NAMIC Wiki - User contributions [en]

2010 Summer Project Week EMSegmentation kmeans

2010-06-25T14:14:10Z

Priya:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* BWH: Priya Srinivasan, Daniel Haehn, Sylvain Bouix
* UPenn: Kilian Pohl

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
To implement as one of the options: KMeans automatic initialization of tissue class intensities in the EMSegmentation Module in Slicer3.

</div>

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

<h3>Approach, Plan</h3>
Currently we have stand alone python scripts that take in 3 inputs: a template MRML scene, path to the T1 image, path to the atlas images. Intensities are computed using KMeans and a MRML scene is outputted which can directly be loaded in Slicer3 for segmentation. Registration of images (T1 and atlases) has to be done as a preprocessing step before providing as inputs to the python scripts. Meet up during NAMIC week and see how best this process can be integrated as one of the options in the current EMSegmentation pipeline in Slicer3.

</div>

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

<h3>Progress</h3>
Met with Kilian and went over the current processing pipeline with the stand alone Python codes and now have a general understanding of how we should proceed in order to integrate into Slicer 3.6. Will work out the details in the coming weeks. Based on Kilian's suggestions, modified the Python codes to make it more easy to integrate into Slicer 3.6.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a '''Loadable module'''.

References:
*A Hierarchical Algorithm for MR Brain Image Parcellation. K. Pohl, S. Bouix, M. Nakamura, T. Rohlfing, R. McCarley, R. Kikinis, W. Grimson, M. E. Shenton, W. Wells. IEEE Transactions on Medical Imaging. 2007

2010 Summer Project Week EMSegmentation kmeans

2010-06-25T13:59:15Z

Priya:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* BWH: Priya Srinivasan, Daniel Haehn, Sylvain Bouix
* UPenn: Kilian Pohl

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
To implement as one of the options: KMeans automatic initialization of tissue class intensities in the EMSegmentation Module in Slicer3.

</div>

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

<h3>Approach, Plan</h3>
Currently we have stand alone python scripts that take in 3 inputs: a template MRML scene, path to the T1 image, path to the atlas images. Intensities are computed using KMeans and a MRML scene is outputted which can directly be loaded in Slicer3 for segmentation. Registration of images (T1 and atlases) has to be done as a preprocessing step before providing as inputs to the python scripts. Meet up during NAMIC week and see how best this process can be integrated as one of the options in the current EMSegmentation pipeline in Slicer3.

</div>

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

<h3>Progress</h3>
Met with Kilian and went over the current processing pipeline with the Python codes we have and got an understanding of how we should proceed in order to integrate into Slicer 3.6. Will work out the details in the coming weeks. Worked on the Python codes to make it more easy to integrate into Slicer 3.6.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a '''Loadable module'''.

References:
*A Hierarchical Algorithm for MR Brain Image Parcellation. K. Pohl, S. Bouix, M. Nakamura, T. Rohlfing, R. McCarley, R. Kikinis, W. Grimson, M. E. Shenton, W. Wells. IEEE Transactions on Medical Imaging. 2007

2010 Summer Project Week EMSegmentation kmeans

2010-06-25T13:58:40Z

Priya:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* BWH: Priya Srinivasan, Daniel Haehn, Sylvain Bouix
* UPenn: Kilian Pohl

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
To implement as one of the options: KMeans automatic initialization of tissue class intensities in the EMSegmentation Module in Slicer3.

</div>

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

<h3>Approach, Plan</h3>
Currently we have stand alone python scripts that take in 3 inputs: a template MRML scene, path to the T1 image, path to the atlas images. Intensities are computed using KMeans and a MRML scene is outputted which can directly be loaded in Slicer3 for segmentation. Registration of images (T1 and atlases) has to be done as a preprocessing step before providing as inputs to the python scripts. Meet up during NAMIC week and see how best this process can be integrated as one of the options in the current EMSegmentation pipeline in Slicer3.

</div>

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

<h3>Progress</h3>
Met with Kilian and went over the current processing pipeline with the Python codes we have and got an understanding of how we should proceed in order to integrate into Slicer 3.6. Will work more in detail in the coming weeks. Worked on the Python codes to make it more easy to integrate into Slicer 3.6.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a '''Loadable module'''.

References:
*A Hierarchical Algorithm for MR Brain Image Parcellation. K. Pohl, S. Bouix, M. Nakamura, T. Rohlfing, R. McCarley, R. Kikinis, W. Grimson, M. E. Shenton, W. Wells. IEEE Transactions on Medical Imaging. 2007

2010 Summer Project Week EMSegmentation kmeans

2010-06-04T20:54:29Z

Priya:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
To implement as one of the options: KMeans automatic initialization of tissue class intensities in the EMSegmentation Module in Slicer3.

</div>

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

<h3>Approach, Plan</h3>
Currently we have stand alone python scripts that take in 3 inputs: a template MRML scene, path to the T1 image, path to the atlas images. Intensities are computed using KMeans and a MRML scene is outputted which can directly be loaded in Slicer3 for segmentation. Registration of images (T1 and atlases) has to be done as a preprocessing step before providing as inputs to the python scripts. Meet up during NAMIC week and see how best this process can be integrated as one of the options in the current EMSegmentation pipeline in Slicer3.

</div>

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

<h3>Progress</h3>
Will be updated ...

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a '''Loadable module'''.

References:
*A Hierarchical Algorithm for MR Brain Image Parcellation. K. Pohl, S. Bouix, M. Nakamura, T. Rohlfing, R. McCarley, R. Kikinis, W. Grimson, M. E. Shenton, W. Wells. IEEE Transactions on Medical Imaging. 2007

2010 Summer Project Week EMSegmentation kmeans

2010-06-04T20:51:09Z

Priya:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
To implement as one of the options: KMeans automatic initialization of tissue class intensities in the EMSegmentation Module in Slicer3.

</div>

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

<h3>Approach, Plan</h3>
Currently we have stand alone python scripts that take in 3 inputs: a template MRML scene, path to the T1 image, path to the atlas images. Intensities are computed using KMeans and a MRML scene is outputted which can directly be loaded in Slicer3 for segmentation. Registration of images (T1 and atlases) has to be done as a preprocessing step before providing as inputs to the python scripts. Meet up during NAMIC week and see how best this process can be integrated as one of the options with the current EMSegmentation pipeline in Slicer3.

</div>

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

<h3>Progress</h3>
Will be updated ...

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a '''Loadable module'''.

References:
*A Hierarchical Algorithm for MR Brain Image Parcellation. K. Pohl, S. Bouix, M. Nakamura, T. Rohlfing, R. McCarley, R. Kikinis, W. Grimson, M. E. Shenton, W. Wells. IEEE Transactions on Medical Imaging. 2007

2010 Summer Project Week EMSegmentation kmeans

2010-06-04T20:49:27Z

Priya:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* BWH: Ryan Eckbo

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
To implement as one of the options: KMeans automatic initialization of tissue class intensities in the EMSegmentation Module in Slicer3.

</div>

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

<h3>Approach, Plan</h3>
Currently we have stand alone python scripts that take in 3 inputs: a template MRML scene, path to the T1 image, path to the atlas images. Intensities are computed using KMeans and a MRML scene is outputted which can directly be loaded in Slicer3 for segmentation. Registration of images (T1 and atlases) has to be done as a preprocessing step before providing as inputs to the python scripts. Meet up during NAMIC week and see how best this process can be integrated as one of the options with the current EMSegmentation pipeline in Slicer3.

</div>

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

<h3>Progress</h3>
Will be updated ...

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a '''Loadable module'''.

References:
*A Hierarchical Algorithm for MR Brain Image Parcellation. K. Pohl, S. Bouix, M. Nakamura, T. Rohlfing, R. McCarley, R. Kikinis, W. Grimson, M. E. Shenton, W. Wells. IEEE Transactions on Medical Imaging. 2007

2010 Summer Project Week EMSegmentation kmeans

2010-06-04T20:49:14Z

Priya:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* BWH: Ryan Eckbo

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
To implement as one of the options: KMeans automatic initialization of tissue class intensities in the EMSegmentation Module in Slicer3.

</div>

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

<h3>Approach, Plan</h3>
Currently we have stand alone python scripts that take in 3 inputs: a template MRML scene, path to the T1 image, path to the atlas images. Intensities are computed using KMeans and a MRML scene is outputted which can directly be loaded in Slicer3 for segmentation. Registration of images (T1 and atlases) has to be done as a preprocessing step before providing as inputs to the python scripts. Meet up during NAMIC week and see how best this process can be integrated as one of the options with the current EMSegmentation pipeline in Slicer3.

</div>

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

<h3>Progress</h3>
Will be updated

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a '''Loadable module'''.

References:
*A Hierarchical Algorithm for MR Brain Image Parcellation. K. Pohl, S. Bouix, M. Nakamura, T. Rohlfing, R. McCarley, R. Kikinis, W. Grimson, M. E. Shenton, W. Wells. IEEE Transactions on Medical Imaging. 2007

2010 Summer Project Week EMSegmentation kmeans

2010-06-04T20:48:56Z

Priya: Created page with '__NOTOC__ <gallery> Image:PW-MIT2010.png|Projects List </gallery> ==Key Investigators== * BWH: Ryan Eckbo <div style="margin: 20px;"> <div…'

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* BWH: Ryan Eckbo

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
To implement as one of the options: KMeans automatic initialization of tissue class intensities in the EMSegmentation Module in Slicer3.

</div>

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

<h3>Approach, Plan</h3>
Currently we have stand alone python scripts that take in 3 inputs: a template MRML scene, path to the T1 image, path to the atlas images. Intensities are computed using KMeans and a MRML scene is outputted which can directly be loaded in Slicer3 for segmentation. Registration of images (T1 and atlases) has to be done as a preprocessing step before providing as inputs to the python scripts. Meet up during NAMIC week and see how best this process can be integrated as one of the options with the current EMSegmentation pipeline in Slicer3.

</div>

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

<h3>Progress</h3>
To be announced

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a '''Loadable module'''.

References:
*A Hierarchical Algorithm for MR Brain Image Parcellation. K. Pohl, S. Bouix, M. Nakamura, T. Rohlfing, R. McCarley, R. Kikinis, W. Grimson, M. E. Shenton, W. Wells. IEEE Transactions on Medical Imaging. 2007

2010 Summer Project Week

2010-06-04T18:56:03Z

Priya:

__NOTOC__

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

[[Image:PW-MIT2010.png|300px]]

==Background==

We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 21-25, 2010
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here] to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&app=resvlink&fromDate=6/20/10&toDate=6/25/10 Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process.

''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''
''' $189/night/room (plus tax).'''
''' This rate is good only through June 1.'''

Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290.

*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

==Agenda==
=== Monday, June 21, 2010 ===
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)

=== Tuesday, June 22, 2010 ===
** 8:30am breakfast
**9-9:45am: NA-MIC Kit Update (Jim Miller) - include Module nomenclature (Extensions: cmdline vs loadable, Built-in), QT, Include Superbuild demo by Dave P.
**9:45-10:30am 3D Slicer Update (Steve Pieper)
**10:30-11am OpenIGTLink Update (Junichi Tokuda)
**11-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
** noon lunch
** 1-3pm: Breakout Session: QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)
** 3pm: [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
** 4-5pm [[2010 Summer Project Week Breakout Session: Data Management]] (Dan Marcus, Stephen Aylward)
** 5:30pm adjourn for day

=== Wednesday, June 23, 2010 ===
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2010 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
**12:45pm: [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
**1-3pm: Breakout Session: [[Microscopy_Image_Analysis]] (Sean Megason)
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:QA Training]] (Luis Ibanesz)
**3-4pm: Breakout Session: [[2010 Summer Project Week Breakout Session:VTK Widget]] (Nicole, Kilian, JC)
** 5:30pm adjourn for day

=== Thursday, June 24, 2010 ===
** 8:30am breakfast

** 9am-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
** noon lunch
** 1-2pm: [[2010 Summer Project Week Breakout Session:GWE]] (Marco Ruiz)
** 2-2:30pm: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)
** 5:30pm adjourn for day

=== Friday, June 25, 2010 ===
** 8:30am breakfast
** 10am-noon: [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2011|in Utah, Fill in Dates]]

==Projects==

=== Segmentation ===
*[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
*[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
*[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)
*[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)
*[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping integration with Slicer]] (Nicole Aucoin, Min Chen)
*[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)
*[[2010_Summer_Project_Week_Left ventricular scar segmentation| LV scar segmentation display and fusion]] (Dana C. Peters, Felix Liu, BIDMC, Boston)
*[[2010_Summer_Project_Week_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans ]](Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)
=== Registration ===
*[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
*[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Nadya Shusharina, Greg Sharp)
*[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)
*[[2010_Summer_Project_Week_Best_Regularization_Term_for_Demons_Registration_Algorithm|Best Regularization Term for Demons Registration Algorithm]] (Rui Li, Greg Sharp)
*[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)
*[[2010_Summer_Project_Week_MR_to_Ultrasound_Registration_Methodology|MR to Ultrasound Registration Methodology]] (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward)
*[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)

=== IGT ===
*[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Planning|MR to CT Registration for Prostate Brachytherapy Planning]] (Andriy Fedorov, Dominik Meier, Hans Johnson)
*Prostate Intervention(Junichi, Sam Song, Tamas Ungi?)
* Liver Ablation (Haiying Liu)
* BrainLab-Aurora HybridNav (Isaiah Norton, Dan Marcus)
*[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)

=== Radiotherapy ===
*[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp)
*[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)

=== Analysis ===
*Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
*Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)
*[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
*[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
*[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)

===[[Microscopy Image Analysis]] ===
* Malaterre, Gouaillard: DICOM supplement [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf 145]: Microscopy Image in the Dicom Standard
* Laehman, Gouaillard: Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more
* Gouaillard: Flow Cytometry
* [[Import/Export Farsight-GoFigure results]] (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)
* [[Farsight nuclear segmentation as GoFigure plugin]] (Arnaud Gelas, Sean Megason, Badri Roysam)
* [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju)
* [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Stever Pieper)
* [[Seedings results comparison]] (Antonin Perrot-Audet, Kishore Mosaliganti, Sean Megason, Badri Roysam)
* [[ITK GPAC level set]] (K. Palaniappan, Kishore Mosaliganti, Sean Megason)
* [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)

=== Shape Analysis ===
*[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)
* [[Shape Analysis projects, integration with Slicer3]] (Beatriz Paniagua, Martin Styner)

=== Informatics ===
* Computer Aided Photodynamic Therapy (Pietka, Spinczyk)

=== Diffusion ===
*Fluid Mechanics Based Tractography (Nathan Hageman)
*[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)

=== NA-MIC Kit Internals ===
*Module Inventory (Steve, Jim)
*Viewer Manager Factory (Alex Y., Kilian, Steve, Nicole)
* [[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andrey Fedorov, Yanling Liu, Alex Yarmarkovich)
*XNAT Enterprise webservices client for Slicer (Wendy, Mark)
*[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)

*VTKWidgets (JC, will, Schroeder, Nicole, Ron)
*Superbuild (Dave Partika, Steve Pieper, Katie Hayes)
*[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on June 10, 2009: [[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.
# By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## 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. XNAT/MIDAS). 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)
# 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...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Attendee List==

<big>'''NOTE:'''</big> <font color="maroon">THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD '''NOT''' EDIT THIS, BUT [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 REGISTER BY CLICKING HERE.]</font>

#Aucoin, Nicole, BWH
#Audette, Michel, Kitware
#Aylward, Stephen, Kitware, Inc
#Boucharin, Alexis, UNC Neuro Image Research and Analysis Laboratories
#Bouix, Sylvain, BWH
#Budin, Francois, UNC
#Burdette, Everette, Acoustic MedSystems, Inc.
#Chen, Min, Johns Hopkins University
#Datar, Manasi, SCI Institute
#Eckbo, Ryan, BWH
#Fedorov, Andriy, Surgical Planning Lab
#Fillion-Robin, Jean-Christophe, Kitware Inc.
#Finet, Julien, Kitware Inc
#Fishbaugh, James, SCI Institute
#Gao, Yi, Gerogia Tech
#GELAS, Arnaud, Harvard Medical School
#gouaillard, alexandre, CoSMo Software
#Gouttard, Sylvain, SCI Institute
#Haehn, Daniel, University of Pennsylvania
#Hageman, Nathan
#Hahn, Dieter, University Erlangen
#Hamel, Corentin, UNC Chapel Hill
#Hata, Nobuhiko, Brigham and Women's Hospital
#Hayes, Kathryn, Brigham and Women's Hospital
#Holton, Leslie, Medtronic Navigation
#Ibanez, Luis, KITWARE Inc.
#Johnson, Hans, University of Iowa
#Kapur, Tina, Brigham and Women's Hospital
#Kikinis, Ron, Brigham and Women's Hospital
#Kim, Minjeong, UNC-Chapel Hill
#Kolesov, Ivan, Georgia Institute of Technology
#Larson, Garrett, UNC-CH
#Li, Rui, MGH
#Lisle, Curtis, KnowledgeVis, LLC
#Liu, Haiying, Brigham and Women's Hospital
#Liu, Yanling, SAIC-Frederick, Inc.
#Magnotta, Vincent, The University of Iowa
#malaterre, mathieu, CoSMo Software
#Mastrogiacomo, Katie, Brigham and Women's Hospital
#Matsui, Joy, University
#Megason, Sean, Harvard Medical School
#Meier, Dominik, BWH, Boston MA
#menze, bjoern, CSAIL MIT
#Mosaliganti, Kishore, Harvard Medical School
#Niethammer, Marc, UNC Chapel Hill
#Norton, Isaiah, BWH Neurosurgery
#Paniagua, Beatriz, University of North Caolina at Chapel Hill
#Papademetris, Xenophon, Yale University
#Partyka, David, Kitware Inc
#Pathak, Sudhir, Univeristy Of Pittsburgh
#Peroni, Marta, Politecnico di Milano
#Perrot-Audet, Antonin, Harvard Medical School
#Pieper, Steve, Isomics, Inc.
#Plesniak, Wendy, BWH
#Pohl, Kilian, IBM
#Pujol, Sonia, Brigham and Women's Hospital
#Rannou, Nicolas, Harvard Medical School
#Riklin Raviv, Tammy, MIT, CSAIL
#Ruiz, Marco, UCSD
#Schroeder, William, Kitware
#Scully, Mark, The Mind Research Network
#Sharp, Greg, MGH
#Shi, Yundi, UNC Chapel Hill
#Shusharina, Nadya, MGH
#Smith, Gareth, Wolfson Medical Imaging Centre (WMIC)
#Souhait, Lydie, Harvard Medical School
#Spinczyk, Dominik, Silesian University of Technology
#Srinivasan, Padmapriya
#Tao, Xiaodong, GE Research
#Ungi, Tamas, Queen's University
#Vachet, Clement, UNC Chapel Hill
#Veni, Gopalkrishna, SCI Institute
#Wassermann, Demian, SPL/LMI/PNL
#Wells, Sandy, BWH
#Wu, Guorong, University of North Carolina at Chapel Hill

2010 Summer Project Week

2010-06-04T18:53:42Z

Priya:

__NOTOC__

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

[[Image:PW-MIT2010.png|300px]]

==Background==

We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 21-25, 2010
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here] to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&app=resvlink&fromDate=6/20/10&toDate=6/25/10 Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process.

''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''
''' $189/night/room (plus tax).'''
''' This rate is good only through June 1.'''

Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290.

*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

==Agenda==
=== Monday, June 21, 2010 ===
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)

=== Tuesday, June 22, 2010 ===
** 8:30am breakfast
**9-9:45am: NA-MIC Kit Update (Jim Miller) - include Module nomenclature (Extensions: cmdline vs loadable, Built-in), QT, Include Superbuild demo by Dave P.
**9:45-10:30am 3D Slicer Update (Steve Pieper)
**10:30-11am OpenIGTLink Update (Junichi Tokuda)
**11-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
** noon lunch
** 1-3pm: Breakout Session: QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)
** 3pm: [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
** 4-5pm [[2010 Summer Project Week Breakout Session: Data Management]] (Dan Marcus, Stephen Aylward)
** 5:30pm adjourn for day

=== Wednesday, June 23, 2010 ===
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2010 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
**12:45pm: [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
**1-3pm: Breakout Session: [[Microscopy_Image_Analysis]] (Sean Megason)
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:QA Training]] (Luis Ibanesz)
**3-4pm: Breakout Session: [[2010 Summer Project Week Breakout Session:VTK Widget]] (Nicole, Kilian, JC)
** 5:30pm adjourn for day

=== Thursday, June 24, 2010 ===
** 8:30am breakfast

** 9am-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
** noon lunch
** 1-2pm: [[2010 Summer Project Week Breakout Session:GWE]] (Marco Ruiz)
** 2-2:30pm: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)
** 5:30pm adjourn for day

=== Friday, June 25, 2010 ===
** 8:30am breakfast
** 10am-noon: [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2011|in Utah, Fill in Dates]]

==Projects==

=== Segmentation ===
*[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
*[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
*[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)
*[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)
*[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping integration with Slicer]] (Nicole Aucoin, Min Chen)
*[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)
*[[2010_Summer_Project_Week_Left ventricular scar segmentation| LV scar segmentation display and fusion]] (Dana C. Peters, Felix Liu, BIDMC, Boston)
*[[2010_Summer_Project_Week_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans ]](Daniel Haehn, Kilian Pohl, Sylvain Bouix, Priya Srinivasan)
=== Registration ===
*[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
*[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Nadya Shusharina, Greg Sharp)
*[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)
*[[2010_Summer_Project_Week_Best_Regularization_Term_for_Demons_Registration_Algorithm|Best Regularization Term for Demons Registration Algorithm]] (Rui Li, Greg Sharp)
*[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)
*[[2010_Summer_Project_Week_MR_to_Ultrasound_Registration_Methodology|MR to Ultrasound Registration Methodology]] (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward)
*[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)

=== IGT ===
*[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Planning|MR to CT Registration for Prostate Brachytherapy Planning]] (Andriy Fedorov, Dominik Meier, Hans Johnson)
*Prostate Intervention(Junichi, Sam Song, Tamas Ungi?)
* Liver Ablation (Haiying Liu)
* BrainLab-Aurora HybridNav (Isaiah Norton, Dan Marcus)
*[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)

=== Radiotherapy ===
*[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp)
*[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)

=== Analysis ===
*Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
*Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)
*[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
*[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
*[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)

===[[Microscopy Image Analysis]] ===
* Malaterre, Gouaillard: DICOM supplement [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf 145]: Microscopy Image in the Dicom Standard
* Laehman, Gouaillard: Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more
* Gouaillard: Flow Cytometry
* [[Import/Export Farsight-GoFigure results]] (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)
* [[Farsight nuclear segmentation as GoFigure plugin]] (Arnaud Gelas, Sean Megason, Badri Roysam)
* [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju)
* [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Stever Pieper)
* [[Seedings results comparison]] (Antonin Perrot-Audet, Kishore Mosaliganti, Sean Megason, Badri Roysam)
* [[ITK GPAC level set]] (K. Palaniappan, Kishore Mosaliganti, Sean Megason)
* [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)

=== Shape Analysis ===
*[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)
* [[Shape Analysis projects, integration with Slicer3]] (Beatriz Paniagua, Martin Styner)

=== Informatics ===
* Computer Aided Photodynamic Therapy (Pietka, Spinczyk)

=== Diffusion ===
*Fluid Mechanics Based Tractography (Nathan Hageman)
*[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)

=== NA-MIC Kit Internals ===
*Module Inventory (Steve, Jim)
*Viewer Manager Factory (Alex Y., Kilian, Steve, Nicole)
* [[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andrey Fedorov, Yanling Liu, Alex Yarmarkovich)
*XNAT Enterprise webservices client for Slicer (Wendy, Mark)
*[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)

*VTKWidgets (JC, will, Schroeder, Nicole, Ron)
*Superbuild (Dave Partika, Steve Pieper, Katie Hayes)
*[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on June 10, 2009: [[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.
# By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## 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. XNAT/MIDAS). 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)
# 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...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Attendee List==

<big>'''NOTE:'''</big> <font color="maroon">THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD '''NOT''' EDIT THIS, BUT [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 REGISTER BY CLICKING HERE.]</font>

#Aucoin, Nicole, BWH
#Audette, Michel, Kitware
#Aylward, Stephen, Kitware, Inc
#Boucharin, Alexis, UNC Neuro Image Research and Analysis Laboratories
#Bouix, Sylvain, BWH
#Budin, Francois, UNC
#Burdette, Everette, Acoustic MedSystems, Inc.
#Chen, Min, Johns Hopkins University
#Datar, Manasi, SCI Institute
#Eckbo, Ryan, BWH
#Fedorov, Andriy, Surgical Planning Lab
#Fillion-Robin, Jean-Christophe, Kitware Inc.
#Finet, Julien, Kitware Inc
#Fishbaugh, James, SCI Institute
#Gao, Yi, Gerogia Tech
#GELAS, Arnaud, Harvard Medical School
#gouaillard, alexandre, CoSMo Software
#Gouttard, Sylvain, SCI Institute
#Haehn, Daniel, University of Pennsylvania
#Hageman, Nathan
#Hahn, Dieter, University Erlangen
#Hamel, Corentin, UNC Chapel Hill
#Hata, Nobuhiko, Brigham and Women's Hospital
#Hayes, Kathryn, Brigham and Women's Hospital
#Holton, Leslie, Medtronic Navigation
#Ibanez, Luis, KITWARE Inc.
#Johnson, Hans, University of Iowa
#Kapur, Tina, Brigham and Women's Hospital
#Kikinis, Ron, Brigham and Women's Hospital
#Kim, Minjeong, UNC-Chapel Hill
#Kolesov, Ivan, Georgia Institute of Technology
#Larson, Garrett, UNC-CH
#Li, Rui, MGH
#Lisle, Curtis, KnowledgeVis, LLC
#Liu, Haiying, Brigham and Women's Hospital
#Liu, Yanling, SAIC-Frederick, Inc.
#Magnotta, Vincent, The University of Iowa
#malaterre, mathieu, CoSMo Software
#Mastrogiacomo, Katie, Brigham and Women's Hospital
#Matsui, Joy, University
#Megason, Sean, Harvard Medical School
#Meier, Dominik, BWH, Boston MA
#menze, bjoern, CSAIL MIT
#Mosaliganti, Kishore, Harvard Medical School
#Niethammer, Marc, UNC Chapel Hill
#Norton, Isaiah, BWH Neurosurgery
#Paniagua, Beatriz, University of North Caolina at Chapel Hill
#Papademetris, Xenophon, Yale University
#Partyka, David, Kitware Inc
#Pathak, Sudhir, Univeristy Of Pittsburgh
#Peroni, Marta, Politecnico di Milano
#Perrot-Audet, Antonin, Harvard Medical School
#Pieper, Steve, Isomics, Inc.
#Plesniak, Wendy, BWH
#Pohl, Kilian, IBM
#Pujol, Sonia, Brigham and Women's Hospital
#Rannou, Nicolas, Harvard Medical School
#Riklin Raviv, Tammy, MIT, CSAIL
#Ruiz, Marco, UCSD
#Schroeder, William, Kitware
#Scully, Mark, The Mind Research Network
#Sharp, Greg, MGH
#Shi, Yundi, UNC Chapel Hill
#Shusharina, Nadya, MGH
#Smith, Gareth, Wolfson Medical Imaging Centre (WMIC)
#Souhait, Lydie, Harvard Medical School
#Spinczyk, Dominik, Silesian University of Technology
#Srinivasan, Padmapriya
#Tao, Xiaodong, GE Research
#Ungi, Tamas, Queen's University
#Vachet, Clement, UNC Chapel Hill
#Veni, Gopalkrishna, SCI Institute
#Wassermann, Demian, SPL/LMI/PNL
#Wells, Sandy, BWH
#Wu, Guorong, University of North Carolina at Chapel Hill

2010 Summer Project Week EMSegmenter kmeans

2010-06-04T18:49:26Z

Priya: Created page with 'http://wiki.na-mic.org/Wiki/index.php?title=2010_Summer_Project_Week_EMSegmenter_kmeans'

[[http://wiki.na-mic.org/Wiki/index.php?title=2010_Summer_Project_Week_EMSegmenter_kmeans]]

2008 Summer Project Week:LobeParcellation

2008-06-21T02:44:39Z

Priya:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:RoiPar.PNG|thumb|320px|Lobe parcellations in a coronal slice]]
|}

__NOTOC__

===Key Investigators===

* BWH: Sylvain Bouix, Yogesh Rathi, Padmapriya Srinivasan
* SPL: Kilian Pohl
* Kitware: Brad Davis

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

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

<h1>Objective</h1>
To build a lobe parcellation algorithm for our 3T data set. The spatial priors are based on 100 existing manually-lobe parcellated 1.5T data.

</div>

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

<h1>Approach, Plan</h1>
Our plan is to use an algorithm described in Reference 1 to construct probability maps of the lobes using an unbiased registration approach. The algorithm uses a ''label space'' representation that allows for direct registration.
We will then tune the EMsegmenter of Slicer3 to perform the segmentation.

</div>

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

<h1>Progress</h1>
We have been using a MATLAB(R) implementation of the atlas building algorithm to construct the atlas and fine tuning it for 10 subjects.

</div>

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

</div>

===References===

#James Malcolm, Yogesh Rathi,and Allen Tannenbaum, "Label Space: A multi-object Shape Representation", IWCIA 2008,LNCS 4958, pp. 185-196.
#Motoaki Nakamura, Dean F. Salisbury, Yoshio Hirayasu, Sylvain Bouix, Kilian M. Pohl, Takeshi Yoshida, Min-Seong Koo, Martha E. Shenton, and Robert W. McCarley, "Neocortical Gray Matter Volume in First-Episode Schizophrenia and First-Episode Affective Psychosis: A Cross-Sectional and Longitudinal MRI Study", Biol Psychiatry 2007;62:773–783

2008 Summer Project Week:LobeParcellation

2008-06-21T02:43:17Z

Priya:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:RoiPar.PNG|thumb|320px|Coronal slice of lobe parcellations]]
|}

__NOTOC__

===Key Investigators===

* BWH: Sylvain Bouix, Yogesh Rathi, Padmapriya Srinivasan
* SPL: Kilian Pohl
* Kitware: Brad Davis

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

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

<h1>Objective</h1>
To build a lobe parcellation algorithm for our 3T data set. The spatial priors are based on 100 existing manually-lobe parcellated 1.5T data.

</div>

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

<h1>Approach, Plan</h1>
Our plan is to use an algorithm described in Reference 1 to construct probability maps of the lobes using an unbiased registration approach. The algorithm uses a ''label space'' representation that allows for direct registration.
We will then tune the EMsegmenter of Slicer3 to perform the segmentation.

</div>

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

<h1>Progress</h1>
We have been using a MATLAB(R) implementation of the atlas building algorithm to construct the atlas and fine tuning it for 10 subjects.

</div>

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

</div>

===References===

#James Malcolm, Yogesh Rathi,and Allen Tannenbaum, "Label Space: A multi-object Shape Representation", IWCIA 2008,LNCS 4958, pp. 185-196.
#Motoaki Nakamura, Dean F. Salisbury, Yoshio Hirayasu, Sylvain Bouix, Kilian M. Pohl, Takeshi Yoshida, Min-Seong Koo, Martha E. Shenton, and Robert W. McCarley, "Neocortical Gray Matter Volume in First-Episode Schizophrenia and First-Episode Affective Psychosis: A Cross-Sectional and Longitudinal MRI Study", Biol Psychiatry 2007;62:773–783

2008 Summer Project Week:LobeParcellation

2008-06-21T02:20:37Z

Priya:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:RoiPar.PNG|thumb|320px|]]
|}

__NOTOC__

===Key Investigators===

* BWH: Sylvain Bouix, Yogesh Rathi, Padmapriya Srinivasan
* SPL: Kilian Pohl
* Kitware: Brad Davis

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

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

<h1>Objective</h1>
To build a lobe parcellation algorithm for our 3T data set. The spatial priors are based on 100 existing manually-lobe parcellated 1.5T data.

</div>

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

<h1>Approach, Plan</h1>
Our plan is to use an algorithm described in Reference 1 to construct probability maps of the lobes using an unbiased registration approach. The algorithm uses a ''label space'' representation that allows for direct registration.
We will then tune the EMsegmenter of Slicer3 to perform the segmentation.

</div>

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

<h1>Progress</h1>
We have been using a MATLAB(R) implementation of the atlas building algorithm to construct the atlas and fine tuning it for 10 subjects.

</div>

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

</div>

===References===

#James Malcolm, Yogesh Rathi,and Allen Tannenbaum, "Label Space: A multi-object Shape Representation", IWCIA 2008,LNCS 4958, pp. 185-196.
#Motoaki Nakamura, Dean F. Salisbury, Yoshio Hirayasu, Sylvain Bouix, Kilian M. Pohl, Takeshi Yoshida, Min-Seong Koo, Martha E. Shenton, and Robert W. McCarley, "Neocortical Gray Matter Volume in First-Episode Schizophrenia and First-Episode Affective Psychosis: A Cross-Sectional and Longitudinal MRI Study", Biol Psychiatry 2007;62:773–783

2008 Summer Project Week:LobeParcellation

2008-06-21T02:19:17Z

Priya:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:RoiPar.PNG|320px]]
|}

__NOTOC__

===Key Investigators===

* BWH: Sylvain Bouix, Yogesh Rathi, Padmapriya Srinivasan
* SPL: Kilian Pohl
* Kitware: Brad Davis

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

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

<h1>Objective</h1>
To build a lobe parcellation algorithm for our 3T data set. The spatial priors are based on 100 existing manually-lobe parcellated 1.5T data.

</div>

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

<h1>Approach, Plan</h1>
Our plan is to use an algorithm described in Reference 1 to construct probability maps of the lobes using an unbiased registration approach. The algorithm uses a ''label space'' representation that allows for direct registration.
We will then tune the EMsegmenter of Slicer3 to perform the segmentation.

</div>

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

<h1>Progress</h1>
We have been using a MATLAB(R) implementation of the atlas building algorithm to construct the atlas and fine tuning it for 10 subjects.

</div>

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

</div>

===References===

#James Malcolm, Yogesh Rathi,and Allen Tannenbaum, "Label Space: A multi-object Shape Representation", IWCIA 2008,LNCS 4958, pp. 185-196.
#Motoaki Nakamura, Dean F. Salisbury, Yoshio Hirayasu, Sylvain Bouix, Kilian M. Pohl, Takeshi Yoshida, Min-Seong Koo, Martha E. Shenton, and Robert W. McCarley, "Neocortical Gray Matter Volume in First-Episode Schizophrenia and First-Episode Affective Psychosis: A Cross-Sectional and Longitudinal MRI Study", Biol Psychiatry 2007;62:773–783

2008 Summer Project Week:LobeParcellation

2008-06-21T02:17:58Z

Priya:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]

|}

__NOTOC__

===Key Investigators===
[[Image:RoiPar.PNG|320px]]
* BWH: Sylvain Bouix, Yogesh Rathi, Padmapriya Srinivasan
* SPL: Kilian Pohl
* Kitware: Brad Davis

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

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

<h1>Objective</h1>
To build a lobe parcellation algorithm for our 3T data set. The spatial priors are based on 100 existing manually-lobe parcellated 1.5T data.

</div>

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

<h1>Approach, Plan</h1>
Our plan is to use an algorithm described in Reference 1 to construct probability maps of the lobes using an unbiased registration approach. The algorithm uses a ''label space'' representation that allows for direct registration.
We will then tune the EMsegmenter of Slicer3 to perform the segmentation.

</div>

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

<h1>Progress</h1>
We have been using a MATLAB(R) implementation of the atlas building algorithm to construct the atlas and fine tuning it for 10 subjects.

</div>

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

</div>

===References===

#James Malcolm, Yogesh Rathi,and Allen Tannenbaum, "Label Space: A multi-object Shape Representation", IWCIA 2008,LNCS 4958, pp. 185-196.
#Motoaki Nakamura, Dean F. Salisbury, Yoshio Hirayasu, Sylvain Bouix, Kilian M. Pohl, Takeshi Yoshida, Min-Seong Koo, Martha E. Shenton, and Robert W. McCarley, "Neocortical Gray Matter Volume in First-Episode Schizophrenia and First-Episode Affective Psychosis: A Cross-Sectional and Longitudinal MRI Study", Biol Psychiatry 2007;62:773–783

File:RoiPar.PNG

2008-06-21T02:14:00Z

Priya:

2008 Summer Project Week:LobeParcellation

2008-06-20T12:35:30Z

Priya:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]

|}

__NOTOC__

===Key Investigators===
* BWH: Sylvain Bouix, Yogesh Rathi

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

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

<h1>Objective</h1>
To build an atlas based on 100 existing manually-lobe parcellated 1.5T data to aid in automatic lobe parcellation of 3T data.

</div>

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

<h1>Approach, Plan</h1>
Our plan is to use an algorithm described in Reference 1 to construct probability maps of the lobes using an unbiased registration approach. The algorithm uses a ''label space'' representation that allows for direct registration.

</div>

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

<h1>Progress</h1>
We are using a MATLAB(R) implementation of the algorithm to construct the atlas and fine tuning it for 10 subjects.

</div>

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

</div>

===References===

#James Malcolm, Yogesh Rathi,and Allen Tannenbaum, "Label Space: A multi-object Shape Representation", IWCIA 2008,LNCS 4958, pp. 185-196.
#Motoaki Nakamura, Dean F. Salisbury, Yoshio Hirayasu, Sylvain Bouix, Kilian M. Pohl, Takeshi Yoshida, Min-Seong Koo, Martha E. Shenton, and Robert W. McCarley, "Neocortical Gray Matter Volume in First-Episode Schizophrenia and First-Episode Affective Psychosis: A Cross-Sectional and Longitudinal MRI Study", Biol Psychiatry 2007;62:773–783

2008 Summer Project Week:LobeParcellation

2008-06-20T12:34:49Z

Priya:

2008 Summer Project Week:LobeParcellation

2008-06-20T12:33:25Z

Priya:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]

|}

__NOTOC__

===Key Investigators===
* BWH: Sylvain Bouix, Yogesh Rathi

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

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

<h1>Objective</h1>
To build an atlas based on 100 existing manually-lobe parcellated 1.5T data to aid in automatic lobe parcellation of 3T data.

</div>

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

<h1>Approach, Plan</h1>
Our plan is to use an algorithm described in Reference 1 to construct probability maps of the lobes using an unbiased registration approach. The algorithm uses a ''label space'' representation that allows for direct registration.

</div>

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

<h1>Progress</h1>
We are using a MATLAB(R) implementation of the algorithm to construct the atlas and fine tuning it for 10 subjects.

</div>

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

</div>

===References===

#James Malcolm, Yogesh Rathi,and Allen Tannenbaum,"Label Space: A multi-object Shape Representation", IWCIA 2008,LNCS 4958, pp. 185-196.
#Motoaki Nakamura, Dean F. Salisbury, Yoshio Hirayasu, Sylvain Bouix, Kilian M. Pohl, Takeshi Yoshida,
Min-Seong Koo, Martha E. Shenton, and Robert W. McCarley, "Neocortical Gray Matter Volume in First-Episode Schizophrenia and First-Episode Affective Psychosis: A Cross-Sectional and Longitudinal MRI Study", BIOL PSYCHIATRY 2007;62:773–783

2008 Summer Project Week:LobeParcellation

2008-06-20T12:32:59Z

Priya:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]

|}

__NOTOC__

===Key Investigators===
* BWH: Sylvain Bouix, Yogesh Rathi

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

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

<h1>Objective</h1>
To build an atlas based on 100 existing manually-lobe parcellated 1.5T data to aid in automatic lobe parcellation of 3T data.

</div>

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

<h1>Approach, Plan</h1>
Our plan is to use an algorithm described in Reference 1 to construct probability maps of the lobes using an unbiased registration approach. The algorithm uses a ''label space'' representation that allows for direct registration.

</div>

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

<h1>Progress</h1>
We are using a MATLAB(R) implementation of the algorithm to construct the atlas and fine tuning it for 10 subjects.

</div>

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

</div>

===References===

#James Malcolm, Yogesh Rathi,and Allen Tannenbaum,"Label Space: A multi-object Shape Representation", IWCIA 2008,LNCS 4958, pp. 185-196.

#Motoaki Nakamura, Dean F. Salisbury, Yoshio Hirayasu, Sylvain Bouix, Kilian M. Pohl, Takeshi Yoshida,
Min-Seong Koo, Martha E. Shenton, and Robert W. McCarley, "Neocortical Gray Matter Volume in First-Episode Schizophrenia and First-Episode Affective Psychosis: A Cross-Sectional and Longitudinal MRI Study", BIOL PSYCHIATRY 2007;62:773–783

2008 Summer Project Week:LobeParcellation

2008-06-20T12:31:49Z

Priya:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]

|}

__NOTOC__

===Key Investigators===
* BWH: Sylvain Bouix, Yogesh Rathi

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

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

<h1>Objective</h1>
To build an atlas based on 100 existing manually-lobe parcellated 1.5T data to aid in automatic lobe parcellation of 3T data.

</div>

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

<h1>Approach, Plan</h1>
Our plan is to use an algorithm described in Reference 1 to construct probability maps of the lobes using an unbiased registration approach. The algorithm uses a ''label space'' representation that allows for direct registration.

</div>

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

<h1>Progress</h1>
We are using a MATLAB(R) implementation of the algorithm to construct the atlas and fine tuning it for 10 subjects.

</div>

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

</div>

===References===

#James Malcolm, Yogesh Rathi,and Allen Tannenbaum,"Label Space: A multi-object Shape Representation", IWCIA 2008,LNCS 4958, pp. 185-196.
#Motoaki Nakamura, Dean F. Salisbury, Yoshio Hirayasu, Sylvain Bouix, Kilian M. Pohl, Takeshi Yoshida,
Min-Seong Koo, Martha E. Shenton, and Robert W. McCarley, "Neocortical Gray Matter Volume in First-Episode Schizophrenia and First-Episode Affective Psychosis: A Cross-Sectional and Longitudinal MRI Study", BIOL PSYCHIATRY 2007;62:773–783

2008 Summer Project Week:LobeParcellation

2008-06-20T12:24:58Z

Priya:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]

|}

__NOTOC__

===Key Investigators===
* BWH: Sylvain Bouix, Yogesh Rathi

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

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

<h1>Objective</h1>
To build an atlas based on 100 existing manually-lobe parcellated 1.5T data to aid in automatic lobe parcellation of 3T data.

</div>

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

<h1>Approach, Plan</h1>
Our plan is to use an algorithm described in Reference 1 to construct probability maps of the lobes using an unbiased registration approach. The algorithm uses a ''label space'' representation that allows for direct registration.

</div>

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

<h1>Progress</h1>
We are using a MATLAB(R) implementation of the algorithm to construct the atlas and fine tuning it for 10 subjects.

</div>

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

</div>

===References===

#James Malcolm, Yogesh Rathi,and Allen Tannenbaum,"Label Space: A multi-object Shape Representation", IWCIA 2008,LNCS 4958, pp. 185-196.

2008 Summer Project Week:LobeParcellation

2008-06-20T11:10:15Z

Priya:

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:genuFAp.jpg|thumb|320px|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.]]
|[[Image:genuFA.jpg|thumb|320px|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.]]
|}

__NOTOC__

===Instructions for Use of this Template===
#Please create a new wiki page with an appropriate title for your project using the convention NA-MIC/Projects/Theme-Name/Project-Name
#Copy the entire text of this page into the page created above
#Link the created page into the list of projects for the project event
#Delete this section from the created page
#Send an email to tkapur at bwh.harvard.edu if you are stuck

===Key Investigators===
* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
* Utah: Tom Fletcher, Ross Whitaker

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

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

<h1>Objective</h1>
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.

</div>

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

<h1>Approach, Plan</h1>

Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.

Our plan for the project week is to first try out <bar>,...
</div>

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

<h1>Progress</h1>

Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.

</div>

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

</div>

===References===
* Fletcher, P.T., Tao, R., Jeong, W.-K., Whitaker, R.T., "A Volumetric Approach to Quantifying Region-to-Region White Matter Connectivity in Diffusion Tensor MRI," to appear Information Processing in Medical Imaging (IPMI) 2007.
* Corouge, I., Fletcher, P.T., Joshi, S., Gilmore, J.H., and Gerig, G., "Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis," Medical Image Analysis 10 (2006), 786--798.
* Corouge, I., Fletcher, P.T., Joshi, S., Gilmore J.H., and Gerig, G., Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis, Lecture Notes in Computer Science LNCS, James S. Duncan and Guido Gerig, editors, Springer Verlag, Vol. 3749, Oct. 2005, pp. 131 -- 138
* C. Goodlett, I. Corouge, M. Jomier, and G. Gerig, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .

2008 Summer Project Week:LobeParcellation

2008-06-20T11:09:03Z

Priya: New page: t

2008 Summer Project Week

2008-06-20T11:08:30Z

Priya: /* DBP II */

Back to [[Engineering:Programming_Events|Programming/Project Events]]

[[Image:ProjectWeek-2008.png|thumb|220px|right|Summer 2008]]

== Logistics ==
*'''Dates:''' June 23-27, 2008
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. If you are attending for one day only, the registration fee is not required.
*'''Registration Method''' The event is full. [[User:Tkapur|Tkapur]] 18:12, 17 June 2008 (UTC)
*'''Hotel:''' We have a group rate of $239/night (plus tax) for a room with either 1 king or 2 queen beds at the [http://www.hotelatmit.com Hotel at MIT (now called Le Meridien)]. [http://www.starwoodmeeting.com/StarGroupsWeb/booking/reservation?id=0805167317&key=4FD1B Please click here to reserve.] This rate is good only through June 1.
*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*2008 Summer Project Week [[NA-MIC/Projects/Theme/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 in Utah -- January 5-9, 2009

==Introduction to NA-MIC Project Week==
Please read an introduction about these events [[Project_Events#Introduction|here]].

== Agenda==
* Monday
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process
** 10-10:30am [http://www.slicer.org/slicerWiki/index.php/Announcements:Slicer3.2 Slicer 3.2 Update] (Jim Miller, Steve Pieper)
** 11-12noon [[Project Week 2008 Slicer Tuning| Performance tuning for Slicer 3.2]] (Ron Kikinis)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: XNAT Database]] (Daniel Marcus)
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Luis Ibanez)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-rigid Registration]] (Stephen Aylward)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** noon lunch
**2:30-3:30pm [[Project Week 2008 Special topic breakout: GWE]] (Marco Ruiz)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn. (Next one [[AHM_2009| in Utah the week of Jan 5, 2009]])

== Projects ==

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
##[[2008_Summer_Project_Week:DWIRegistrationOMT|DWI Registration using Optimal Mass Transport]] (Sylvain Bouix BWH, Tauseef Rehman GATech)
##[[2008_Summer_Project_Week:EddyCurrentCorrection|EPI-DWI Eddy Current distortion correction]] (Sylvain Bouix BWH, Ran Tao Utah)
##[[2008_Summer_Project_Week:LobeParcellation| Parcellation of 3T MR data]] - need help parametrization (Sylvain Bouix BWH, Priya Srinivasan BWH, Brad Davis Kitware)
##[[2008_Summer_Project_Week:GMLongDistanceTractography|GM Long Distance Tractography]] (John Melonakos GATech, Marek Kubicki BWH)
##[[2008_Summer_Project_Week:PopulationDTIApplication|Group Analysis of DTI]] (Casey Goodlett Utah, Marek Kubicki BWH)
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
##[[2008_Summer_Project_Week:RegionalCorticalThicknessTool|Work Flow Tool for regional cortical thickness pipeline]] (Clement Vachet UNC)
##[[2008_Summer_Project_Week:NITRCRegistration|NITRC registration of cortical thickness modules]] (Clement Vachet UNC)
##[[2008_Summer_Project_Week:DWI-DTI_PrepTools|DWI DTI Prep Tools]] (Zhexing Liu UNC)
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
##[[DBP2:MIND:RoadmapProject|Finish Roadmap Project]]
##[[DBP2:MIND:LongitudinalRegistrationProject|Longitudinal Registration]]
##[[DBP2:MIND:BeyondLesionsProject|Beyond Lesions]]
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)
##[[2008_Summer_Project_Week:TransRectal_Prostate_Biopsy_Module|Trans-Rectal Prostate Biopsy module]] (David Gobbi, Gabor Fichtinger, Queens/JHU)
##[[2008_Summer_Project_Week:ProstateSegReg|Prostate Segmentation and Registration]] (Yi Gao GATech, Gabor Fichtinger JHU)
##[[2008_Summer_Project_Week:PerkStation|Hardware/software overlay for percutaneous intervention (PERK Station)]] (Siddharth Vikal, Gabor Fichtinger, Queens/JHU)

===Other Projects===
#[[2008_Summer_Project_Week:EddyCurrentCorrection|Eddy current and head motion correction of DWIs]] (Ran Tao, Utah, Sylvain Bouix, BWH, Xiaodong Tao, GE, Tom Fletcher, Utah)
#[[2008_Summer_Project_Week:GroupwiseBSplineForDTI| Integraton of groupwise b-spline registration into atlas building]] (Casey Goodlett, Serdar Balci)
# CVS / SVN auto synchronization
# [[2008_Summer_Project_Week:3DWidgetsInSlicer|3D Widgets in Slicer]] (Nicole Aucoin, Will Schroeder)
## Issues with existing widgets
## Design of new widgets
# Batch processing in the NAMIC Kit (Julien, Marco, Steve, Jim)
#[[2008_Summer_Project_Week:ModuleChaining|Module Chaining]] (Marco, Jim, Steve, Dan B., Luca)
# Nonlinear transforms (Jim, Steve, Luis)
## TransformToWorld/TransformFromWorld, integration with slice viewing
# [[2008_Summer_Project_Week:XNATandXCEDE| Slicer3, XNAT integration and XCEDE Web Services ]] (Dan M., Steve, Julien, Dan B.)
## Review and enrich use cases
# [[2008_Summer_Project_Week:PythonInSlicer| Python in Slicer]] (Dan B., Michael Halle, Steve, Luca)
# [[2008_Summer_Project_Week:PerformanceTuningFiducials|Performance Tuning of Fiducials]] using the EventBroker and other tools (Nicole Aucoin, Alex Yarmarkovich, Steve Pieper, Will Schroeder)
# [[2008_Summer_Project_Week:FocusedGUIRefinement|Focused GUI Refinement and Strategies for Consistency]] (Wendy, Sebastien) [http://www.na-mic.org/Bug/view.php?id=242]
# [[2008_Summer_Project_Week:fMRIconnectivity|fMRI connectivity]] (Bryce Kim, MIT)
# [[2008_Summer_Project_Week:AtlasFreeSegmentation|Atlas free Segmentation]] (Tammy Riklin-Raviv, MIT)
#[[NA-MIC/Projects/Collaboration/EM Bias Field Correction | New Bias Field Correction in EM]] (Carlos Sánchez Mendoza, Kilian Pohl - SPL, Brad Davis - Kitware)
# [[2008_Summer_Project_Week:FluidMechanicsTractographyUCLA|Fluid Mechanics Based DTI Tractography]] (Nathan Hageman, UCLA)

===External Collaborations===
#[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Adam Wittek)
#[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)
#[[NA-MIC/Projects/Collaboration/NIREP: Non-rigid Image Registration Evaluation]] (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/Lung Atlas]] (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/Non-rigid image registration]] (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/SARP phantom]] (Keith Gunderson)
#[[FMA (Protege) links to Slicer]] (Vish, Mike, Florin, Jim, Steve, Wendy)
#[[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction]]
#[[NA-MIC/Projects/External Collaboration/Slicer3-vmtk Integration]] (Luca Antiga, Dan Blezek, Mike Halle, Steve Piper)
#[[NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008]] (Iowa Group)
#[[NA-MIC/Projects/Collaboration/Carto_scar_BIDMC]] (Dana Peters Group)
#[[NA-MIC/Projects/Collaboration/3D Ultrasound Module in Slicer3]] (Junichi, Haiying and Noby - SPL, David - Queen's), Danielle - Robarts) )
#[[NA-MIC/Projects/Collaboration/MGH RadOnc]] (Greg Sharp, MGH)
#[[NA-MIC/Projects/External Collaboration/W&M CRTC]] Non-rigid registration for neurosurgery (Nikos Chrisochoides, Andriy Fedorov, College of William&Mary)
#[[NA-MIC/Projects/Collaboration/SBIA UPenn]] Non-rigid DTI Registration(Ragini Verma, SBIA Upenn)

===Non-Medical Collaborations===
#[[NA-MIC/Projects/Non-Medical Collaborations/Astronomical Medicine|Astronomical Medicine]] (Harvard IIC: Douglas Alan, Michael Halle)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list

# [[Engineering:TCON_2008|May 08 and May 15 TCON DBPs ONLY]] at 3pm ET to discuss NA-MIC DBP Projects ONLY.
# [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams
# [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded "collaborations with NCBC" leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 12 TCON#4]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 19 TCON#5]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 12, 2008: [[NA-MIC/Projects/Theme/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.
# By 3pm on June 19, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## 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)
# 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...

==Attendee List==
# Jack Blevins Acoustic Med
# Pratik Patel Brainlab
# Mark Anderson BWH
# Nicole Aucoin BWH
# Sylvain Bouix BWH
# Michael Halle BWH
# Nobuhiko Hata BWH
# Katie Hayes BWH
# Scott Hoge BWH
# Marianna Jakab BWH
# Tina Kapur BWH
# Ron Kikinis BWH
# Jacek Kukluk BWH
# Haying Liu BWH
# Bjoern Menze BWH
# Wendy Plesniak BWH
# Kilian Pohl BWH
# Sonia Pujol BWH
# Carlos Sánchez Mendoza BWH
# Priya Srinivasan BWH
# Junichi Tokuda BWH
# Demian Wasserman BWH (INRIA)
# C-F Westin BWH
# Xiaodong Tao GE
# Dirk Padfield GE
# Jim Miller GE
# Surprise Guest from EAB
# Viswanath Avasarala GE
# John Melonakos GA Tech
# Yi Gao GA Tech
# Tauseef Rehman GA Tech
# Sean Megason Harvard Med
# Alex Gouaillard Harvard Med
# Kishore Mosaliganti Harvard Med
# Arnaud Gelas Harvard Med
# Dana Peters Harvard Med
# Jason Taclas Harvard Med
# Douglas Alan Harvard
# Toru Higaki Hiroshima U
# Daniel Blezek Isomics
# Curtis Lisle Isomics
# Steve Pieper Isomics
# Alex Yarmarkovich Isomics
# Csaba Csoma JHU
# Peter Kazanzides JHU
# Will Schroeder Kitware
# Sebastien Barre Kitware
# Julien Jomier Kitware
# Bill Hoffman Kitware
# Luis Ibanez Kitware
# Luca Antiga Mario Negri Inst
# Randy Gollub MGH
# Silas Mann MGH
# Greg Sharp MGH
# Marta Peroni MGH
# Serdar Balci MIT
# Bryce Kim MIT
# Clare Poynton MIT
# Tammy Riklin Raviv MIT
# Polina Golland MIT
# Jeremy Bockholt MRN Lupus DBP
# Mark Scully MRN Lupus DBP
# Gabor Fichtinger Queen's
# David Gobbi Queen's
# Purang Abolmaesumi Queen's
# Siddharth Vikal Queen's
# Zhen Qian Rutgers
# Jinghao Zhou Rutgers
# Jeffrey Grethe UCSD
# Marco Ruiz UCSD
# Chris Churas UCSD
# Nathan Hageman UCLA
# Keith Gunderson U Iowa
# Gary Christensen U Iowa
# Jeffrey Hawley U Iowa
# Kate Raising U Iowa
# Nathan Fritze U Iowa
# Paul Song U Iowa
# Cheng Zhang U Iowa
# Ying Wei U Iowa
# Nathan Burnette U Iowa
# Hans Johnson U Iowa
# Vincent Magnotta U Iowa
# Clement Vachet UNC
# Zhexing Liu UNC
# Ragini Verma U Penn
# Luke Bloy U Penn
# Yang Li U Penn
# Ran Tao Utah
# Marcel Prastawa Utah
# Casey Goodlett Utah
# Ross Whitaker Utah
# John Hale U Tulsa
# Cody Pollet U Tulsa
# Nikeisha Schimke U Tulsa
# Adam Wittek Western Australia
# Grand Joldes Western Australia
# Jamie Berger Western Australia
# Carling Cheung Western Ontario
# Danielle Pace Western Ontario
# Vidya Rajagopalan VA Tech
# Nikos Chrisochoides William and Mary
# Andriy Fedorov William and Mary
# Dan Marcus Washington U
# Tim Olsen Washington U
# Kevin Archie Washington U
# Misha Milchenko Washington U
# Xenophon Papademetris Yale U
# John Onofrey Yale U
# Yifeng Jiang Yale U
# Dustin Scheinost Yale U
#* Please note that Registration is closed. Do not add names here. [[User:Tkapur|Tkapur]] 18:19, 19 June 2008 (UTC)

==Pictures==
To be added.

2008 Summer Project Week

2008-06-20T11:07:14Z

Priya: /* DBP II */

Back to [[Engineering:Programming_Events|Programming/Project Events]]

[[Image:ProjectWeek-2008.png|thumb|220px|right|Summer 2008]]

== Logistics ==
*'''Dates:''' June 23-27, 2008
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. If you are attending for one day only, the registration fee is not required.
*'''Registration Method''' The event is full. [[User:Tkapur|Tkapur]] 18:12, 17 June 2008 (UTC)
*'''Hotel:''' We have a group rate of $239/night (plus tax) for a room with either 1 king or 2 queen beds at the [http://www.hotelatmit.com Hotel at MIT (now called Le Meridien)]. [http://www.starwoodmeeting.com/StarGroupsWeb/booking/reservation?id=0805167317&key=4FD1B Please click here to reserve.] This rate is good only through June 1.
*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*2008 Summer Project Week [[NA-MIC/Projects/Theme/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 in Utah -- January 5-9, 2009

==Introduction to NA-MIC Project Week==
Please read an introduction about these events [[Project_Events#Introduction|here]].

== Agenda==
* Monday
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
** 9:00-9:45am: NA-MIC Software Process
** 10-10:30am [http://www.slicer.org/slicerWiki/index.php/Announcements:Slicer3.2 Slicer 3.2 Update] (Jim Miller, Steve Pieper)
** 11-12noon [[Project Week 2008 Slicer Tuning| Performance tuning for Slicer 3.2]] (Ron Kikinis)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: XNAT Database]] (Daniel Marcus)
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Luis Ibanez)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-rigid Registration]] (Stephen Aylward)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** noon lunch
**2:30-3:30pm [[Project Week 2008 Special topic breakout: GWE]] (Marco Ruiz)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn. (Next one [[AHM_2009| in Utah the week of Jan 5, 2009]])

== Projects ==

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
##[[2008_Summer_Project_Week:DWIRegistrationOMT|DWI Registration using Optimal Mass Transport]] (Sylvain Bouix BWH, Tauseef Rehman GATech)
##[[2008_Summer_Project_Week:EddyCurrentCorrection|EPI-DWI Eddy Current distortion correction]] (Sylvain Bouix BWH, Ran Tao Utah)
##[[2008_Summer_Project_Week:LobeParcellationLobe| Parcellation of 3T MR data]] - need help parametrization (Sylvain Bouix BWH, Priya Srinivasan BWH, Brad Davis Kitware)
##[[2008_Summer_Project_Week:GMLongDistanceTractography|GM Long Distance Tractography]] (John Melonakos GATech, Marek Kubicki BWH)
##[[2008_Summer_Project_Week:PopulationDTIApplication|Group Analysis of DTI]] (Casey Goodlett Utah, Marek Kubicki BWH)
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
##[[2008_Summer_Project_Week:RegionalCorticalThicknessTool|Work Flow Tool for regional cortical thickness pipeline]] (Clement Vachet UNC)
##[[2008_Summer_Project_Week:NITRCRegistration|NITRC registration of cortical thickness modules]] (Clement Vachet UNC)
##[[2008_Summer_Project_Week:DWI-DTI_PrepTools|DWI DTI Prep Tools]] (Zhexing Liu UNC)
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
##[[DBP2:MIND:RoadmapProject|Finish Roadmap Project]]
##[[DBP2:MIND:LongitudinalRegistrationProject|Longitudinal Registration]]
##[[DBP2:MIND:BeyondLesionsProject|Beyond Lesions]]
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)
##[[2008_Summer_Project_Week:TransRectal_Prostate_Biopsy_Module|Trans-Rectal Prostate Biopsy module]] (David Gobbi, Gabor Fichtinger, Queens/JHU)
##[[2008_Summer_Project_Week:ProstateSegReg|Prostate Segmentation and Registration]] (Yi Gao GATech, Gabor Fichtinger JHU)
##[[2008_Summer_Project_Week:PerkStation|Hardware/software overlay for percutaneous intervention (PERK Station)]] (Siddharth Vikal, Gabor Fichtinger, Queens/JHU)

===Other Projects===
#[[2008_Summer_Project_Week:EddyCurrentCorrection|Eddy current and head motion correction of DWIs]] (Ran Tao, Utah, Sylvain Bouix, BWH, Xiaodong Tao, GE, Tom Fletcher, Utah)
#[[2008_Summer_Project_Week:GroupwiseBSplineForDTI| Integraton of groupwise b-spline registration into atlas building]] (Casey Goodlett, Serdar Balci)
# CVS / SVN auto synchronization
# [[2008_Summer_Project_Week:3DWidgetsInSlicer|3D Widgets in Slicer]] (Nicole Aucoin, Will Schroeder)
## Issues with existing widgets
## Design of new widgets
# Batch processing in the NAMIC Kit (Julien, Marco, Steve, Jim)
#[[2008_Summer_Project_Week:ModuleChaining|Module Chaining]] (Marco, Jim, Steve, Dan B., Luca)
# Nonlinear transforms (Jim, Steve, Luis)
## TransformToWorld/TransformFromWorld, integration with slice viewing
# [[2008_Summer_Project_Week:XNATandXCEDE| Slicer3, XNAT integration and XCEDE Web Services ]] (Dan M., Steve, Julien, Dan B.)
## Review and enrich use cases
# [[2008_Summer_Project_Week:PythonInSlicer| Python in Slicer]] (Dan B., Michael Halle, Steve, Luca)
# [[2008_Summer_Project_Week:PerformanceTuningFiducials|Performance Tuning of Fiducials]] using the EventBroker and other tools (Nicole Aucoin, Alex Yarmarkovich, Steve Pieper, Will Schroeder)
# [[2008_Summer_Project_Week:FocusedGUIRefinement|Focused GUI Refinement and Strategies for Consistency]] (Wendy, Sebastien) [http://www.na-mic.org/Bug/view.php?id=242]
# [[2008_Summer_Project_Week:fMRIconnectivity|fMRI connectivity]] (Bryce Kim, MIT)
# [[2008_Summer_Project_Week:AtlasFreeSegmentation|Atlas free Segmentation]] (Tammy Riklin-Raviv, MIT)
#[[NA-MIC/Projects/Collaboration/EM Bias Field Correction | New Bias Field Correction in EM]] (Carlos Sánchez Mendoza, Kilian Pohl - SPL, Brad Davis - Kitware)
# [[2008_Summer_Project_Week:FluidMechanicsTractographyUCLA|Fluid Mechanics Based DTI Tractography]] (Nathan Hageman, UCLA)

===External Collaborations===
#[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Adam Wittek)
#[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)
#[[NA-MIC/Projects/Collaboration/NIREP: Non-rigid Image Registration Evaluation]] (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/Lung Atlas]] (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/Non-rigid image registration]] (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/SARP phantom]] (Keith Gunderson)
#[[FMA (Protege) links to Slicer]] (Vish, Mike, Florin, Jim, Steve, Wendy)
#[[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction]]
#[[NA-MIC/Projects/External Collaboration/Slicer3-vmtk Integration]] (Luca Antiga, Dan Blezek, Mike Halle, Steve Piper)
#[[NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008]] (Iowa Group)
#[[NA-MIC/Projects/Collaboration/Carto_scar_BIDMC]] (Dana Peters Group)
#[[NA-MIC/Projects/Collaboration/3D Ultrasound Module in Slicer3]] (Junichi, Haiying and Noby - SPL, David - Queen's), Danielle - Robarts) )
#[[NA-MIC/Projects/Collaboration/MGH RadOnc]] (Greg Sharp, MGH)
#[[NA-MIC/Projects/External Collaboration/W&M CRTC]] Non-rigid registration for neurosurgery (Nikos Chrisochoides, Andriy Fedorov, College of William&Mary)
#[[NA-MIC/Projects/Collaboration/SBIA UPenn]] Non-rigid DTI Registration(Ragini Verma, SBIA Upenn)

===Non-Medical Collaborations===
#[[NA-MIC/Projects/Non-Medical Collaborations/Astronomical Medicine|Astronomical Medicine]] (Harvard IIC: Douglas Alan, Michael Halle)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list

# [[Engineering:TCON_2008|May 08 and May 15 TCON DBPs ONLY]] at 3pm ET to discuss NA-MIC DBP Projects ONLY.
# [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams
# [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded "collaborations with NCBC" leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 12 TCON#4]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 19 TCON#5]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 12, 2008: [[NA-MIC/Projects/Theme/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.
# By 3pm on June 19, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## 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)
# 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...

==Attendee List==
# Jack Blevins Acoustic Med
# Pratik Patel Brainlab
# Mark Anderson BWH
# Nicole Aucoin BWH
# Sylvain Bouix BWH
# Michael Halle BWH
# Nobuhiko Hata BWH
# Katie Hayes BWH
# Scott Hoge BWH
# Marianna Jakab BWH
# Tina Kapur BWH
# Ron Kikinis BWH
# Jacek Kukluk BWH
# Haying Liu BWH
# Bjoern Menze BWH
# Wendy Plesniak BWH
# Kilian Pohl BWH
# Sonia Pujol BWH
# Carlos Sánchez Mendoza BWH
# Priya Srinivasan BWH
# Junichi Tokuda BWH
# Demian Wasserman BWH (INRIA)
# C-F Westin BWH
# Xiaodong Tao GE
# Dirk Padfield GE
# Jim Miller GE
# Surprise Guest from EAB
# Viswanath Avasarala GE
# John Melonakos GA Tech
# Yi Gao GA Tech
# Tauseef Rehman GA Tech
# Sean Megason Harvard Med
# Alex Gouaillard Harvard Med
# Kishore Mosaliganti Harvard Med
# Arnaud Gelas Harvard Med
# Dana Peters Harvard Med
# Jason Taclas Harvard Med
# Douglas Alan Harvard
# Toru Higaki Hiroshima U
# Daniel Blezek Isomics
# Curtis Lisle Isomics
# Steve Pieper Isomics
# Alex Yarmarkovich Isomics
# Csaba Csoma JHU
# Peter Kazanzides JHU
# Will Schroeder Kitware
# Sebastien Barre Kitware
# Julien Jomier Kitware
# Bill Hoffman Kitware
# Luis Ibanez Kitware
# Luca Antiga Mario Negri Inst
# Randy Gollub MGH
# Silas Mann MGH
# Greg Sharp MGH
# Marta Peroni MGH
# Serdar Balci MIT
# Bryce Kim MIT
# Clare Poynton MIT
# Tammy Riklin Raviv MIT
# Polina Golland MIT
# Jeremy Bockholt MRN Lupus DBP
# Mark Scully MRN Lupus DBP
# Gabor Fichtinger Queen's
# David Gobbi Queen's
# Purang Abolmaesumi Queen's
# Siddharth Vikal Queen's
# Zhen Qian Rutgers
# Jinghao Zhou Rutgers
# Jeffrey Grethe UCSD
# Marco Ruiz UCSD
# Chris Churas UCSD
# Nathan Hageman UCLA
# Keith Gunderson U Iowa
# Gary Christensen U Iowa
# Jeffrey Hawley U Iowa
# Kate Raising U Iowa
# Nathan Fritze U Iowa
# Paul Song U Iowa
# Cheng Zhang U Iowa
# Ying Wei U Iowa
# Nathan Burnette U Iowa
# Hans Johnson U Iowa
# Vincent Magnotta U Iowa
# Clement Vachet UNC
# Zhexing Liu UNC
# Ragini Verma U Penn
# Luke Bloy U Penn
# Yang Li U Penn
# Ran Tao Utah
# Marcel Prastawa Utah
# Casey Goodlett Utah
# Ross Whitaker Utah
# John Hale U Tulsa
# Cody Pollet U Tulsa
# Nikeisha Schimke U Tulsa
# Adam Wittek Western Australia
# Grand Joldes Western Australia
# Jamie Berger Western Australia
# Carling Cheung Western Ontario
# Danielle Pace Western Ontario
# Vidya Rajagopalan VA Tech
# Nikos Chrisochoides William and Mary
# Andriy Fedorov William and Mary
# Dan Marcus Washington U
# Tim Olsen Washington U
# Kevin Archie Washington U
# Misha Milchenko Washington U
# Xenophon Papademetris Yale U
# John Onofrey Yale U
# Yifeng Jiang Yale U
# Dustin Scheinost Yale U
#* Please note that Registration is closed. Do not add names here. [[User:Tkapur|Tkapur]] 18:19, 19 June 2008 (UTC)

==Pictures==
To be added.