructure available in ITK. And Python and vmtk in Slicer, but that's another story (we're almost there with that!).

*Piccinelli M, Bacigaluppi S, Boccardi E, Ene-Iordache B, Remuzzi A, Veneziani A, Antiga L Influence of internal carotid artery geometry on aneurysm location and orientation: a computational geometry study. Submitted.
*Thomas JB, Antiga L, Che S, Milner JS, Hangan Steinman DA, Spence JD, Rutt BK and Steinman DA. Variation in the carotid bifurcation geometry of young vs. older adults: Implications for "geometric risk" of atherosclerosis. Stroke, 36(11): 2450-2456, Nov 2005.
*Antiga L, Steinman DA. Robust and objective decomposition and mapping of bifurcating vessels. IEEE Transactions on Medical Imaging, 23(6): 704-713, June 2004.
*Antiga L, Ene-Iordache B and Remuzzi A. Computational geometry for patient-specific reconstruction and meshing of blood vessels from MR and CT angiography. IEEE Transactions on Medical Imaging, 22(5): 674-684, May 2003.
*Antiga L, Ene-Iordache B, Caverni L, Cornalba GP and Remuzzi A. Geometric reconstruction for computational mesh generation of arterial bifurcations from CT angiography. Computerized Medical Imaging and Graphics, 26(4): 227-235, June 2002.

[[Image:VoronoiVortices lowres.png]]
Shape and flow in an intracranial aneurysm.

----

Back to [[AHM_2008]], [[Events]]

AHM 2008 fMRI

2008-01-05T22:04:42Z

Padma:

Back to [[AHM_2008]]

Time: Wednesday, Jan 9, 2008

Topic: fmri

Attendees:
*kinh tieu
*sandy wells
*Janoos Firdaus <firdaus@ieee.org>,
*Kishore Rao Mosaliganti" < mosaligk@cse.ohio-state.edu>,
*Raghu Machiraju [raghu@cse.ohio-state.edu]
*Randy Gollub [rgollub at partners.org] I'll join you if I am able to take a break from the Tractography sessions
*Padma Sundaram

2008 Winter Project Week:fmri eeg analysis

2007-12-20T17:24:51Z

Padma: /* Key Investigators */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:padma_eeg.jpg|thumb|400px|Visualization of Electromagnetic Activity (Sleep, Epilepsy)]]
|}

__NOTOC__
===Key Investigators===
* BWH: Padma Sundaram, Darren Orbach

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
We are interested in visualizing electromagnetic activity in the brain using
MR imaging with concurrent EEG.
We are particularly interested in inspecting epileptic foci and sleeping individuals.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan </h1>
We would like to analyze the fMRI data within the slicer framework and also use SCIRun to analyze the EEG and visualize the bioelectric fields.
</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>
Data currently acquired:
* Rest-state fMRI and concurrent EEG (normal healthy volunteer)
* EEG of a sleeping individual (no MRI yet, but data covers 8 pm to 10 am and all sleep stages)

</div>

<br style="clear: both;" />

</div>

===References===
* Direct detection of neuronal activity with MRI: fantasy, possibility, or reality?, Bandettini, N. Petridou and J. Bodurka, Appl. Magn. Reson. 29 (2005), pp. 65–88.
* Visual Analysis of Bioelectric Fields, Xavier Trioche, Rob MacLeod, Chris Johnson.

2008 Winter Project Week:fmri eeg analysis

2007-12-20T17:23:30Z

Padma: /* References */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:padma_eeg.jpg|thumb|400px|Visualization of Electromagnetic Activity (Sleep, Epilepsy)]]
|}

__NOTOC__
===Key Investigators===
* BWH: Padma Sundaram

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
We are interested in visualizing electromagnetic activity in the brain using
MR imaging with concurrent EEG.
We are particularly interested in inspecting epileptic foci and sleeping individuals.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan </h1>
We would like to analyze the fMRI data within the slicer framework and also use SCIRun to analyze the EEG and visualize the bioelectric fields.
</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>
Data currently acquired:
* Rest-state fMRI and concurrent EEG (normal healthy volunteer)
* EEG of a sleeping individual (no MRI yet, but data covers 8 pm to 10 am and all sleep stages)

</div>

<br style="clear: both;" />

</div>

===References===
* Direct detection of neuronal activity with MRI: fantasy, possibility, or reality?, Bandettini, N. Petridou and J. Bodurka, Appl. Magn. Reson. 29 (2005), pp. 65–88.
* Visual Analysis of Bioelectric Fields, Xavier Trioche, Rob MacLeod, Chris Johnson.

2008 Winter Project Week:fmri eeg analysis

2007-12-20T17:23:23Z

Padma:

2008 Winter Project Week:fmri eeg analysis

2007-12-20T17:22:10Z

Padma:

2008 Winter Project Week:fmri eeg analysis

2007-12-20T17:20:39Z

Padma:

2008 Winter Project Week:fmri eeg analysis

2007-12-20T17:19:58Z

Padma:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:padma_eeg.jpg|thumb|400px|Title Here]]
|}

__NOTOC__
===Key Investigators===
* BWH: Padma Sundaram

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
We are interested in visualizing electromagnetic activity in the brain using
MR imaging with concurrent EEG.
We are particularly interested in inspecting epileptic foci and sleeping individuals.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan </h1>
Our approach
</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

</div>

<br style="clear: both;" />

</div>

===References===
* Direct detection of neuronal activity with MRI: fantasy, possibility, or reality?, Bandettini, N. Petridou and J. Bodurka, Appl. Magn. Reson. 29 (2005), pp. 65–88.
* Visual Analysis of Bioelectric Fields, Xavier Trioche, Rob MacLeod, Chris Johnson.

2008 Winter Project Week:fmri eeg analysis

2007-12-20T17:18:39Z

Padma:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:padma_eeg.jpg|thumb|480px|Title Here]]
|}

__NOTOC__
===Key Investigators===
* BWH: Padma Sundaram

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
We are interested in visualizing electromagnetic activity in the brain using
MR imaging with concurrent EEG.
We are particularly interested in inspecting epileptic foci and sleeping individuals.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan </h1>
Our approach
</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

</div>

<br style="clear: both;" />

</div>

===References===
* Direct detection of neuronal activity with MRI: fantasy, possibility, or reality?, Bandettini, N. Petridou and J. Bodurka, Appl. Magn. Reson. 29 (2005), pp. 65–88.
* Visual Analysis of Bioelectric Fields, Xavier Trioche, Rob MacLeod, Chris Johnson.

2008 Winter Project Week:fmri eeg analysis

2007-12-20T17:18:03Z

Padma:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:padma_eeg.jpg |thumb|320px|Title Here]]
|}

__NOTOC__
===Key Investigators===
* BWH: Padma Sundaram

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
We are interested in visualizing electromagnetic activity in the brain using
MR imaging with concurrent EEG.
We are particularly interested in inspecting epileptic foci and sleeping individuals.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan </h1>
Our approach
</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

</div>

<br style="clear: both;" />

</div>

===References===
* Direct detection of neuronal activity with MRI: fantasy, possibility, or reality?, Bandettini, N. Petridou and J. Bodurka, Appl. Magn. Reson. 29 (2005), pp. 65–88.
* Visual Analysis of Bioelectric Fields, Xavier Trioche, Rob MacLeod, Chris Johnson.

File:Padma eeg.jpg

2007-12-20T17:17:36Z

Padma:

2008 Winter Project Week:fmri eeg analysis

2007-12-20T17:16:40Z

Padma: /* Update */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:padma_eeg.png |thumb|320px|Title Here]]
|}

__NOTOC__
===Key Investigators===
* BWH: Padma Sundaram

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
We are interested in visualizing electromagnetic activity in the brain using
MR imaging with concurrent EEG.
We are particularly interested in inspecting epileptic foci and sleeping individuals.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan </h1>
Our approach
</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

</div>

<br style="clear: both;" />

</div>

===References===
* Direct detection of neuronal activity with MRI: fantasy, possibility, or reality?, Bandettini, N. Petridou and J. Bodurka, Appl. Magn. Reson. 29 (2005), pp. 65–88.
* Visual Analysis of Bioelectric Fields, Xavier Trioche, Rob MacLeod, Chris Johnson.

2008 Winter Project Week:fmri eeg analysis

2007-12-20T17:16:10Z

Padma: /* References */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:padma_eeg.png |thumb|320px|Title Here]]
|}

__NOTOC__
===Key Investigators===
* BWH: Padma Sundaram

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
We are interested in visualizing electromagnetic activity in the brain using
MR imaging with concurrent EEG.
We are particularly interested in inspecting epileptic foci and sleeping individuals.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan </h1>
Our approach
</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

====Update====
During this Project Week

====Project Half Week====
More here

</div>

<br style="clear: both;" />

</div>

===References===
* Direct detection of neuronal activity with MRI: fantasy, possibility, or reality?, Bandettini, N. Petridou and J. Bodurka, Appl. Magn. Reson. 29 (2005), pp. 65–88.
* Visual Analysis of Bioelectric Fields, Xavier Trioche, Rob MacLeod, Chris Johnson.

2008 Winter Project Week:fmri eeg analysis

2007-12-20T17:15:42Z

Padma: /* References */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:padma_eeg.png |thumb|320px|Title Here]]
|}

__NOTOC__
===Key Investigators===
* BWH: Padma Sundaram

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
We are interested in visualizing electromagnetic activity in the brain using
MR imaging with concurrent EEG.
We are particularly interested in inspecting epileptic foci and sleeping individuals.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan </h1>
Our approach
</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

====Update====
During this Project Week

====Project Half Week====
More here

</div>

<br style="clear: both;" />

</div>

===References===
* Direct detection of neuronal activity with MRI: fantasy, possibility, or reality?', Bandettini, N. Petridou and J. Bodurka, Appl. Magn. Reson. 29 (2005), pp. 65–88.

2008 Winter Project Week:fmri eeg analysis

2007-12-20T17:14:30Z

Padma:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:padma_eeg.png |thumb|320px|Title Here]]
|}

__NOTOC__
===Key Investigators===
* BWH: Padma Sundaram

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
We are interested in visualizing electromagnetic activity in the brain using
MR imaging with concurrent EEG.
We are particularly interested in inspecting epileptic foci and sleeping individuals.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan </h1>
Our approach
</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

====Update====
During this Project Week

====Project Half Week====
More here

</div>

<br style="clear: both;" />

</div>

===References===
* J. Melonakos, M. Niethammer, V. Mohan, M. Kubicki, J. Miller, A. Tannenbaum. Locally-Constrained Region-Based Methods for DW-MRI Segmentation. Submitted to MMBIA 2007.

2008 Winter Project Week:fmri eeg analysis

2007-12-20T15:43:15Z

Padma: New page: {| |Return to [[2008_Winter_Project_Week ]] |valign="top"|Title Here |} __NOTOC__ ===Key Investigators=== * BWH: P...

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:padma_eeg.png |thumb|320px|Title Here]]
|}

__NOTOC__
===Key Investigators===
* BWH: Padma Sundaram

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
More details.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan </h1>
Our approach
</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

====Update====
During this Project Week

====Project Half Week====
More here

</div>

<br style="clear: both;" />

</div>

===References===
* J. Melonakos, M. Niethammer, V. Mohan, M. Kubicki, J. Miller, A. Tannenbaum. Locally-Constrained Region-Based Methods for DW-MRI Segmentation. Submitted to MMBIA 2007.

2008 Winter Project Week

2007-12-20T15:37:33Z

Padma: /* All Other Projects */

Back to [[Project Events]], [[AHM_2008]], [[Events]]

== Projects ==
*2008 Project Week [[2008_Winter_Project_Week_Template|'''Template''']]
*[[2007_Programming/Project_Week_MIT#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]
*Next Project Week is at MIT -- June 23-27, 2008

===DBP Roadmap Projects===
Please note that the first four categories below correspond to four clinical Roadmap application projects that will be pursued in focused parallel tracks at the meeting, each corresponding to a DBP problem.
====[[DBP2:Harvard:Brain_Segmentation_Roadmap|DBP Harvard Roadmap Project: Stochastic Tractography for Velocardio Facial Syndrome (VCFS)]]====
*[[2008_Winter_Project_Week:StochasticTract_Arcuate|Stochastic tractography of the arcuate fasciculus in schizophrenia]] (Marek Kubicki, Tri Ngo, Doug Markant)

====[[DBP2:UNC:Cortical_Thickness_Roadmap|DBP UNC Roadmap Project: Cortical Thickness Measurement for Autism]]====
*[[2008_Winter_Project_Week:Cortical_Thickness|Cortical thickness analysis of pediatric brains]] (Heather Cody Hazlett, Martin Styner, Clement Vachet, Jim Miller)

====[[DBP2:MIND:Roadmap|DBP MIND Roadmap Project: Brain Lesion Analysis in Neuropsychiatric Systemic Lupus Erythematosus]]====
*[[2008_Winter_Project_Week:Lesions|Towards an end to end lesion analysis feature in Slicer3]] (Mark Scully, Jeremy Bockholt, Brad Davis, Marcel Prastawa, Sonia Pujol, Vincent Magnotta)

====[[DBP2:JHU:Roadmap|DBP JHU Roadmap Project: Segmentation and Registration for Robotic Prostate Intervention]]====
#[[2008_Winter_Project_Week:Robotic_Prostate_Interventions | Robotic Prostate Interventions]] (David Gobbi, Csaba Csoma, Junichi Tokuda, Katie Hayes)
#[[2008_Winter_Project_Week:Prostate_Segmentation|Prostate Segmentation]], (Yi Gao, Ponnappan Arumuganainar, John Melonakos, Allen Tannenbaum, Gabor Fichtinger)

===All Other Projects===
# [[2008_Winter_Project_Week_GroupwiseReg | Groupwise Registration and Atlas Building]] (Brad Davis, Serdar Balci, Casey Goodlett)
# [[2008_Winter_Project_Week:MRISC|Joint Segmentation and Classification of MR Images Based on Structure-specific Affine Registration]] (Mert Sabuncu, Kilian Pohl)
# [[2008_Winter_Project_Week:CorPar|Cortical Surface Parcellation]] (Thomas Yeo, Mert Sabuncu)
# [[2008_Winter_Project_Week:Dorsolateral_Prefrontal_Cortex_Segmentation|Dorsolateral Prefrontal Cortex Segmentation]] (Marek Kubicki, Sylvain Bouix, John Melonakos, Brad Davis, Polina Golland)
#[[2008_Winter_Project_Week:Particle_Correspondence_DTI|Incorporating DTI data into entropy-based particle system for cortical correspondence]] (Ipek Oguz, Josh Cates, Tom Fletcher, Martin Styner)
#[[2008_Winter_Project_Week:Population_DTI|Integrating population based DTI tools into NAMIC Kit]] (Casey Goodlett)
#[[2008_Winter_Project_Week:Population_DTI_Application|Application of population based DTI tools to Schizophrenia]] (Casey Goodlett, Marek Kubicki)
#[[2008_Winter_Project_Week:Geodesic_Tractography_Segmentation|Geodesic Tractography Segmentation]], (John Melonakos, Allen Tannenbaum, Marek Kubicki)
#[[2008_Winter_Project_Week:Fluid_Mechanics_Tractography|Fluid Mechanics Based DTI Tractography]] (Nathan Hageman)
#[[2008_Winter_Project_Week:MRMLScenesForExecutionModel |MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
#Unstructured Grids and Mesh Support(Curt, Alex, Steve, Will, Vince, Bob O'Bara)
#[[2008_Winter_Project_Week:PythonSupport |Python Support in Slicer 3]] (Luca, Bryan Smith, Dan Blezek)
#[[2008_Winter_Project_Week:MRMLTransformHardening |Transform hardening in MRML]] (Luca Antiga, Steve Pieper)
#[[2008_Winter_Project_Week:EventBrokerInSlicer3 |Event broker in Slicer3]] (Jim, Steve, Alex Y, Luca, Dan Blezek)
#[[2008_Winter_Project_Week:CPack |CPack]], CTest, CMake infrastructure Improvements(Katie, Steve, Bill Hoffman, Sebastien)
#[[2008_Winter_ProjectWeek:SlicerCookbook | Slicer GUI Style Guide and Cookbook]] (Wendy Plesniak, Sebastien Barre)
#Shape Descriptor Functions for Dendritic Spine Morphometrics and Colon Polyps (Bryan Smith, Padma Sundaram, Martin Styner)
#[[2008_Winter_Project_Week_VolumeRendering|Volume rendering]] (Andy Freudling, Steve Pieper, Grauer)
#[[2008_Winter_Project_Week_VolumeRenderingUsingCuda|Volume rendering using Cuda]] (Andy Freudling, Steve Pieper, Grauer)
#[[2008_Winter_Project_Week:3DWWidgets |3D W Widgets and Picking]] (Will Schroeder, Nicole Aucoin, Curt Lisle, Kiran Shivana)
#[[2008_Winter_Project_Week:OutOfCoreMRML | MRML support for out of core processing with fMRI and DTI as use cases]] (Steve Pieper, Jim Miller, Wendy Plesniak, Alex Yarmakovich, Will Schroeder)
#[[2008_Winter_Project_Week:XNAT_Integration | XNAT Integration]] ([http://www.xnat.org XNAT], [http://www.slicer.org Slicer], [http://www.Xcede.org XCEDE], [http://www.batchmake.org Batchmake]) (Dan Marcus, Steve Pieper, Stephen Aylward, Jeff Grethe, Julien Jomier)
#KWWidgets Roadmap (Sebastien Barre, Wendy Plesniak, Katie Hayes)
#Circuit Annotation Capability (for example drawing arrows above regions that are connected functionally, structurally, etc), (Mark Scully, others)
#Astronomical coordinate system support (Mike Halle, Doug Alan)
#[[2008_Winter_Project_Week:Meshing Techniques into NA-MIC Toolkit|New Meshing Techniques into NA-MIC]] [Univ. of Iowa] (Nicole Grosland, Vince Magnotta)
#[[2008_Winter_Project_Week:Finite Element Meshing into NA-MIC|Meshing Workflow into Slicer]] [Univ. of Iowa] (Nicole Grosland, Vince Magnotta, Kiran Shivana, Steve Pieper, Curt Lisle, Brad Davis)
#[[2008_Winter_Project_Week:SmallAnimalEvalNCI |Evaluating NA-MIC Tools for Small Animal Imaging Workflows]] [NCI] (Curt Lisle, Jack Collins, Killian Pohl)
#[[2008_Winter_Project_Week:GoFigure |GoFigure:High-Level Microscopy Image analysis Application and Algorithms]] [CalTech-Harvard Medical School] (Alex G, Sean Megason, Arnaud Gelas?)
#[[2008_Winter_Project_Week:IGT_IGSTK_Slicer| IGSTK-Slicer]] [Georgetown] (Haiying Liu, Patrick Cheng, Noby Hata, Junichi Tokuda)
#[[2008_Winter_Project_Week:IGT_Intelligent_Surgical_Instrument_Projects| Japanese Intelligent Surgical Instrument Project]] [AIST] (Noby Hata, Chinzei, Hong)
#[[2008_Winter_Project_Week:microslicer_3 | Doing microscopy image analysis with Slicer3]] [The Ohio State University](Kishore Mosaliganti, Raghu Machiraju, Brad Davis,Stephen Aylward, Steve Pieper)
#[[2008_Winter_Project_Week:fmri_image_analysis | fMRI Analysis with Slicer 3]] [The Ohio State University](Firdaus Janoos,Raghu Machiraju, Luis Ibanez,Steve Pieper, Wendy Plesniak)
#[[2008_Winter_Project_Week:Resampling_DTIs_with_Slicer3|Resampling DTIs with Slicer 3]] (Francois Budin, Sylvain Bouix)
#[[2008_Winter_Project_Week:fmri_eeg_analysis | Analyzing fMRI and concurrent EEG with Slicer and SCIRun]] [BWH] (Padma Sundaram)

== Dates.Venue.Registration ==

'''Dates:'''
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 10th'''.
* Project Activities will be held rest of the week between '''Monday, January 7th and Friday, January 11th'''.

'''Venue:''' The venue for the meeting is [http://www.marriott.com/hotels/travel/slccc-salt-lake-city-marriott-city-center/ Marriot City Center, Salt Lake City, Utah] Mariott City Center, Salt Lake City, Utah. [http://marriott.com/property/meetingsandevents/floorplans/slccc (Floorplan)]. To reserve rooms at the meeting rate of $129/night, please call the hotel at 1-801-961-8700 or 1-866-961-8700 (toll free) and mention that you are attending the NAMIC meeting. Please note that we do need attendees to use this hotel in order to not incur additional charges for the use of conference rooms.

<big> '''Registration:''' We are charging a registration fee to all participants. The fee covers the costs of the facilities and food provided. In order to keep the fee low, we need to get a sufficient number of hotel nights by our participants. See above for more on this. Please click [http://www.sci.utah.edu/namic2008/registration.html '''here'''] for online registration. This registration must be completed by Friday, December 14, 2007. </big>

Please note that this information can also be found [[AHM_2008#Dates.Venue.Registration|here.]]

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

===Introduction to NA-MIC Project Week===

Please read the introduction to these events [[Project_Events#Introduction|here]].

=== Agenda===

[[AHM_2008#Agenda|Agenda for AHM 2008 and Project Week]]

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
# [[Engineering:TCON_2007#2007-11-29|November 29, 2007: Kickoff TCON#1 (w/ NA-MIC Engeering Core only) to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-12-06|December 6, 2007: TCON#2 with all participants to Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-12-13|December 13, 2007: TCON#3 with Breakout Session owners to review agendas]]
# [[Engineering:TCON_2007#2007-12-13|December 20, 2007: TCON#4 to discuss outstanding projects and teams]]
# [[Engineering:TCON_2007#2008-01-03|January 3, 2008: TCON#5 to discuss outstanding projects and teams]]
# December 20, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# January 3, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# By December 17, 2008: [[2008_Winter_Project_Week_Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== Previous Project Events ==

A history of all the programming/project events in NA-MIC is available by following [[Project Events|this link]].

2008 Winter Project Week

2007-12-20T15:37:16Z

Padma: /* All Other Projects */

Back to [[Project Events]], [[AHM_2008]], [[Events]]

== Projects ==
*2008 Project Week [[2008_Winter_Project_Week_Template|'''Template''']]
*[[2007_Programming/Project_Week_MIT#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]
*Next Project Week is at MIT -- June 23-27, 2008

===DBP Roadmap Projects===
Please note that the first four categories below correspond to four clinical Roadmap application projects that will be pursued in focused parallel tracks at the meeting, each corresponding to a DBP problem.
====[[DBP2:Harvard:Brain_Segmentation_Roadmap|DBP Harvard Roadmap Project: Stochastic Tractography for Velocardio Facial Syndrome (VCFS)]]====
*[[2008_Winter_Project_Week:StochasticTract_Arcuate|Stochastic tractography of the arcuate fasciculus in schizophrenia]] (Marek Kubicki, Tri Ngo, Doug Markant)

====[[DBP2:UNC:Cortical_Thickness_Roadmap|DBP UNC Roadmap Project: Cortical Thickness Measurement for Autism]]====
*[[2008_Winter_Project_Week:Cortical_Thickness|Cortical thickness analysis of pediatric brains]] (Heather Cody Hazlett, Martin Styner, Clement Vachet, Jim Miller)

====[[DBP2:MIND:Roadmap|DBP MIND Roadmap Project: Brain Lesion Analysis in Neuropsychiatric Systemic Lupus Erythematosus]]====
*[[2008_Winter_Project_Week:Lesions|Towards an end to end lesion analysis feature in Slicer3]] (Mark Scully, Jeremy Bockholt, Brad Davis, Marcel Prastawa, Sonia Pujol, Vincent Magnotta)

====[[DBP2:JHU:Roadmap|DBP JHU Roadmap Project: Segmentation and Registration for Robotic Prostate Intervention]]====
#[[2008_Winter_Project_Week:Robotic_Prostate_Interventions | Robotic Prostate Interventions]] (David Gobbi, Csaba Csoma, Junichi Tokuda, Katie Hayes)
#[[2008_Winter_Project_Week:Prostate_Segmentation|Prostate Segmentation]], (Yi Gao, Ponnappan Arumuganainar, John Melonakos, Allen Tannenbaum, Gabor Fichtinger)

===All Other Projects===
# [[2008_Winter_Project_Week_GroupwiseReg | Groupwise Registration and Atlas Building]] (Brad Davis, Serdar Balci, Casey Goodlett)
# [[2008_Winter_Project_Week:MRISC|Joint Segmentation and Classification of MR Images Based on Structure-specific Affine Registration]] (Mert Sabuncu, Kilian Pohl)
# [[2008_Winter_Project_Week:CorPar|Cortical Surface Parcellation]] (Thomas Yeo, Mert Sabuncu)
# [[2008_Winter_Project_Week:Dorsolateral_Prefrontal_Cortex_Segmentation|Dorsolateral Prefrontal Cortex Segmentation]] (Marek Kubicki, Sylvain Bouix, John Melonakos, Brad Davis, Polina Golland)
#[[2008_Winter_Project_Week:Particle_Correspondence_DTI|Incorporating DTI data into entropy-based particle system for cortical correspondence]] (Ipek Oguz, Josh Cates, Tom Fletcher, Martin Styner)
#[[2008_Winter_Project_Week:Population_DTI|Integrating population based DTI tools into NAMIC Kit]] (Casey Goodlett)
#[[2008_Winter_Project_Week:Population_DTI_Application|Application of population based DTI tools to Schizophrenia]] (Casey Goodlett, Marek Kubicki)
#[[2008_Winter_Project_Week:Geodesic_Tractography_Segmentation|Geodesic Tractography Segmentation]], (John Melonakos, Allen Tannenbaum, Marek Kubicki)
#[[2008_Winter_Project_Week:Fluid_Mechanics_Tractography|Fluid Mechanics Based DTI Tractography]] (Nathan Hageman)
#[[2008_Winter_Project_Week:MRMLScenesForExecutionModel |MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
#Unstructured Grids and Mesh Support(Curt, Alex, Steve, Will, Vince, Bob O'Bara)
#[[2008_Winter_Project_Week:PythonSupport |Python Support in Slicer 3]] (Luca, Bryan Smith, Dan Blezek)
#[[2008_Winter_Project_Week:MRMLTransformHardening |Transform hardening in MRML]] (Luca Antiga, Steve Pieper)
#[[2008_Winter_Project_Week:EventBrokerInSlicer3 |Event broker in Slicer3]] (Jim, Steve, Alex Y, Luca, Dan Blezek)
#[[2008_Winter_Project_Week:CPack |CPack]], CTest, CMake infrastructure Improvements(Katie, Steve, Bill Hoffman, Sebastien)
#[[2008_Winter_ProjectWeek:SlicerCookbook | Slicer GUI Style Guide and Cookbook]] (Wendy Plesniak, Sebastien Barre)
#Shape Descriptor Functions for Dendritic Spine Morphometrics and Colon Polyps (Bryan Smith, Padma Sundaram, Martin Styner)
#[[2008_Winter_Project_Week_VolumeRendering|Volume rendering]] (Andy Freudling, Steve Pieper, Grauer)
#[[2008_Winter_Project_Week_VolumeRenderingUsingCuda|Volume rendering using Cuda]] (Andy Freudling, Steve Pieper, Grauer)
#[[2008_Winter_Project_Week:3DWWidgets |3D W Widgets and Picking]] (Will Schroeder, Nicole Aucoin, Curt Lisle, Kiran Shivana)
#[[2008_Winter_Project_Week:OutOfCoreMRML | MRML support for out of core processing with fMRI and DTI as use cases]] (Steve Pieper, Jim Miller, Wendy Plesniak, Alex Yarmakovich, Will Schroeder)
#[[2008_Winter_Project_Week:XNAT_Integration | XNAT Integration]] ([http://www.xnat.org XNAT], [http://www.slicer.org Slicer], [http://www.Xcede.org XCEDE], [http://www.batchmake.org Batchmake]) (Dan Marcus, Steve Pieper, Stephen Aylward, Jeff Grethe, Julien Jomier)
#KWWidgets Roadmap (Sebastien Barre, Wendy Plesniak, Katie Hayes)
#Circuit Annotation Capability (for example drawing arrows above regions that are connected functionally, structurally, etc), (Mark Scully, others)
#Astronomical coordinate system support (Mike Halle, Doug Alan)
#[[2008_Winter_Project_Week:Meshing Techniques into NA-MIC Toolkit|New Meshing Techniques into NA-MIC]] [Univ. of Iowa] (Nicole Grosland, Vince Magnotta)
#[[2008_Winter_Project_Week:Finite Element Meshing into NA-MIC|Meshing Workflow into Slicer]] [Univ. of Iowa] (Nicole Grosland, Vince Magnotta, Kiran Shivana, Steve Pieper, Curt Lisle, Brad Davis)
#[[2008_Winter_Project_Week:SmallAnimalEvalNCI |Evaluating NA-MIC Tools for Small Animal Imaging Workflows]] [NCI] (Curt Lisle, Jack Collins, Killian Pohl)
#[[2008_Winter_Project_Week:GoFigure |GoFigure:High-Level Microscopy Image analysis Application and Algorithms]] [CalTech-Harvard Medical School] (Alex G, Sean Megason, Arnaud Gelas?)
#[[2008_Winter_Project_Week:IGT_IGSTK_Slicer| IGSTK-Slicer]] [Georgetown] (Haiying Liu, Patrick Cheng, Noby Hata, Junichi Tokuda)
#[[2008_Winter_Project_Week:IGT_Intelligent_Surgical_Instrument_Projects| Japanese Intelligent Surgical Instrument Project]] [AIST] (Noby Hata, Chinzei, Hong)
#[[2008_Winter_Project_Week:microslicer_3 | Doing microscopy image analysis with Slicer3]] [The Ohio State University](Kishore Mosaliganti, Raghu Machiraju, Brad Davis,Stephen Aylward, Steve Pieper)
#[[2008_Winter_Project_Week:fmri_image_analysis | fMRI Analysis with Slicer 3]] [The Ohio State University](Firdaus Janoos,Raghu Machiraju, Luis Ibanez,Steve Pieper, Wendy Plesniak)
#[[2008_Winter_Project_Week:Resampling_DTIs_with_Slicer3|Resampling DTIs with Slicer 3]] (Francois Budin, Sylvain Bouix)
#[[2008_Winter_Project_Week:fmri_eeg_analysis | Analyzing fMRI and concurrent EEG with Slicer]] [BWH] (Padma Sundaram)

== Dates.Venue.Registration ==

'''Dates:'''
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 10th'''.
* Project Activities will be held rest of the week between '''Monday, January 7th and Friday, January 11th'''.

'''Venue:''' The venue for the meeting is [http://www.marriott.com/hotels/travel/slccc-salt-lake-city-marriott-city-center/ Marriot City Center, Salt Lake City, Utah] Mariott City Center, Salt Lake City, Utah. [http://marriott.com/property/meetingsandevents/floorplans/slccc (Floorplan)]. To reserve rooms at the meeting rate of $129/night, please call the hotel at 1-801-961-8700 or 1-866-961-8700 (toll free) and mention that you are attending the NAMIC meeting. Please note that we do need attendees to use this hotel in order to not incur additional charges for the use of conference rooms.

<big> '''Registration:''' We are charging a registration fee to all participants. The fee covers the costs of the facilities and food provided. In order to keep the fee low, we need to get a sufficient number of hotel nights by our participants. See above for more on this. Please click [http://www.sci.utah.edu/namic2008/registration.html '''here'''] for online registration. This registration must be completed by Friday, December 14, 2007. </big>

Please note that this information can also be found [[AHM_2008#Dates.Venue.Registration|here.]]

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

===Introduction to NA-MIC Project Week===

Please read the introduction to these events [[Project_Events#Introduction|here]].

=== Agenda===

[[AHM_2008#Agenda|Agenda for AHM 2008 and Project Week]]

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
# [[Engineering:TCON_2007#2007-11-29|November 29, 2007: Kickoff TCON#1 (w/ NA-MIC Engeering Core only) to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-12-06|December 6, 2007: TCON#2 with all participants to Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-12-13|December 13, 2007: TCON#3 with Breakout Session owners to review agendas]]
# [[Engineering:TCON_2007#2007-12-13|December 20, 2007: TCON#4 to discuss outstanding projects and teams]]
# [[Engineering:TCON_2007#2008-01-03|January 3, 2008: TCON#5 to discuss outstanding projects and teams]]
# December 20, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# January 3, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# By December 17, 2008: [[2008_Winter_Project_Week_Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== Previous Project Events ==

A history of all the programming/project events in NA-MIC is available by following [[Project Events|this link]].