NAMIC Wiki - User contributions [en]

2009 Summer project week adaptive radiation planning visualization

2009-06-22T16:36:41Z

Khisley:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Des Moines University, Department of Anatomy: Cal Hisley, Ph.D.
* Mercy Des Moines Medical Center, Department of Radiology, William Young, MD
* Mercy Des Moines Medical Center, Department of Radiation Oncology, Richard Deming, MD
* Mercy Des Moines Medical Center, Department of Radiation Oncology, Kenneth Berstein, Ph.D.

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

<h3>Objective</h3>
We are applying functional magnetic resonance imaging, including BOLD and DTI to study the feasibility of adaptive radiation therapy treatment planning and longitudinal tracking/visualization. This is our initial effort and we are concentrating on the application of white matter tractography to improved clinical target volume delineation, tumor characterization and theraputic effects tracking.

</div>

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

<h3>Approach, Plan</h3>

Our approach will be to add DTI pulse sequences to the end of the standard brain MT protocol on our GE HDx 3T magnet and then, along with the routine tissue density mapping performed in RadOnc using CT, perform parallel dosimetry planning procedures - one using just the standard brain MR protocol and one fusing the added white matter tractography FA maps/reconstructions with the MR and CT images. We expect to observe improved delineation of tumor margins, improvements in treatment responses as measured by standard clinical measures and potential prognostic value for patient signs/symptoms course based on the identified white matter tracks involved.<foo>.

Our plan for the project week is to find out what, if any, DICOM-RT import/export functions are available in slicer and design a composite visualization method able to overlay the results from sequential followup scans as a longitudinal tracking tool.
</div>

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

<h3>Progress</h3>
Scanning is ready to begin and we are ready to begin accumulating cases. We are now working on our SLICER foundation.

</div>
</div>

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

==References==
1. Purdy JA. et. al.; Dose to normal tissue outside the radiation therapy patient's treat volume.; Health Physics 95(5):666-676; 2008.
2. Burnet NG. et. al.; Defining the tumor and target volumes for radiotherapy; Cancer Imaging (2004) 4, 153-161.
3. Jena R. et. al.; Diffusion Tensor Imaging: possible implications for radiotherapy treatment planning of patients with high-grade glioma.; Clinical Oncology (2005 17:581-590.
4. Wei CW. et. al.; Tumor effects on cerebral white matter as characterized by diffusion tensor tractography; Ca. J. Neurological Sciences 2007; 34:62-69.
5. Lu S. et. al.; Diffusion-Tensor MR imaging of intracranial neoplasia and associated peritumoral edema: introduction to the tumor infiltration index.; Radiology 2004 232:221-228.
6. Goebell E. et. al.; Low-grade and anaplastic gliomas: differences in architecture evaluated with diffusion-tensor MR imaging.; Radiology V239: Number 1 - April 2006, 217-221.
7. Peng H. et. al.; Development of a human brain diffusion tensor template.; Neuroimage 46 (2009) 967-980.

</div>

2009 Summer project week adaptive radiation planning visualization

2009-06-22T16:33:21Z

Khisley:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Instructions for Use of this Template==
#Please create a new wiki page with an appropriate title for your project using the convention Project/<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%;">

<h3>Objective</h3>
We are applying functional magnetic resonance imaging, including BOLD and DTI to study the feasibility of adaptive radiation therapy treatment planning and longitudinal tracking/visualization. This is our initial effort and we are concentrating on the application of white matter tractography to improved clinical target volume delineation, tumor characterization and theraputic effects tracking.

</div>

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

<h3>Approach, Plan</h3>

Our approach will be to add DTI pulse sequences to the end of the standard brain MT protocol on our GE HDx 3T magnet and then, along with the routine tissue density mapping performed in RadOnc using CT, perform parallel dosimetry planning procedures - one using just the standard brain MR protocol and one fusing the added white matter tractography FA maps/reconstructions with the MR and CT images. We expect to observe improved delineation of tumor margins, improvements in treatment responses as measured by standard clinical measures and potential prognostic value for patient signs/symptoms course based on the identified white matter tracks involved.<foo>.

Our plan for the project week is to find out what, if any, DICOM-RT import/export functions are available in slicer and design a composite visualization method able to overlay the results from sequential followup scans as a longitudinal tracking tool.
</div>

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

<h3>Progress</h3>
Scanning is ready to begin and we are ready to begin accumulating cases. We are now working on our SLICER foundation.

</div>
</div>

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

==References==
1. Purdy JA. et. al.; Dose to normal tissue outside the radiation therapy patient's treat volume.; Health Physics 95(5):666-676; 2008.
2. Burnet NG. et. al.; Defining the tumor and target volumes for radiotherapy; Cancer Imaging (2004) 4, 153-161.
3. Jena R. et. al.; Diffusion Tensor Imaging: possible implications for radiotherapy treatment planning of patients with high-grade glioma.; Clinical Oncology (2005 17:581-590.
4. Wei CW. et. al.; Tumor effects on cerebral white matter as characterized by diffusion tensor tractography; Ca. J. Neurological Sciences 2007; 34:62-69.
5. Lu S. et. al.; Diffusion-Tensor MR imaging of intracranial neoplasia and associated peritumoral edema: introduction to the tumor infiltration index.; Radiology 2004 232:221-228.
6. Goebell E. et. al.; Low-grade and anaplastic gliomas: differences in architecture evaluated with diffusion-tensor MR imaging.; Radiology V239: Number 1 - April 2006, 217-221.
7. Peng H. et. al.; Development of a human brain diffusion tensor template.; Neuroimage 46 (2009) 967-980.

</div>

2009 Summer project week adaptive radiation planning visualization

2009-06-22T16:07:32Z

Khisley:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Instructions for Use of this Template==
#Please create a new wiki page with an appropriate title for your project using the convention Project/<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%;">

<h3>Objective</h3>
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%;">

<h3>Approach, Plan</h3>

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;">

<h3>Progress</h3>
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>
</div>

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

==References==
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
* Goodlett C, Corouge I, Jomier M, Gerig G, 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 .

</div>

2009 Summer project week adaptive radiation planning visualization

2009-06-22T16:06:46Z

Khisley: Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png|Projects List Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus ...'

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
</gallery>

==Instructions for Use of this Template==
#Please create a new wiki page with an appropriate title for your project using the convention Project/<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%;">

<h3>Objective</h3>
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%;">

<h3>Approach, Plan</h3>

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;">

<h3>Progress</h3>
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>
</div>

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

==References==
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
* Goodlett C, Corouge I, Jomier M, Gerig G, 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 .

</div>

2009 Summer Project Week

2009-06-22T16:05:19Z

Khisley: /* Radiotherapy */

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

[[Image:PW2009-v3.png|300px]]

*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*32-D451 (Stata)
** Mon, noon - end
** Tues, Wed, Thurs, all day
*38-413 (Lg Conference room inside EECS Headquarters)
**Mon, noon-end
**Tues, Wed, Thurs, 9-end
**Fri, 9-1:00

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. 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 16th 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 that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

== Agenda==
=== Monday===
** 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 Start project work
=== Tuesday ===
** 8:30am breakfast
**9:30-10am: NA-MIC Kit Overview (Jim Miller)
** 10-10:30am Slicer 3.4 Update (Steve Pieper) ([[media:2009 NA-MIC Project Week Slicer3.4.ppt|Slides]], [[2009_Summer_Project_Week_Extension_Manager|Project Page]])
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)
** noon lunch
** 2:00pm-3.00pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis)
** 4:30pm [http://www.cimit.org/forum-current.html CIMIT Forum (At BWH / Carl J. and Ruth Shapiro Cardiovascular Center) Open Source Software for Translational IGT Research and Commercial Use, Clif Burdette, Acoustic MedSystems, Inc. ]
** 5:30pm adjourn for day
=== Wednesday ===
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (Alexandre Gouaillard)
** 5:30pm adjourn for day
=== Thursday===
** 8:30am breakfast
** 9-11am [[Events:TutorialContestJune2009|Tutorial Contest Presentations]]
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT for Programmers]] (Dan M.)
** 5:30pm adjourn for day
=== Friday===
** 8:30am breakfast
** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#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_2010|in Utah, January 4-8, 2010]]

==Projects==

=== Segmentation ===

#[[2009_Summer_Project_Week_Lupus_Lesion_Segmentation|Lupus Lesion Segmentation]] (Jeremy Bockholt MRN)
#[[2009_Summer_Project_Week_WML_SEgmentation|White Matter Lesion segmentation]] (Minjeong Kim UNC)
#[[2009_Summer_Project_Week_Skull_Stripping|Skull Stripping]] (Snehasish Roy JHU)
#[[EMSegment|EM Segment]] (Sylvain Jaume MIT, Nicolas Rannou BWH)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation|FastMarching for brain tumor segmentation]] (Andrey Fedorov BWH)
#[[2009_Summer_Project_Week_New_ITK_Level_Set_Framework|New Level Set Framework in ITK]] (Arnaud Gelas, Harvard Medical School)
#[[2009_Summer_Project_Week_TubularSurfaceSeg|Tubular Surface Segmentation in Slicer]] (Vandana Mohan, Georgia Tech)
#[[Summer2009:The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn BWH)
#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline]] (Clement Vachet UNC)
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel Prastawa Utah)
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images|Segmentation of Knee Structures]] (Harish Doddi Stanford)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration|Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez Kitware)

=== Registration ===

#[[BSpline Registration in Slicer3|BSpline Registration in Slicer3]] (Samuel Gerber Utah)
#[[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andrey Fedorov BWH)
#[[2009_Summer_project_week_prostate_registration|Prostate Registration Slicer Module]] (Yi Gao, Georgia Tech)
#[[2009_Summer_Project_Week_Slicer3_registration|Slicer 3 registration ]] (Andrew Rausch BWH PNL)
#[[EPI Correction in Slicer3|EPI Correction in Slicer3]] (Ran Tao Utah)
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Tina Kapur BWH)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan Virginia Tech)
#[[2009_Summer_Project_Week_TrigeminalNerve|Atlas to CT Registration in Trigeminal Neuralgia]] (Marta Peroni PoliMI)
#[[2009_Summer_Project_Week_HAMMER_Registration|HAMMER Registration]] (Guorong Wu UNC)

=== IGT ===

#[[2009_Summer_Project_Week_Transrectal_Prostate_biopsy|Transrectal Prostate Biopsy]] (Andras Lasso Queen's)
#[[2009_Summer_Project_Week_Prostate_Robotics|Prostate Robotics]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Ziv Yaniv Georgetown)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|Demo of Neuronavigation using Brainlab, Slicer3, BioImage Suite]] (Haiying Liu BWH)
#[[2009_Summer_Project_Week_3DGRASE|3D GRASE]] (Scott Hoge BWH)
#[[2009_Summer_Project_Week_RTHawk_MR_Navigation|Using RTHawk to Implement MR Navigation]] (Ben Schwartz BWH)
#[[2009_Summer_Project_Week_Slicer|Integration of Flexible Surgical Instrument Modeling and Virtual Catheter with Slicer]] (Jayender Jagadeesan BWH)
#[[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian Robarts Institute)

=== Radiotherapy ===

#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp MGH)
#[[2009_Summer_Project_Week_Adaptive_RT|Adaptive Radiotherapy for Head,Neck, and Thorax]] (Ivan Kolesov GATech)
#[[2009_Summer_Project_Week_Cone_Beam_backprojection]](Zhou Shen U Michigan)
#[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan U Michigan)
#[[2009_Summer_project_week_adaptive_radiation_planning_visualization]](Cal Hisley, Des Moines University/Mercy Des Moines Medical Center)

=== Analysis ===

#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Andrey Fedorov BWH)
#[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Linking atlas data with ontologies of brain morphology and function]] (Ion-Florin Talos BWH)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze MIT)
#[[2009_Summer_Project_Week_4D_Imaging|4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer|Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace Robarts Institute)
#[[2009_Summer_Project_Week_Statistical_Toolbox|multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor Robarts Institute)

=== Informatics ===

#[[2009_Summer_Project_Week_Slicer3_XNAT_UI|XNAT user interface improvements for NA-MIC]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNATFS|XNAT File System with FUSE]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong Harvard)
#[[2009_Summer_Project_Week_GWE_XNAT|GWE-XNAT Integration]] (Marco Ruiz UCSD)
#[[2009_Summer_Project_Week_GWE_Results_Browser|GWE Results Browser Improvements]] (Marco Ruiz UCSD)

=== Diffusion ===

#[[Summer2009:VCFS|Stochastic Tractography to study VCFS and Schizophrenia]] (Sylvain Bouix BWH)
#[[2009_Summer_Project_Week_FunctionalClusteringAnalysis|Functional Analysis of White Matter in Whole Brain Clustering of Schizophrenic Patients]] (Doug Terry BWH)
#[[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev BWH)
#[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep|DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu UNC)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom|DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Hageman_FMTractography|Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[Summer2009:Using_CUDA_for_stochastic_tractography|Developing interactive stochastic tractography using CUDA]] (Julien de Siebenthal BWH)

=== Python ===

#[[Summer2009:Using_ITK_in_python|Using ITK in python]] (Steve Pieper BWH)
#[[Summer2009:Using_cython|Accelerating python with cython: application to stochastic tractography]] (Julien de Siebenthal BWH)
#[[Summer2009:Implementing_parallelism_in_python|Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal BWH)
#[[Summer2009:Using_client_server_paradigm_with_python_and_slicer|Deferring heavy computational tasks with Slicer python]] (Julien de Siebenthal BWH)

=== Slicer Internals ===

#[[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole Aucoin BWH)
#[[2009_Summer_Project_Week_Colors_Module|Updates to Slicer3 Colors module]] (Nicole Aucoin BWH)
#[[2009_Summer_Project_Week_Orthogonal_Reformat_Widget|Orthogonal Planes in Reformat Widget]] (Michal Depa MIT)
#[[Slicer3 Informatics Workflow Design & XNAT updates|Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wendy Plesniak BWH)
#[[Slicer3_FlexibleLayouts | Slicer3 Flexible Layouts]] (Wendy Plesniak BWH)
#[[2009_Summer_Project_Week_Extension_Manager|Slicer3 Extension Manager]] (Katie Hayes BWH)
#[[MeshingSummer2009|IAFE Mesh Modules - improvements and testing]] (Curt Lisle Knowledge Vis)

=== Execution Model ===

#[[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang Siemens Research)
#[[Summer2009:Extension of the Command Line XML Syntax/Interface|Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 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 18, 2009: 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...
# 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-3-4/#dirlist Slicer-3-4 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].

== Logistics ==
*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*32-D451 (Stata)
** Mon, noon - end
** Tues, Wed, Thurs, all day
*38-413 (Lg Conference room inside EECS Headquarters)
**Mon, noon-end
**Tues, Wed, Thurs, 9-end
**Fri, 9-1:00
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. 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 this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.
*'''Registration Method''' Add your name to the Attendee List section of this page
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE 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.
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2008_Summer_Project_Week#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]]

==Attendee List==

'''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''
{|
|-
|
{|class="wikitable"
!Number
|- style=&#34height:50px&#34
|1
|- style=&#34height:50px&#34
|2
|- style=&#34height:50px&#34
|3
|- style=&#34height:50px&#34
|4
|- style=&#34height:50px&#34
|5
|- style=&#34height:50px&#34
|6
|- style=&#34height:50px&#34
|7
|- style=&#34height:50px&#34
|8
|- style=&#34height:50px&#34
|9
|- style=&#34height:50px&#34
|10
|- style=&#34height:50px&#34
|11
|- style=&#34height:50px&#34
|12
|- style=&#34height:50px&#34
|13
|- style=&#34height:50px&#34
|14
|- style=&#34height:50px&#34
|15
|- style=&#34height:50px&#34
|16
|- style=&#34height:50px&#34
|17
|- style=&#34height:50px&#34
|18
|- style=&#34height:50px&#34
|19
|- style=&#34height:50px&#34
|20
|- style=&#34height:50px&#34
|21
|- style=&#34height:50px&#34
|22
|- style=&#34height:50px&#34
|23
|- style=&#34height:50px&#34
|24
|- style=&#34height:50px&#34
|25
|- style=&#34height:50px&#34
|26
|- style=&#34height:50px&#34
|27
|- style=&#34height:50px&#34
|28
|- style=&#34height:50px&#34
|29
|- style=&#34height:50px&#34
|30
|- style=&#34height:50px&#34
|31
|- style=&#34height:50px&#34
|32
|- style=&#34height:50px&#34
|33
|- style=&#34height:50px&#34
|34
|- style=&#34height:50px&#34
|35
|- style=&#34height:50px&#34
|36
|- style=&#34height:50px&#34
|37
|- style=&#34height:50px&#34
|38
|- style=&#34height:50px&#34
|39
|- style=&#34height:50px&#34
|40
|- style=&#34height:50px&#34
|41
|- style=&#34height:50px&#34
|42
|- style=&#34height:50px&#34
|43
|- style=&#34height:50px&#34
|44
|- style=&#34height:50px&#34
|45
|- style=&#34height:50px&#34
|46
|- style=&#34height:50px&#34
|47
|- style=&#34height:50px&#34
|48
|- style=&#34height:50px&#34
|49
|- style=&#34height:50px&#34
|50
|- style=&#34height:50px&#34
|51
|- style=&#34height:50px&#34
|52
|- style=&#34height:50px&#34
|53
|- style=&#34height:50px&#34
|54
|- style=&#34height:50px&#34
|55
|- style=&#34height:50px&#34
|56
|- style=&#34height:50px&#34
|57
|- style=&#34height:50px&#34
|58
|- style=&#34height:50px&#34
|59
|- style=&#34height:50px&#34
|60
|- style=&#34height:50px&#34
|61
|- style=&#34height:50px&#34
|62
|- style=&#34height:50px&#34
|63
|- style=&#34height:50px&#34
|64
|- style=&#34height:50px&#34
|65
|- style=&#34height:50px&#34
|66
|- style=&#34height:50px&#34
|67
|- style=&#34height:50px&#34
|68
|- style=&#34height:50px&#34
|69
|- style=&#34height:50px&#34
|70
|- style=&#34height:50px&#34
|71
|- style=&#34height:50px&#34
|72
|- style=&#34height:50px&#34
|73
|- style=&#34height:50px&#34
|74
|- style=&#34height:50px&#34
|75
|- style=&#34height:50px&#34
|76
|- style=&#34height:50px&#34
|77
|- style=&#34height:50px&#34
|78
|- style=&#34height:50px&#34
|79
|- style=&#34height:50px&#34
|80
|- style=&#34height:50px&#34
|81
|- style=&#34height:50px&#34
|82
|- style=&#34height:50px&#34
|83
|- style=&#34height:50px&#34
|84
|- style=&#34height:50px&#34
|85
|- style=&#34height:50px&#34
|86
|- style=&#34height:50px&#34
|87
|- style=&#34height:50px&#34
|88
|- style=&#34height:50px&#34
|89
|- style=&#34height:50px&#34
|90
|- style=&#34height:50px&#34
|93
|- style=&#34height:50px&#34
|91
|- style=&#34height:50px&#34
|92
|- style=&#34height:50px&#34
|94
|- style=&#34height:50px&#34
|95
|- style=&#34height:50px&#34
|96
|- style=&#34height:50px&#34
|97
|- style=&#34height:50px&#34
|98
|- style=&#34height:50px&#34
|99
|- style=&#34height:50px&#34
|100
|- style=&#34height:50px&#34
|101
|- style=&#34height:50px&#34
|102
|- style=&#34height:50px&#34
|103
|- style=&#34height:50px&#34
|104
|- style=&#34height:50px&#34
|105
|- style=&#34height:50px&#34
|106
|- style=&#34height:50px&#34
|107
|- style=&#34height:50px&#34
|108
|- style=&#34height:50px&#34
|109
|- style=&#34height:50px&#34
|110
|- style=&#34height:50px&#34
|111
|- style=&#34height:50px&#34
|112
|- style=&#34height:50px&#34
|113
|- style=&#34height:50px&#34
|114
|- style=&#34height:50px&#34
|115
|- style=&#34height:50px&#34
|116
|- style=&#34height:50px&#34
|117
|- style=&#34height:50px&#34
|118
|- style=&#34height:50px&#34
|119
|- style=&#34height:50px&#34
|120
|- style=&#34height:50px&#34
|121
|- style=&#34height:50px&#34
|122
|- style=&#34height:50px&#34
|123
|- style=&#34height:50px&#34
|124
|- style=&#34height:50px&#34
|}
|
{| class="wikitable sortable"
!First
!Last
!Affiliation
|- style=&#34height:50px&#34
|John
|Melonakos
|AccelerEyes (Wed & Thu morning)
|- style=&#34height:50px&#34
|Jack
|Blevins
|Acoustic Med
|- style=&#34height:50px&#34
|Clif
|Burdette
|Acoustic Med (Mon-Wed)
|- style=&#34height:50px&#34
|Dana
|Peters
|Beth Israel Deaconess
|- style=&#34height:50px&#34
|Nicole
|Aucoin
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Giovanna
|Danagoulian
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Haytham
|Elhawary
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Andriy
|Fedorov
|BWH (NAMIC Collaborator)
|- style=&#34height:50px&#34
|Daniel
|Haehn
|BWH (NAC)
|- style=&#34height:50px&#34
|Michael
|Halle
|BWH (NAC)
|- style=&#34height:50px&#34
|Nobuhiko
|Hata
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Katie
|Hayes
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Scott
|Hoge
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Tina
|Kapur
|BWH (NCIGT, NAMIC)
|- style=&#34height:50px&#34
|Ron
|Kikinis
|BWH (NAMIC, NAC, NCIGT)
|- style=&#34height:50px&#34
|Jayender
|Jagadeesan
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Haying
|Liu
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Lauren
|O'Donnell
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Wendy
|Plesniak
|BWH (NAC)
|- style=&#34height:50px&#34
|Megumi
|Nakao
|BWH (NAIST)
|- style=&#34height:50px&#34
|Sonia
|Pujol
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Lei
|Qin
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Nicolas
|Rannou
|BWH (NAC)
|- style=&#34height:50px&#34
|Petter
|Risholm
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Florin
|Talos
|BWH (NAC)
|- style=&#34height:50px&#34
|Clare
|Tempany
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Junichi
|Tokuda
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Demian
|Wasserman
|BWH (INRIA)
|- style=&#34height:50px&#34
|Carl-Fredrik
|Westin
|BWH (NAC)
|- style=&#34height:50px&#34
|Sandy
|Wells
|BWH (NAC, NCIGT)
|- style=&#34height:50px&#34
|Lilla
|Zollei
|MGH (NAC)
|- style=&#34height:50px&#34
|Padma
|Akella
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Sylvain
|Bouix
|BWH (PNL)
|- style=&#34height:50px&#34
|Julien
|de Siebenthal
|BWH (PNL)
|- style=&#34height:50px&#34
|Marek
|Kubicki
|BWH (NAMIC DBP PNL)
|- style=&#34height:50px&#34
|Juhana
|Frosen
|BWH Tues only
|- style=&#34height:50px&#34
|Sun Woo
|Lee
|BWH (PNL)
|- style=&#34height:50px&#34
|Jimi
|Malcolm
|BWH (PNL)
|- style=&#34height:50px&#34
|Eric
|Melonakos
|BWH (PNL)
|- style=&#34height:50px&#34
|Yogesh
|Rathi
|BWH (PNL)
|- style=&#34height:50px&#34
|Peter
|Savadjiev
|BWH (PNL)
|- style=&#34height:50px&#34
|Doug
|Terry
|BWH (PNL)
|- style=&#34height:50px&#34
|Andrew
|Rausch
|BWH (Mon only)
|- style=&#34height:50px&#34
|Cal
|Hisley
|Des Moines Unive
|- style=&#34height:50px&#34
|Jim
|Miller
|GE
|- style=&#34height:50px&#34
|Xiaodong
|Tao
|GE
|- style=&#34height:50px&#34
|Vandana
|Mohan
|GA Tech
|- style=&#34height:50px&#34
|Yi
|Gao
|GA Tech
|- style=&#34height:50px&#34
|Ivan
|Kolosev
|GA Tech
|- style=&#34height:50px&#34
|Behnood
|Gholami
|GA Tech
|- style=&#34height:50px&#34
|Ziv
|Yaniv
|Georgetown
|- style=&#34height:50px&#34
|Alex
|Gouaillard
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Arnaud
|Gelas
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Sean
|Megason
|Harvard Systems Biology (Wed only)
|- style=&#34height:50px&#34
|Lydie
|Souhait
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Moti
|Freiman
|Hebrew University of Jerusalem
|- style=&#34height:50px&#34
|Amanda
|Peters
|Harvard SEAS
|- style=&#34height:50px&#34
|Maria Francesca
|Spadea
|Italy
|- style=&#34height:50px&#34
|Curtis
|Lisle
|KnowledgeVis
|- style=&#34height:50px&#34
|Steve
|Pieper
|Isomics
|- style=&#34height:50px&#34
|Alex
|Yarmarkovich
|Isomics
|- style=&#34height:50px&#34
|Nathan
|Cho
|JHU
|- style=&#34height:50px&#34
|Bennett
|Landman
|JHU
|- style=&#34height:50px&#34
|Snehashis
|Roy
|JHU
|- style=&#34height:50px&#34
|Sam
|Song
|JHU
|- style=&#34height:50px&#34
|Sebastien
|Barre
|Kitware
|- style=&#34height:50px&#34
|Luis
|Ibanez
|Kitware
|- style=&#34height:50px&#34
|Daniel
|Blezek
|Mayo
|- style=&#34height:50px&#34
|Yong
|Gao
|MGH
|- style=&#34height:50px&#34
|Randy
|Gollub
|MGH
|- style=&#34height:50px&#34
|Rui
|Li
|MGH
|- style=&#34height:50px&#34
|Greg
|Sharp
|MGH
|- style=&#34height:50px&#34
|Robert
|Yaffe
|MGH - Mon
|- style=&#34height:50px&#34
|Sylvain
|Jaume
|MIT
|- style=&#34height:50px&#34
|Bjoern
|Menze
|MIT
|- style=&#34height:50px&#34
|Jeremy
|Bockholt
|MRN (NAMIC Lupus DBP)
|- style=&#34height:50px&#34
|Mark
|Scully
|MRN (NAMIC Lupus DBP) Tue-Th
|- style=&#34height:50px&#34
|Joe
|Stam
|NVIDIA (Wed & Thurs)
|- style=&#34height:50px&#34
|Kimberly
|Powell
|NVIDIA (Wed)
|- style=&#34height:50px&#34
|Marta
|Peroni
|Politecnico di Milano
|- style=&#34height:50px&#34
|Andras
|Lasso
|Queen's (NAMIC DBP)
|- style=&#34height:50px&#34
|Yanling
|Liu
|SAIC/NCI-Frederick
|- style=&#34height:50px&#34
|Melanie
|Grebe
|Siemens Corporate Research
|- style=&#34height:50px&#34
|Lining
|Yang
|Siemens Corporate Research
|- style=&#34height:50px&#34
|Harish
|Doddi
|Stanford University
|- style=&#34height:50px&#34
|Marco
|Ruiz
|UCSD
|- style=&#34height:50px&#34
|Nathan
|Hageman
|UCLA (Mon-Thurs)
|- style=&#34height:50px&#34
|Hans
|Johnson
|U Iowa
|- style=&#34height:50px&#34
|Vincent
|Magnotta
|U Iowa
|- style=&#34height:50px&#34
|Jeffrey
|Yager
|U Iowa
|- style=&#34height:50px&#34
|Manasi
|Ramachandran
|U Iowa
|- style=&#34height:50px&#34
|Dave
|Welch
|U Iowa
|- style=&#34height:50px&#34
|Andrzej
|Przybyszewski
|UMass Med (Mon)
|- style=&#34height:50px&#34
|James
|Balter
|U Michigan
|- style=&#34height:50px&#34
|Dan
|McShan
|U Michigan
|- style=&#34height:50px&#34
|Zhou
|Shen
|U Michigan
|- style=&#34height:50px&#34
|Beatriz
|Paniagua
|UNC
|- style=&#34height:50px&#34
|Minjeong
|Kim
|UNC
|- style=&#34height:50px&#34
|Zhexing
|Liu
|UNC
|- style=&#34height:50px&#34
|Clement
|Vachet
|UNC (NAMIC DBP)
|- style=&#34height:50px&#34
|Guorong
|Wu
|UNC
|- style=&#34height:50px&#34
|Samuel
|Gerber
|SCI, Utah
|- style=&#34height:50px&#34
|Ran
|Tao
|SCI, Utah
|- style=&#34height:50px&#34
|Marcel
|Prastawa
|SCI, Utah
|- style=&#34height:50px&#34
|Ross
|Whitaker
|SCI, Utah
|- style=&#34height:50px&#34
|Curtis
|Rueden
|UW-Madison
|- style=&#34height:50px&#34
|Dan
|Marcus
|WUSTL
|- style=&#34height:50px&#34
|Misha
|Milchenko
|WUSTL
|- style=&#34height:50px&#34
|Kevin
|Archie
|WUSTL
|- style=&#34height:50px&#34
|Tim
|Olsen
|WUSTL
|- style=&#34height:50px&#34
|Mehdi
|Esteghamatian
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Diego
|Cantor
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Danielle
|Pace
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Vidya
|Rajagopalan
|VA Tech
|- style=&#34height:50px&#34
|Gregory
|Fischer
|WPI
|- style=&#34height:50px&#34
|Dominique
|Belhachemi
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Alark
|Joshi
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Xenios
|Papademetris
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Dustin
|Scheinost
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Michelle
|Borkin
|Harvard SEAS (Mon only)
|- style=&#34height:50px&#34
|Renxin
|Chu
|BWH (NCIGT) (Mon, Tue)
|- style=&#34height:50px&#34
|Ben
|Schwartz
|BWH (NCIGT) (Mon, Tue)
|- style=&#34height:50px&#34
|Marianna
|Jakab
|BWH (NCIGT, NAC) (Mon, Tue)
|- style=&#34height:50px&#34
|Viswanath
|Avasarala
|GE (Wed, Thurs)
|- style=&#34height:50px&#34
|}
|}

'''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''

The following was used to convert from excel to mediawiki markup: http://area23.brightbyte.de/csv2wp.php

2009 Summer Project Week

2009-06-16T03:15:38Z

Khisley:

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

[[Image:PW2009-v3.png|300px]]

*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. 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 will begin on''' Thursday, April 16th 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 that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

== Agenda==
* Monday
** 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 Start project work
* Tuesday
** 8:30am breakfast
**9:30-10am: NA-MIC Kit Overview (Jim Miller)
** 10-10:30am Slicer 3.4 Update (Steve Pieper)
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)
** noon lunch
** 2:30pm-5pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis)
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (Alex G.)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** 9-11am [[Events:TutorialContestJune2009|Tutorial Contest Presentations]]
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT for Programmers]] (Dan M.)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#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_2010|in Utah, January 4-8, 2010]]

== Projects ==

#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline]] (Clement Vachet UNC)
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_Lupus_Lesion_Segmentation |Lupus Lesion Segmentation]] (Jeremy Bockholt MRN)
#[[Summer2009:VCFS| Pipeline development for VCFS]] (Marek Kubicki BWH)
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]] (Harish Doddi Stanford)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Ziv Yaniv Georgetown)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan Virginia Tech)
#[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Snehasish Roy JHU)
# [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt Lisle Knowledge Vis)
#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp MGH)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|SLicer3, BioImage Suite and Brainlab - Introduction to UCLA]] (Haiying Liu BWH)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Demo|Demo Brainlab-BioImage Suite-Slicer in BWH OR]] (Haiying Liu BWH)
#[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Segmentation of thalamic nuclei from DTI]] (Ion-Florin Talos BWH)
#[[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev BWH)
#[[2009_Summer_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep | DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu UNC)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom | DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao Utah)
#[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim UNC)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Andrey Fedorov BWH)
# [[EMSegment|EM Segment]] (Sylvain Jaume BWH)
#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Andrey Fedorov BWH)
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel Prastawa Utah)
#[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu UNC)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez Kitware)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber Utah)
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze MIT)
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer |Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace Robarts Institute)
# [[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian Robarts Institute)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor Robarts Institute)
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve Pieper BWH)
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal BWH)
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with Slicer python]] (Julien de Siebenthal BWH)
# [[Summer2009:Using_cython| Accelerating python with cython: application to stochastic tractography]] (Julien de Siebenthal BWH)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole Aucoin BWH)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole Aucoin BWH)
# [[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang Siemens Research)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wendy Plesniak BWH)
# [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andrey Fedorov BWH)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn BWH)
# [[Summer2009:Extension of the Command Line XML Syntax/Interface | Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)
#[[2009_Summer_Project_Week_Slicer3_XNAT_UI | XNAT user interface improvements for NA-MIC]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNATFS | XNAT File System with FUSE]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong Harvard)
#[[2009_Summer_Project_Week_Slicer3_registration| Slicer 3 registration ]] (Andrew Rausch)
#[[2009_Summer_Project_Week_Transrectal_Prostate_biopsy|Transrectal Prostate Biopsy]] (Andras Lasso Queen's)
#[[2009_Summer_Project_Week_3DGRASE|3D GRASE]] (Scott Hoge BWH)
#[[2009_Summer_Project_Week_TrigeminalNerve|Atlas to CT Registration in Trigeminal Neuralgia]] (Marta Peroni PoliMI, Maria Francesca Spadea UMG, Greg Sharp MGH)

===CUDA Projects===

This is a list of candidate cuda projects that will be discussed with Joe Stam shortly:

#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Tina Kapur BWH)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor Robarts Institute)
#[[2009_Summer_Project_Week_Dose_Calculation |accelerate calculation for LDR seeds]] (Jack Blevins Acousticmed)
#[[2009_Summer_Project_Week_Cone_Beam_backprojection]](Zhou Shen U Michigan)
#[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan U Michigan)
#[[Summer2009:Using_CUDA_for_stochastic_tractography|Developing interactive stochastic tractography using CUDA]] (Julien de Siebenthal BWH)
#acceleration of parallel real time processing of strain and elasticity images for monitoring of ablative therapy (Clif Burdette Acousticmed)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 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 18, 2009: 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...
# 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-3-4/#dirlist Slicer-3-4 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==
If you plan to attend, please add your name here.

#Ron Kikinis, BWH (NA-MIC, NAC, NCIGT)
#Clare Tempany, BWH (NCIGT)
#Tina Kapur, BWH (NA-MIC, NCIGT)
#Steve Pieper, Isomics Inc
#Jim Miller, GE Research
#Xiaodong Tao, GE Research
#Randy Gollub, MGH
#Nicole Aucoin, BWH (NA-MIC) (Attending Tuesday-Friday)
#Dan Marcus, WUSTL
#Junichi Tokuda, BWH (NCIGT)
#Alex Gouaillard, Harvard Systems Biology
#Arnaud Gelas, Harvard Systems Biology
#Kishore Mosanliganti, Harvard Systems Biology
#Lydie Souhait, Harvard Systems Biology
#Luis Ibanez, Kitware Inc (Attending: Monday/Tuesday/Wednesday)
#Vincent Magnotta, UIowa
#Hans Johnson, UIowa
#Xenios Papademetris, Yale
#Gregory S. Fischer, WPI (Mon, Tue, Wed)
#Daniel Blezek, Mayo (Tue-Fri)
#Danielle Pace, Robarts Research Institute / UWO
#Clement Vachet, UNC-Chapel Hill
#Dave Welch, UIowa
#Demian Wassermann, Odyssée lab, INRIA, France
#Manasi Ramachandran, UIowa
#Greg Sharp, MGH
#Rui Li, MGH
#Mehdi Esteghamatian, Robarts Research Institute / UWO
#Misha Milchenko, WUSTL
#Kevin Archie, WUSTL
#Tim Olsen, WUSTL
#Wendy Plesniak BWH (NAC)
#Haiying Liu BWH (NCIGT)
#Curtis Lisle, KnowledgeVis / Isomics
#Diego Cantor, Robarts Research Institute / UWO
#Daniel Haehn, BWH
#Nicolas Rannou, BWH
#Sylvain Jaume, MIT
#Alex Yarmarkovich, Isomics
#Marco Ruiz, UCSD
#Andriy Fedorov, BWH (NA-MIC)
#Harish Doddi, Stanford University
#Scott Hoge, BWH (NCIGT)
#Vandana Mohan, Georgia Tech
#Ivan Kolosev, Georgia Tech
#Behnood Gholami, Georgia Tech
#James Balter, U Michigan
#Dan McShan, U Michigan
#Zhou Shen, U Michigan
#Maria Francesca Spadea, Italy
#Lining Yang, Siemens Corporate Research
#Beatriz Paniagua, UNC-Chapel Hill
#Bennett Landman, Johns Hopkins University
#Snehashis Roy, Johns Hopkins University
#Marta Peroni, Politecnico di Milano
#Sebastien Barre, Kitware, Inc.
#Samuel Gerber, SCI University of Utah
#Ran Tao, SCI University of Utah
#Marcel Prastawa, SCI University of Utah
#Katie Hayes, BWH (NA-MIC)
#Sonia Pujol, BWH (NA-MIC)
#Andras Lasso, Queen's University
#Yong Gao, MGH
#Minjeong Kim, UNC-Chapel Hill
#Guorong Wu, UNC-Chapel Hill
#Jeffrey Yager, UIowa
#Yanling Liu, SAIC/NCI-Frederick
#Ziv Yaniv, Georgetown
#Bjoern Menze, MIT
#Vidya Rajagopalan, Virginia Tech
#Sandy Wells, BWH (NAC, NCIGT)
#Lilla Zollei, MGH (NAC)
#Lauren O'Donnell, BWH
#Florin Talos, BWH (NAC)
#Nobuhiko Hata, BWH (NCIGT)
#Alark Joshi, Yale
#Yogesh Rathi, BWH
#Jimi Malcolm, BWH
#Dustin Scheinost, Yale
#Dominique Belhachemi, Yale
#Sam Song, JHU
#Nathan Cho, JHU
#Julien de Siebenthal, BWH
#Peter Savadjiev, BWH
#Carl-Fredrik Westin, BWH
#John Melonakos, AccelerEyes (Wed & Thu morning)
#Yi Gao, Georgia Tech
#Sylvain Bouix, BWH
#Zhexing Liu, UNC-CH
#Eric Melonakos, BWH
#Lei Qin, BWH
#Giovanna Danagoulian, BWH
#Andrew Rausch, BWH (Monday)
#Haytham Elhawary, BWH
#Jayender Jagadeesan, BWH
#Marek Kubicki, BWH
#Doug Terry, BWH
#Nathan Hageman, LONI (UCLA)
#Dana Peters, Beth Israel Deaconess
#Sun Woo Lee, BWH
# Melanie Grebe, Siemens Corporate Research
# Megumi Nakao, BWH/NAIST
# Moti Freiman, The Hebrew Univ. of Jerusalem
#Jack Blevins, Acoustic Med Systems
#Michael Halle, BWH
#Amanda Peters, Harvard SEAS
#Joe Stam, NVIDIA (Wednesday, Thursday)
#Petter Risholm, BWH (NCIGT)
#Kimberly Powell, NVIDIA (Wednesday)
#Padma Akella, BWH (NCIGT)
#Clif Burdette, Acousticmed (Mon, Tue, Wed)
#Mark Scully, MRN
#Jeremy Bockholt, MRN (tues-thurs)
#Curtis Rueden, UW-Madison
#Juhana Frosen, BWH (Tuesday)
#Andrzej Przybyszewski, UMass Medical School (Monday)
#Robert Yaffe, MGH
#Kenneth (Cal) Hisley, Des Moines University

== Logistics ==
*'''Dates:''' June 22-26, 2009
*'''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 12th, 2009. 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 this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.
*'''Registration Method''' Add your name to the Attendee List section of this page
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE 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.
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2008_Summer_Project_Week#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]]

User:Khisley

2008-02-06T17:21:34Z

Khisley: SLICER and 3D tracking eqwuipment interface assistance

Hello.

Does anyone in the SLICER community have experience with
using 3D SLICER with Accension Technologies "Flock of Birds"
equipment.

We're putting together an initial medical education
VR application with SLICER linking stethoscope position with
various MR and CT reconstructions.

We need to interface the FOB to the serial port of a Windows machine
running SLICER and then presumably use a plugin/driver to manage the
coordinate input stream.

Many Thanks

Ken Hisley