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Back to [[Events]]
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__NOTOC__
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Back to [[Events]]
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[[image:PW-MIT2013.png|300px]]
 
[[image:PW-MIT2013.png|300px]]
  
Dates: June 17-21, 2013.
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=Welcome to the web page for the 17th Project Week!=
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<gallery widths="800px" heights="300px" perrow="1" caption="Lunch in the Amphitheater at the Stata Building, June 20, 2013.">
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Image:Lunch at Project week IMG 0367.JPG|Shade was a popular commodity.
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</gallery>
  
Location: MIT, Cambridge, MA.
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==Summary==
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The 17th PROJECT EVENT was held on June 17-21, 2013 at MIT. It recorded 104 registered attendees, who worked on 75 projects. These attendees represented 22 academic sites (Brigham and Women’s Hospital, Massachusetts General Hospital, Boston Children’s Hospital, MIT, WPI, WIT, University of Alabama, Rochester Institute of Technology, University of Utah, University of Iowa, University of Michigan, UCLA, Rutgers University, University del Estado de Mexico,  Ecole Polytechnique Federale de Lausanne, Zhejiang University of Technology, Queen’s University, University of Sydney, University of Western Australia, University Sao Paulo, Leibniz University, Hannover, University Magna Graecia of Catanzaro) and 13 companies (NIRAL-UNC, Radnostics, GE Healthcare, GE Global Research, Kitware, zSpace, AZE Technology Inc, IEEE, Medical Science & Computing Inc, Fraunhofer MEVIS, Isomics Inc, IGI Technologies, KUKA Laboratories). The agenda and projects are detailed below.
  
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A [[Project_Events#Past_Project_Weeks|summary]] of all past Project Events.
  
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==Logistics==
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*Dates: June 17-21, 2013.
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*Location: MIT, Cambridge, MA.
 
==Agenda==
 
==Agenda==
  
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|bgcolor="#ffffdd"|'''9am-12pm'''
 
|bgcolor="#ffffdd"|'''9am-12pm'''
 
|
 
|
|'''10-11am''' [[2013 Project Week Breakout Session:Slicer4Python|Slicer4 Python Modules, Testing, Q&A]] <br>
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|'''10-11am''' [[2013 Project Week Breakout Session:Slicer4Python|Slicer4 Python Modules, Testing, Q&A]] (Steve Pieper) <br>
 
[[MIT_Project_Week_Rooms|Grier Room (Left)]]  
 
[[MIT_Project_Week_Rooms|Grier Room (Left)]]  
|'''9:30-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans)
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|'''9:30-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans Johnson, Brad Lowekamp)
 
[[MIT_Project_Week_Rooms#32-D507|32-D507]]
 
[[MIT_Project_Week_Rooms#32-D507|32-D507]]
|'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2013 Project Week Breakout Session: IGT|Image-Guided Therapy]] (Tina)
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|
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'''9:30-10:30am''' [[2013_Tutorial_Contest|Tutorial Contest Presentations]] <br>
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[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
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<br>----------------------------------------<br>
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'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2013 Project Week Breakout Session: IGT|Image-Guided Therapy]] (Tina Kapur)
 
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
 
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
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|'''10am-12pm:''' [[#Projects|Project Progress Updates]] <br>
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'''12pm''' [[Events:TutorialContestJune2013|Tutorial Contest Winner Announcement]]
 
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
 
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
 
|-
 
|-
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|bgcolor="#ffffaa"|Lunch
 
|bgcolor="#ffffaa"|Lunch
 
|bgcolor="#ffffaa"|Lunch
 
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
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|bgcolor="#ffffaa"|[http://www.na-mic.org/Wiki/index.php/File:NamicToAmphi.png Lunch in Outdoor Amphitheather!]
 
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
 
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
 
|-
 
|-
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[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
 
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
 
|'''1-3pm:''' [[Renewal-06-2013|NA-MIC Renewal]] <br>PIs <br>Closed Door Session with Ron
 
|'''1-3pm:''' [[Renewal-06-2013|NA-MIC Renewal]] <br>PIs <br>Closed Door Session with Ron
[[MIT_Project_Week_Rooms#32-D407|32-D407]]  
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[[MIT_Project_Week_Rooms#32-D407|32-262]]  
<br>----------------------------------------<br>
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|
'''3-4pm:''' [[2013_Tutorial_Contest|Tutorial Contest Presentations]] <br>
 
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
 
|'''12:45-1pm:''' [[Events:TutorialContestJune2013|Tutorial Contest Winner Announcement]]
 
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
 
 
|<br>----------------------------------------<br>'''3-5:30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Summer Project Week Breakout Session:RT|Radiation Therapy]] (Greg, Csaba)
 
|<br>----------------------------------------<br>'''3-5:30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Summer Project Week Breakout Session:RT|Radiation Therapy]] (Greg, Csaba)
 
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
 
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
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Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template this template] to create wiki pages for your project. Then link the page here with a list of key personnel.  
 
Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template this template] to create wiki pages for your project. Then link the page here with a list of key personnel.  
  
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 +
==Some Stats==
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75 Projects, 104 Attendees.  First time attendees 25.
  
 
===Huntington's Disease===
 
===Huntington's Disease===
* [[Dynamically Configurable Quality Assurance Module for Large Huntington's Disease Database Frontend]] (Dave)
 
* [[DWIConvert]] (Kent Williams)
 
 
* [[Learn and Apply FiberBundleLabelSelect for Huntington's Disease Data]] (Hans, Demian)
 
* [[Learn and Apply FiberBundleLabelSelect for Huntington's Disease Data]] (Hans, Demian)
 
* [[Investigate Potential Tensor Computation Improvement via Positive Semi-Definite (PSD) Tensor Estimation]] (Hans)
 
* [[Investigate Potential Tensor Computation Improvement via Positive Semi-Definite (PSD) Tensor Estimation]] (Hans)
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* [[2013_Summer_Project_Week:SinglePrecisionRegistrationITK| Single Precision Registration]] (Hans, Brad Lowekamp, Dave, Ali Ghayoor)
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* [[Dynamically Configurable Quality Assurance Module for Large Huntington's Disease Database Frontend]] (Dave)
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* [[DWIConvert]] (Dave, Kent Williams)
 
* [[Enhance and update SPL atlas]] (Dave, Hans)
 
* [[Enhance and update SPL atlas]] (Dave, Hans)
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* [[Linear Mixed-effects shape model to explore Huntington's Disease Data]] (Manasi, Dave, Josh, Hans, Ross)
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 +
<!-- If it applies, update the project count reported below and at the top of the page -->
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7 projects
  
 
===Traumatic Brain Injury===
 
===Traumatic Brain Injury===
* Validation and testing of 3D Slicer modules implementing the Utah segmentation algorithm for traumatic brain injury (Andrei Irimia, Micah Chambers, Bo Wang, Marcel Prastawa, Guido Gerig, Jack van Horn)
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* [[Visualization and quantification of peri-contusional white matter bundles in traumatic brain injury using diffusion tensor imaging]] (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* Visualization and quantification of peri-contusional white matter bundles in traumatic brain injury using diffusion tensor imaging (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
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* [[Clinically oriented assessment of local changes in the properties of white matter affected by intra-cranial hemorrhage]] (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* Clinically oriented assessment of local changes in the properties of white matter affected by intra-cranial hemorrhage (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
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* [[Validation and testing of 3D Slicer modules implementing the Utah segmentation algorithm for traumatic brain injury]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Guido Gerig, Jack van Horn)
* Investigation of the peri-lesional penumbra in traumatic brain injury using diffusion tensor imaging to isolate longitudinal changes in white matter integrity (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
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* [[Exploring multi-modal registration for improved longitudinal modeling of patient-specific 4D DTI data]] (Anuja Sharma, Bo Wang, Andrei Irimia, Micah Chambers, Guido Gerig, Jack van Horn)
* Reconstruction and visualization of the corticospinal tract in traumatic brain injury in the presence of severe hematoma and CSF-perfused edematous tissue using diffusion tensor imaging (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
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* [[2013_Summer_Project_Week: A Portable Ultrasound Device for Intracranial Hemorrhage Detection|A Portable Ultrasound Device for Intracranial Hemorrhage Detection]] (Jason White, Vicki Noble, Kirby Vosburgh)
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<!-- If it applies, update the project count reported below and at the top of the page -->
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5 projects
  
===Atrial Fibrillation===
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===Atrial Fibrillation and Cardiac Image Analysis===
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* [[2013_Summer_Project_Week:Fibrosis_analysis|Fibrosis distribution analysis]] (Yi Gao, LiangJia Zhu, Josh Cates, Rob MacLeod, Sylvain Bouix, Ron Kikinis, Allen Tannenbaum)
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* [[2013_Summer_Project_Week:SegmentationAidedRegistration|Segmentation Aided Registration]] (Yi Gao, LiangJia Zhu, Josh Cates, Rob MacLeod, Sylvain Bouix, Ron Kikinis, Allen Tannenbaum)
 
* [[2013_Summer_Project_Week:CARMA_workflow_wizard|Cardiac MRI Toolkit LA segmentation and enhancement quantification workflow wizard]] (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
 
* [[2013_Summer_Project_Week:CARMA_workflow_wizard|Cardiac MRI Toolkit LA segmentation and enhancement quantification workflow wizard]] (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
 
* [[2013_Summer_Project_Week:CARMA_Documentataion|Cardiac MRI Toolkit Documentation Project]] (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
 
* [[2013_Summer_Project_Week:CARMA_Documentataion|Cardiac MRI Toolkit Documentation Project]] (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
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* [[2013_Summer_Project_Week:CARMA_AutoLASeg|Cardiac MRI Toolkit: Automatic LA Segmentation with Graph Cuts Module]] (Salma Bengali, Alan Morris, Josh Cates, Gopal, Ross Whitaker, Rob MacLeod)
 
* [[2013_Summer_Project_Week:CARMA_AutoLASeg|Cardiac MRI Toolkit: Automatic LA Segmentation with Graph Cuts Module]] (Salma Bengali, Alan Morris, Josh Cates, Gopal, Ross Whitaker, Rob MacLeod)
 
* [[2013_Summer_Project_Week:Sobolev_Segmenter|Medical Volume Segmentation Using Sobolev Active Contours]] (Arie Nakhmani, Yi Gao, LiangJia Zhu, Rob MacLeod, Josh Cates, Ron Kikinis, Allen Tannenbaum)
 
* [[2013_Summer_Project_Week:Sobolev_Segmenter|Medical Volume Segmentation Using Sobolev Active Contours]] (Arie Nakhmani, Yi Gao, LiangJia Zhu, Rob MacLeod, Josh Cates, Ron Kikinis, Allen Tannenbaum)
* [[2013_Summer_Project_Week:Fibrosis_analysis|Fibrosis distribution analysis]] (Yi Gao, LiangJia Zhu, Rob MacLeod, Josh Cates, Ron Kikinis, Allen Tannenbaum)
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* [[2013_Summer_Project_Week:Left_Ventricle_Motion_Analysis_using_Tagged_MRI|Left Ventricle Motion Analysis using Tagged MRI]] (Yang Yu, Shaoting Zhang, Dimitris Metaxas)
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<!-- If it applies, update the project count reported below and at the top of the page -->
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8 projects
  
 
===Radiation Therapy===
 
===Radiation Therapy===
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* [[2013_Summer_Project_Week:Slicer_RT:_DICOM-RT_Export | SlicerRT: Dicom-RT Export]] (Greg Sharp, Kevin Wang, Csaba Pinter)
 
* [[2013_Summer_Project_Week:Slicer_RT:_DICOM-RT_Export | SlicerRT: Dicom-RT Export]] (Greg Sharp, Kevin Wang, Csaba Pinter)
 
* [[2013_Summer_Project_Week:Proton_dose_calculation | Proton dose calculation]]  (Greg Sharp, Kevin Wang, Maxime Desplanques)
 
* [[2013_Summer_Project_Week:Proton_dose_calculation | Proton dose calculation]]  (Greg Sharp, Kevin Wang, Maxime Desplanques)
* [[2013_Summer_Project_Week:Deformable_registration_validation_toolkit | Deformable registration validation toolkit]] (Greg Sharp, Kevin Wang, Andrey Fedorov, anyone else?)
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* [[2013_Summer_Project_Week:Deformable_registration_validation_toolkit | Deformable registration validation toolkit]] (Greg Sharp, Kevin Wang, Andrey Fedorov)
* [[Analysis of different atlas-based segmentation techniques for parotid glands]] (Christian Wachinger, Karl Fritscher, Greg Sharp, Matthew Brennan)
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* [[2013_Summer_Project_Week:Deformable_transforms | Deformable transform handling in Transforms module]] (Csaba Pinter, Alex Yarmarkovich, Andras Lasso)
* [[2013_Summer_Project_Week:Deformable_transforms | Deformable transform handling in Transforms module]] (Csaba Pinter, Alex Yarmarkovich, Andras Lasso, ?)
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* [[2013_Summer_Project_Week:Brachy_HDR_Ultrasound | Creating DICOM series from ultrasound for prostate HDR brachytherapy]] (Adam Rankin)
* [[2013_Summer_Project_Week:CMFReg | Cranio-Maxillofacial Registration]] (Vinicius Boen)
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* [[Analysis of different atlas-based segmentation techniques for parotid glands]] (Karl Fritscher, Christian Wachinger, Greg Sharp, Matthew Brennan)
 +
* [[2013_Summer_Project_Week:Prostate_radiotherapy_DICOM_communication|DICOM communication between Slicer and Oncentra Prostate radiation therapy planning system]] (Andrey Fedorov, Csaba Pinter, Emily Neubauer-Sugar, Alireza Mehrtash)
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 +
<!-- If it applies, update the project count reported below and at the top of the page -->
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10 projects
  
===Device Integration with Slicer===
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===IGT and Device Integration with Slicer===
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* [[2013_Summer_Project_Week:TractAtlasCluster| Tract Atlas and Clustering for Neurosurgery]] (Lauren O'Donnell)
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* [[2013_Summer_Project_Week:SlicerIGT_Extension| SlicerIGT extension]] (Tamas Ungi, Junichi Tokuda, Laurent Chauvin)
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* [[2013_Summer_Project_Week:Ultrasound_Calibration| Ultrasound Calibration]] (Matthew Toews, Daniel Kostro, William Wells, Stephen Aylward, Isaiah Norton, Tamas Ungi)
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* [[2013_Summer_Project_Week:Ultrasound_Needle_Detection| Ultrasound Needle Detection]] (Alireza Mehrtash, Daniel Kostro, Matthew Toews, Tamas Ungi, William Wells, Tina Kapur)
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* [[2013_Summer_Project_Week:Liver_Trajectory_Management| Liver Trajectory Management]] (Laurent Chauvin, Junichi Tokuda)
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* [[2013_Summer_Project_Week:LabelMapStatistics| Label map statistics]] (Laurent Chauvin, Csaba Pinter)
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* [[2013_Summer_Project_Week:PerkTutorExtension| Perk Tutor Extension]] (Matthew Holden, Tamas Ungi)
 
* [[2013_Summer_Project_Week:Open_source_electromagnetic_trackers_using_OpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
 
* [[2013_Summer_Project_Week:Open_source_electromagnetic_trackers_using_OpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
* [[2013_Summer_Project_Week:kukarobot| Interface for the integration of a KUKA robot using OpnIGTLink]] (Sebastian Tauscher, Nobuhiko Hata)
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* [[2013_Summer_Project_Week:3D_prostate_segmentation_of_Ultrasound_image| Segmentation of Prostate Gland from 3D US for Prostate Interventions]] (Xu Li, Andriy Fedorov, Tina Kapur, William Wells)
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* [[2013_Summer_Project_Week:3D_prostate_registration_of_Ultrasound_image_using_MRI| Registration of an MRI delineated image of the Prostate Gland ot a 3D US for Prostate Interventions]] (Demian Wassermann, Andriy Fedorov, Tina Kapur, William Wells)
 +
* [[2013_Summer_Project_Week:ProstateBRP| MRI-guided robotic prostate interventinos]] (Junichi Tokuda, Greg Fischer, Nirav Patel, Nobuhiko Hata, Clare Tempnay)
 +
 
 +
<!-- If it applies, update the project count reported below and at the top of the page -->
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11 projects
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 +
===Chronic Obstructive Pulmonary Disease===
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* [[2013_Summer_Project_Week:Airway_Inspector_Porting | Porting Airway Inspector to Slicer 4]] (Raul San Jose, Demian Wassermann, Rola Harmouche, James Ross)
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* [[2013_Summer_Project_Week:MRML_Infrastructure_Airway_Inspector | Airway Inspector: Slicer Extension and MRML Infrastructure]] (Demian Wassermann,  James, Ross, Rola Harmouche, Raul San Jose)
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* [[2013_Summer_Project_Week:Nipype_CLI_Integration | Integration of Nipype with CLI modules in the Chest Imaging Platform Library ]] (Rola Harmouche,Demian Wassermann, Raul San Jose)
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 +
<!-- If it applies, update the project count reported below and at the top of the page -->
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3 projects
  
===IGT===
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=== '''Additional Collaborations'''===
* [[2013_Summer_Project_Week:SlicerIGT_Extension| SlicerIGT extension]] (Tamas, Junichi, Laurent)
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* [[2013_Summer_Project_Week:VicomTech| VicomTech visit: Imaging solutions and Slicer use]] (Ivan Macia)
* [[2013_Summer_Project_Week:Ultrasound_Calibration| Ultrasound Calibration]] (Matthew Toews, Daniel Kostro, William Wells, Steven Aylward, Tamas Ungi)
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* [[2013_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis)
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* [[2013_Summer_Project_Week: Computer Assisted Surgery| Computer Assisted Reconstruction of Complex Bone Fractures]] (Karl Fritscher, Peter Karasev, Ivan Kolesov, Allen Tannenbaum, Ron Kikinis)
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* [[2013_Summer_Project_Week:XNAT 3D Viewer| XNAT 3D Viewer]] (Amanda Hartung, Steve Pieper, Daniel Haehn)
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* [[2013_Summer_Project_Week:kukarobot| Interface for the integration of a KUKA robot using OpenIGTLink]] (Sebastian Tauscher, Thomas Neff, Junichi Tokuda, Nobuhiko Hata)
 
* [[2013_Summer_Project_Week:Application of Statistical Shape Modeling to Robot Assisted Spine Surgery | Application of Statistical Shape Modeling to Robot Assisted Spine Surgery]] (Marine Clogenson)
 
* [[2013_Summer_Project_Week:Application of Statistical Shape Modeling to Robot Assisted Spine Surgery | Application of Statistical Shape Modeling to Robot Assisted Spine Surgery]] (Marine Clogenson)
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* [[2013_Summer_Project_Week:Robot_Control| Robot Control]] (A.Vilchis, J-C. Avila-Vilchis, S.Pujol)
 
* [[2013_Summer_Project_Week:Epilepsy_Surgery|Identification of MRI Blurring in Temporal Lobe Epilepsy Surgery]] (Luiz Murta)
 
* [[2013_Summer_Project_Week:Epilepsy_Surgery|Identification of MRI Blurring in Temporal Lobe Epilepsy Surgery]] (Luiz Murta)
 
* [[2013_Summer_Project_Week:_Is_Neurosurgical_Rigid_Registration_Really_Rigid%3F| Is Neurosurgical Rigid Registration Really Rigid?]] (Athena)
 
* [[2013_Summer_Project_Week:_Is_Neurosurgical_Rigid_Registration_Really_Rigid%3F| Is Neurosurgical Rigid Registration Really Rigid?]] (Athena)
* [[2013_Summer_Project_Week:Liver_Trajectory_Management| Liver Trajectory Management]] (Laurent, Junichi)
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* [[2013_Summer_Project_Week:_Individualized_Neuroimaging_Content_Analysis_using_3D_Slicer_in_Alzheimer%27s_Disease| Individualized Neuroimaging Content Analysis using 3D Slicer in Alzheimer's Disease]] (Sidong Liu, Weidong Cai, Sonia Pujol, Ron Kikinis)
* [[2013_Summer_Project_Week:4DUltrasound| 4D Ultrasound]] (Laurent, Junichi)
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* [[2013_Summer_Project_Week:CMFReg | Cranio-Maxillofacial Registration]] (Francois Budin, Vinicius Boen)
* [[2013_Summer_Project_Week: Individualized Neuroimaging Content Analysis using 3D Slicer in Alzheimer's Disease| Individualized Neuroimaging Content Analysis using 3D Slicer]] (Sidong Liu, Weidong Cai, Sonia Pujol, Ron Kikinis)
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* [[2013_Summer_Project_Week:DTIPipelineExtensions | DTI Analysis Pipeline as Slicer4 Extensions]] (Francois Budin)
* [[2013_Summer_Project_Week: Computer Assisted Surgery| Computer Assisted Reconstruction of Complex Bone Fractures]] (Karl Fritscher, Peter Karasev, Ron Kikinis)
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*[[2013_Project_Week:WebbasedAnatomicalTeachingFrameworkSummer2013|Web-based anatomical teaching framework]] (Nathaniel Reynolds, Lilla Zollei, Daniel Haehn, Nicolas Rannou, Steve Pieper, Rudolph Pienaar)
* [[2013_Summer_Project_Week:PerkTutorExtension| Perk Tutor Extension]] (Matthew Holden, Tamas Ungi)
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* [[2013_Summer_Project_Week:Biomedical_Image_Computing_Teaching_Modules|3D Slicer based Biomedical image computing teaching modules]]  (A. Vilchis, J-C. Avila-Vilchis, S. Pujol)
* [[2013_Summer_Project_Week:TractAtlasCluster| Tract Atlas and Clustering]] (Lauren O'Donnell)
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* [[2013_Summer_Project_Week:Analyzing Breast Tumor Heterogeneity Using 3D Slicer|Analyzing Breast Tumor Heterogeneity Using 3D Slicer]] (Sneha Durgapal, Jayender Jagadeesan, Tobias Penzkofer, Vivek Narayan)
 +
* [[2013_Summer_Project_Week:WMH Segmentation for Stroke|WMH Segmentation for Stroke]] (Adrian Dalca, Ramesh Sridharan, Kayhan Batmanghelich, Polina Golland)
 +
* [[2013_Summer_Project_Week:WMQL Integration in Slicer|White Matter Query Language (WMQL) Integration in Slicer]] (Demian Wassermann, Carl-Fredrik Westin)
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* [[2013_Summer_Project_Week:Documentation for Slicer 4.2 Data Loading and 3D Visualization|Documentation for Slicer 4.2 Data Loading and 3D Visualization]] (Parth Amin WIT, Matt Flynn WIT, Sonia Pujol, BWH, Sylvain Jaume, WIT)
 +
* [http://wiki.na-mic.org/Wiki/index.php/Projects:WIT_mold_holder 3D Printing of a Prostate Slicer] (Maria Gonzalez-Puente WIT, Andriy Fedorov, BWH, Sylvain Jaume, WIT)
 +
* [[2013_Summer_Project_Week:WM Geometry Tools|Integration in Slicer of white matter geometry tools]] (Peter Savadjiev, Carl-Fredrik Westin)
  
=== '''Informatics'''===
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<!-- If it applies, update the project count reported below and at the top of the page -->
* [[2013_Summer_Project_Week:Biomedical_Image_Computing_Teaching_Modules|3D Slicer based Biomedical image computing teaching modules]]  (A.Vilchis, J-C. Avila-Vilchis, S.Pujol)
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20 projects
* [[2013_Summer_Project_Week:Robot_Control| Robot Control]] (A.Vilchis, J-C. Avila-Vilchis, S.Pujol)
 
  
 
==='''Infrastructure'''===
 
==='''Infrastructure'''===
* [[2013_Summer_Project_Week:MarkupsModuleSummer2013| Markups/Annotations rewrite]] (Nicole Aucoin)
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* [[2013_Summer_Project_Week:MarkupsModuleSummer2013| Markups/Annotations rewrite]] (Nicole Aucoin, Ron Kikinis)
* Provenance
 
 
* [[2013_Summer_Project_Week:Patient_hierarchy | Patient hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper)
 
* [[2013_Summer_Project_Week:Patient_hierarchy | Patient hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper)
* [[2013_Summer_Project_Week:CLI_Improvements | CLI Improvements (hierarchy nodes, related nodes, roles)]] (Andras Lasso, Csaba Pinter, Jc, Steve, Jim, ?)
 
*  [[2013_Summer_Project_Week:Sample_Data | Sample Data]] (Steve Pieper, Jim Miller, Bill Lorensen, Jc)
 
* [[Plastimatch in NiPype]] (Paolo, Dave, Hans)
 
** look for commonalities/reuse of CompareVolumes
 
* iPython in Slicer (Hans, Jc, Dave)
 
* [[2013_Summer_Project_Week:Optimizing start time of slicer| Optimizing start time of slicer]] (Jc, Steve)
 
 
* [[Common resampling and conversion utility functions in Slicer]] (Csaba Pinter, Steve Pieper, Hans, Kevin Wang)
 
* [[Common resampling and conversion utility functions in Slicer]] (Csaba Pinter, Steve Pieper, Hans, Kevin Wang)
 +
* [[2013_Summer_Project_Week:CLI_Matlab | CLI module implementation in Matlab - without building Slicer or Matlab MEX files]] (Andras Lasso, Jc)
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* [[2013_Summer_Project_Week:CLI_Improvements | CLI Improvements (hierarchy nodes, related nodes, roles)]] (Andras Lasso, Csaba Pinter, Jc, Steve, Jim)
 +
* [[2013_Summer_Project_Week:Sample_Data | Sample Data]] (Steve Pieper, Jim Miller, Bill Lorensen, Jc)
 +
* [[ITK -VTK wrapper]] (Paolo Zaffino, Greg Sharp, Steve Pieper)
 
* [[2013_Summer_Project_Week:CLI_modules_in_MeVisLab| Integrating CTK CLI modules into MeVisLab]] (Hans Meine, Steve, Jc)
 
* [[2013_Summer_Project_Week:CLI_modules_in_MeVisLab| Integrating CTK CLI modules into MeVisLab]] (Hans Meine, Steve, Jc)
*[[2013_Project_Week:WebbasedAnatomicalTeachingFrameworkSummer2013|Web-based anatomical teaching framework]] (Daniel Haehn, Steve Pieper, Rudolph Pienaar, Lilla Zollei, Nathaniel Reynolds)
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* [[2013_Summer_Project_Week:SimpleITK_GUI| Common Usage GUI for SimpleITK]] (Dave Welch, Brad Lowekamp, Hans Johnson, Steve)
 
+
* [[2013_Summer_Project_Week:Extension_dependencies| Extension dependencies]] (Jc, Adam Rankin)
==='''Brain & Spine Segmentation'''===
+
* [[2013_Summer_Project_Week:Parameter_heirarchy| Parameter (time) Hierarchy]] (Adam Rankin, Andras Lasso, Steve Pieper)
* [[2013_Summer_Project_Week:Multi_Atlas_Based_Multi_Image_Segmentation | Multi-Atlas-Based Multi-Image Segmentation for Brain MR Images]] (Minjeong Kim, Xiaofeng Liu, Jim Miller, Dinggang Shen)
+
* [[2013_Summer_Project_Week:ITK_Shared_IO_Libraries| ITK Shared I/O Libraries]] (Jim,Brad Lowekamp, Jc)
* [[2013_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis)
+
* [[2013_Summer_Project_Week:Python_Embedding| Python Embedding Library]] (Rui, Jim, Jc, Steve)
 
+
* [[2013_Summer_Project_Week:MaskedFFTNormalizedCorrelationOverlay | Masked FFT Normalized Correlation Overlay]] (Dirk, Hans, Brad)
===""Chronic Obstructive Pulmonary Disease""===
+
<!-- If it applies, update the project count reported below and at the top of the page -->
* [[2013_Summer_Project_Week:Airway_Inspector_Porting | Porting Airway Inspector to Slicer 4]] (Raul San Jose, Demian Wassermann, Rola Harmouche)
+
12 projects
* [[2013_Summer_Project_Week:MRML_Infrastructure_Airway_Inspector | Airway Inspector: Slicer Extension and MRML Infrastructure]] (Demian Wassermann, Raul San Jose, Rola Harmouche)
 
* [[2013_Summer_Project_Week:Nipype_CLI_Integration | Integration of Nipype with CLI modules in the Chest Imaging Platform Library ]] (Rola Harmouche,Demian Wassermann, Raul San Jose)
 
  
 
== '''Background''' ==
 
== '''Background''' ==
Line 168: Line 221:
 
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 40-50 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.
 
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 40-50 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],  [http://www.cimit.org CIMIT], and OCAIRO.  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.   
+
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],  [http://www.cimit.org CIMIT], and OCAIRO.  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 Women's 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]].
+
Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week NA-MIC Project Week mailing list].
  
  
Line 176: Line 229:
  
 
*'''Dates:''' June 17-21, 2013.
 
*'''Dates:''' June 17-21, 2013.
*'''Location:''' MIT.  
+
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]].  
 
*'''REGISTRATION:'''  http://www.regonline.com/namic2013summerprojweek. Please note that  as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
 
*'''REGISTRATION:'''  http://www.regonline.com/namic2013summerprojweek. Please note that  as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
 
*'''Registration Fee:''' $300.
 
*'''Registration Fee:''' $300.
Line 194: Line 247:
 
# 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...
 
# 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.
 
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
+
## See the [https://www.slicer.org/wiki/Documentation/4.0/Developers Developer Section of slicer.org] for information.
 
## Projects to develop extension modules should be built against the latest Slicer4 trunk.
 
## Projects to develop extension modules should be built against the latest Slicer4 trunk.
  
Line 201: Line 254:
 
Do not add your name to this list - it is maintained by the organizers based on your paid registration.  ([http://www.regonline.com/Register/Checkin.aspx?EventID=1233699  Please click here to register.])
 
Do not add your name to this list - it is maintained by the organizers based on your paid registration.  ([http://www.regonline.com/Register/Checkin.aspx?EventID=1233699  Please click here to register.])
  
#Charles Anderson, BWH, canderson26@partners.org
+
# Parth Amin :: Wentworth Institute of Technology :: aminp at wit.edu
#Peter Anderson, retired, traneus@verizon.net
+
# Charles Anderson :: Brigham and Women's Hospital :: canderson26 at partners.org
#Nicole Aucoin, BWH, nicole@bwh.harvard.edu
+
# Peter Anderson :: Retired :: traneus at verizon.net
#Juan Carlos Avila Vilchis, Univ del Estado de Mexico, jc.avila.vilchis@hotmail.com
+
# Nicole Aucoin :: Brigham and Women's Hospital :: nicole at bwh.harvard.edu
#Salma Bengali, Univ UT, salma.bengali@carma.utah.edu
+
# Kayhan Batmanghelich :: Massachusetts Institute of Technology :: kayhan at csail.mit.edu
#Anthony Blumfield, Radnostics, Anthony.Blumfield@Radnostics.com
+
# Salma Bengali :: University of Utah :: salma.bengali at carma.utah.edu
#Vinicius Boen, Univ Michigan, vboen@umich.edu
+
# Anthony Blumfield :: Radnostics :: Anthony.Blumfield at Radnostics.com
#Matthew Brennan, MIT, brennanm@mit.edu
+
# Vinicius Boen :: University of Michigan :: vboen at umich.edu
#Francois Budin, NIRAL-UNC, fbudin@unc.edu
+
# Taylor Braun-Jones :: General Electric :: taylor.braun-jones at ge.com
#Ivan Buzurovic, BWH/HMS, ibuzurovic@lroc.harvard.edu
+
# Matthew Brennan :: Massachusetts Institute of Technology :: brennanm at mit.edu
#Josh Cates, Univ UT, cates@sci.utah.edu
+
# Francois Budin :: University of North Carolina :: fbudin at unc.edu
#Micah Chambers, UCLA, micahcc@ucla.edu
+
# Ivan Buzurovic :: Brigham and Women's Hospital :: ibuzurovic at lroc.harvard.edu
#Marine Clogenson, Ecole Polytechnique Federale de Lausanne (Switzerland), marine.clogenson@epfl.ch
+
# Juan Carlos Avila-Vilchis :: jc.avila.vilchis at hotmail.com
#Adrian Dalca, MIT, adalca@MIT.EDU
+
# Joshua Cates :: University of Utah :: cates at sci.utah.edu
#Manasi Datar, Univ UT-SCI Institute, datar@sci.utah.edu
+
# Micah Chambers :: UCLA :: micahcc at ucla.edu
#Sneha Durgapal, BWH, durgapalsneha@gmail.com
+
# Laurent Chauvin :: Brigham and Women's Hospital :: lchauvin at bwh.harvard.edu
#Luping Fang, Zhejiang Univ of Technology (China), flp@zjut.edu.cn
+
# Marine Clogenson :: Ecole Polytechnique Federale de Lausanne :: marine.clogenson at epfl.ch
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
+
# Matthew D'Artista :: Brigham and Women's Hospital :: mdartista7 at gmail.com
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
+
# Adrian Dalca :: Massachusetts Institute of Technology :: adalca at MIT.EDU
#Gregory Fischer, WPI, gfischer@wpi.edu
+
# Manasi Datar :: University of Utah :: datar at sci.utah.edu
#Karl Fritscher, MGH, kfritscher@gmail.com
+
# Sneha Durgapal :: Brigham and Women's Hospital :: durgapalsneha at gmail.com
#Yi Gao, Univ AL Birmingham, gaoyi.cn@gmail.com
+
# Andriy Fedorov :: Brigham and Women's Hospital :: fedorov at bwh.harvard.edu
#Daniel Haehn, Boston Childrens Hospital, daniel.haehn@childrens.harvard.edu
+
# Jean-Christophe Fillion-Robin :: Kitware, Inc. :: jchris.fillionr at kitware.com
#Michael Halle, BWH-SPL, mhalle@bwh.harvard.edu
+
# Gregory Fischer :: Worcester Polytechnic Institute :: gfischer at wpi.edu
#Rola Harmouche, BWH, rharmo@bwh.harvard.edu
+
# Barton Fiske :: zSpace :: bfiske at zspace.com
#Nobuhiko Hata, BWH, hata@bwh.harvard.edu
+
# Matthew Flynn :: Wentworth Institute of Technology :: flynnm3 at wit.edu
#Nicholas Herlambang, AZE Technology Inc, nicholas.herlambang@azetech.com
+
# Karl Fritscher :: Massachusetts General Hospital :: kfritscher at gmail.com
#Matthew Holden, Queen's Univ (Canada), mholden8@cs.queensu.ca
+
# Yi Gao :: University of Alabama at Birmingham :: gaoyi.cn at gmail.com
#Jayender Jagadeesan, BWH-SPL, jayender@bwh.harvard.edu
+
# Alexandra Golby :: Brigham and Women's Hospital :: agolby at partners.org
#Hans Johnson, Univ Iowa, hans-johnson@uiowa.edu
+
# Maria Gonzalez-Puente :: Wentworth Institute of Technology :: gonzalezpuentem at wit.edu
#Tina Kapur, BWH/HMS, tkapur@bwh.harvard.edu
+
# Dan Groszmann :: General Electric :: daniel.groszmann at ge.com
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
+
# Daniel Haehn :: Boston Children's Hospital :: daniel.haehn at childrens.harvard.edu
#Daniel Kostro, BWH, dkostro@bwh.harvard.edu
+
# Michael Halle :: Brigham and Women's Hospital :: mhalle at bwh.harvard.edu
#Andras Lasso, Queen's Univ (Canada), lasso@cs.queensu.ca
+
# Rola Harmouche :: Brigham and Women's Hospital :: rharmo at bwh.harvard.edu
#Rui Li, GE Global Research, li.rui@ge.com
+
# Amanda Hartung :: Rochester Institute of Technology :: amh1646 at rit.edu
#Xu Li, BWH, lixu0103@gmail.com
+
# Nobuhiko Hata :: Brigham and Women's Hospital :: hata at bwh.harvard.edu
#Sidong Liu, Univ Sydney (Australia), sliu7418@uni.sydney.edu.au
+
# Nicholas Herlambang :: AZE Technology, Inc. :: nicholas.herlambang at azetech.com
#William Lorensen, Bill's Basement, bill.lorensen@gmail.com  
+
# Matthew Holden :: Queen's University :: mholden8 at cs.queensu.ca
#Bradley Lowekamp, Medical Science & Computing Inc, bradley.lowekamp@nih.gov
+
# Andrei Irimia :: UCLA :: andrei.irimia at loni.ucla.edu
#Athena Lyons, Univ Western Australia, 20359511@student.uwa.edu.au
+
# Jayender Jagadeesan :: Brigham and Women's Hospital :: jayender at bwh.harvard.edu
#Alireza Mehrtash, BWH - SPL, mehrtash@bwh.harvard.edu
+
# Sylvain Jaume :: Wentworth Institute of Technology :: jaumes at wit.edu
#Hans Meine, Fraunhofer MEVIS (Germany), hans.meine@mevis.fraunhofer.de
+
# Daniel Jimenez :: Texas A&M University :: daniel.jimenez at gmail.com
#Jim Miller, GE Global Research, millerjv@ge.com
+
# Hans Johnson :: University of Iowa :: hans-johnson at uiowa.edu
#Luis Murta, Univ Sao Paulo (Brazil), lomurta@gmail.com
+
# Tina Kapur :: Brigham and Women's Hospital :: tkapur at bwh.harvard.edu
#Arie Nakhmani, Univ AL Birmingham, anry@uab.edu
+
# Alex Kikinis :: Brigham and Women's Hospital :: alexkikinis at gmail.com
#Isaiah Norton, BWH, inorton@bwh.harvard.edu
+
# Ron Kikinis :: Brigham and Women's Hospital :: kikinis at bwh.harvard.edu
#Lauren O'Donnell, BWH, odonnell@bwh.harvard.edu
+
# Nils Klarlund :: IEEE :: klarlund at ieee.org
#Dirk Padfield, GE Global Research, padfield@research.ge.com
+
# Daniel Kostro :: Brigham and Women's Hospital :: dkostro at bwh.harvard.edu
#Jian Pan, Zhejiang Univ of Technology (China), pj@zjut.edu.cn
+
# Andras Lasso :: Queen's University :: lasso at cs.queensu.ca
#Steve Pieper, Isomics Inc, pieper@isomics.com
+
# Rui Li :: General Electric :: li.rui at ge.com
#Csaba Pinter, Queen's Univ (Canada), pinter@cs.queensu.ca
+
# Xu Li :: Brigham and Women's Hospital :: lixu0103 at gmail.com
#Sonia Pujol, HMS, spujol@bwh.harvard.edu
+
# Lichen Liang :: Massachusetts General Hospital :: lichenl at nmr.mgh.harvard.edu
#Adam Rankin, Queen's Univ (Canada), rankin@cs.queensu.ca
+
# Sidong Liu :: University of Sydney :: sliu7418 at uni.sydney.edu.au
#Nathaniel Reynolds, MGH, reynolds@nmr.mgh.harvard.edu
+
# Bill Lorensen :: Bill's Basement :: bill.lorensen at gmail.com
#Raul San Jose, BWH, rjosest@bwh.harvard.edu
+
# Bradley Lowekamp :: Medical Science & Computing Inc. :: bradley.lowekamp at nih.gov
#Anuja Sharma, Univ UT-SCI Institute, anuja@cs.utah.edu
+
# Athena Lyons :: University of Western Australia :: 20359511 at student.uwa.edu.au
#Greg Sharp, MGH, gcsharp@partners.org
+
# Nikos Makris :: Massachusetts General Hospital :: nikos at nmr.mgh.harvard.edu
#Nadya Shusharina, MGH, nshusharina@partners.org
+
# Katie Mastrogiacomo :: Brigham and Women's Hospital :: kmast at bwh.harvard.edu
#Sebastian Tauscher, Leibniz Univ Hannover (Germany), sebastian.tauscher@imes.uni-hannover.de
+
# Alireza Mehrtash :: Brigham and Women's Hospital :: mehrtash at bwh.harvard.edu
#Matthew Toews, BWH/HMS, mt@bwh.harvard.edu
+
# Hans Meine :: Fraunhofer MEVIS, Bremen :: hans.meine at mevis.fraunhofer.de
#Junichi Tokuda, BWH, tokuda@bwh.harvard.edu
+
# James Miller :: General Electric :: millerjv at ge.com
#Tamas Ungi, Queen's Univ (Canada), ungi@cs.queensu.ca
+
# Luiz Otavio Murta :: University of Sao Paulo :: lomurta at gmail.com
#Adriana Vilchis González, Univ del Estado de Mexico, hvigady@hotmail.com
+
# Arie Nakhmani :: University of Alabama at Birmingham :: anry at uab.edu
#Christian Wachinger, MIT, wachinge@mit.edu
+
# Isaiah Norton :: Brigham and Women's Hospital :: inorton at bwh.harvard.edu
#Bo Wang, Univ UT-SCI Institute, bowang@sci.utah.edu
+
# Lauren O'Donnell :: Brigham and Women's Hospital :: odonnell at bwh.harvard.edu
#Demian Wassermann, BWH, demian@bwh.harvard.edu
+
# Dirk Padfield :: General Electric :: padfield at research.ge.com
#David Welch, Univ Iowa, david-welch@uiowa.edu
+
# Jian Pan :: University of Technology, China :: pj at zjut.edu.cn
#William Wells, BWH/HMS, sw@bwh.harvard.edu
+
# George Papadimitriou :: Massachusetts General Hospital :: georgep at nmr.mgh.harvard.edu
#Phillip White, BWH/HMS, white@bwh.harvard.edu
+
# Nirav Patel :: Worcester Polytechnic Institute :: napatel at wpi.edu
#Alex Yarmarkovich, Isomics Inc, alexy@bwh.harvard.edu
+
# Tobias Penzkofer :: Brigham and Women's Hospital :: pt at bwh.harvard.edu
#Yang Yu, Rutgers Univ, yyu@cs.rutgers.edu
+
# Rudolph Pienaar :: Boston Children's Hospital :: Rudolph.Pienaar at childrens.harvard.edu
#Paolo Zaffino, Univ Magna Graecia of Catanzaro (Italy), p.zaffino@unicz.it
+
# Steve Pieper :: Isomics, Inc. :: pieper at isomics.com
#Lilla Zollei, MGH, lzollei@nmr.mgh.harvard.edu
+
# Csaba Pinter :: Queen's University :: pinter at cs.queensu.ca
 +
# William Plishker :: IGI Technologies :: will at igitechnologies.com
 +
# Sonia Pujol :: Brigham and Women's Hospital :: spujol at bwh.harvard.edu
 +
# Adam Rankin :: Queen's University :: rankin at cs.queensu.ca
 +
# Nathaniel Reynolds :: Massachusetts General Hospital :: reynolds at nmr.mgh.harvard.edu
 +
# Raul San Jose Estepar :: Brigham and Women's Hospital :: rjosest at bwh.harvard.edu
 +
# Peter Savadjiev :: Brigham and Women's Hospital :: petersv at bwh.harvard.edu
 +
# Tobias Schroeder :: General Electric :: tobias.schroeder at ge.com
 +
# Anuja Sharma :: University of Utah :: anuja at cs.utah.edu
 +
# Gregory Sharp :: Massachusetts General Hospital :: gcsharp at partners.org
 +
# Nadya Shusharina :: Massachusetts General Hospital :: nshusharina at partners.org
 +
# Sebastian Tauscher :: Leibniz Universität Hannover :: sebastian.tauscher at imes.uni-hannover.de
 +
# Clare Tempany :: Brigham and Women's Hospital :: ctempanyafdhal at partners.org
 +
# Gaurie Tilak :: Brigham and Women's Hospital :: gaurie_tilak at hms.harvard.edu
 +
# Matthew Toews :: Brigham and Women's Hospital :: mt at bwh.harvard.edu
 +
# Junichi Tokuda :: Brigham and Women's Hospital :: tokuda at bwh.harvard.edu
 +
# Tamas Ungi :: Queen's University :: ungi at cs.queensu.ca
 +
# Adriana Vilchis González :: Universidad Autonoma del Estado de Mexico :: hvigady at hotmail.com
 +
# Cyrill von Tiesenhausen :: KUKA Laboratories :: cyrill.tiesenhausen at kuka.com
 +
# Kirby Vosburgh :: Brigham and Women's Hospital :: kirby at bwh.harvard.edu
 +
# Christian Wachinger :: Massachusetts Institute of Technology :: wachinge at mit.edu
 +
# Bo Wang :: University of Utah :: bowang at sci.utah.edu
 +
# Demian Wassermann :: Brigham and Women's Hospital :: demian at bwh.harvard.edu
 +
# David Welch :: University of Iowa :: david-welch at uiowa.edu
 +
# Sandy Wells :: Brigham and Women's Hospital :: sw at bwh.harvard.edu
 +
# Jason White :: Brigham and Women's Hospital :: white at bwh.harvard.edu
 +
# Alexander Yarmarkovich :: Isomics, Inc. :: alexy at bwh.harvard.edu
 +
# Kitaro Yoshimitsu :: Brigham and Women's Hospital :: kitarof1 at bwh.harvard.edu
 +
# Yang Yu :: Rutgers University :: yyu at cs.rutgers.edu
 +
# Paolo Zaffino :: Magna Græcia University of Catanzaro :: p.zaffino at unicz.it
 +
# Luping Fang Zhejiang :: University of Technology, China :: flp at zjut.edu.cn
 +
# Lilla Zollei :: Massachusetts General Hospital :: lzollei at nmr.mgh.harvard.edu

Latest revision as of 17:37, 10 July 2017

Home < 2013 Summer Project Week

Back to Events

PW-MIT2013.png

Welcome to the web page for the 17th Project Week!

Summary

The 17th PROJECT EVENT was held on June 17-21, 2013 at MIT. It recorded 104 registered attendees, who worked on 75 projects. These attendees represented 22 academic sites (Brigham and Women’s Hospital, Massachusetts General Hospital, Boston Children’s Hospital, MIT, WPI, WIT, University of Alabama, Rochester Institute of Technology, University of Utah, University of Iowa, University of Michigan, UCLA, Rutgers University, University del Estado de Mexico, Ecole Polytechnique Federale de Lausanne, Zhejiang University of Technology, Queen’s University, University of Sydney, University of Western Australia, University Sao Paulo, Leibniz University, Hannover, University Magna Graecia of Catanzaro) and 13 companies (NIRAL-UNC, Radnostics, GE Healthcare, GE Global Research, Kitware, zSpace, AZE Technology Inc, IEEE, Medical Science & Computing Inc, Fraunhofer MEVIS, Isomics Inc, IGI Technologies, KUKA Laboratories). The agenda and projects are detailed below.

A summary of all past Project Events.

Logistics

  • Dates: June 17-21, 2013.
  • Location: MIT, Cambridge, MA.

Agenda

Time Monday, June 17 Tuesday, June 18 Wednesday, June 19 Thursday, June 20 Friday, June 21
Project Presentations NA-MIC Update Day IGT and RT Day Reporting Day
8:30am Breakfast Breakfast Breakfast Breakfast
9am-12pm 10-11am Slicer4 Python Modules, Testing, Q&A (Steve Pieper)

Grier Room (Left)

9:30-11pm: Breakout Session:
Slicer and SimpleITK (Hans Johnson, Brad Lowekamp)

32-D507

9:30-10:30am Tutorial Contest Presentations
Grier Rooms
----------------------------------------
10am-12pm: Breakout Session:
Image-Guided Therapy (Tina Kapur) 32-D407

10am-12pm: Project Progress Updates

12pm Tutorial Contest Winner Announcement Grier Rooms

12pm-1pm Lunch Lunch Lunch Lunch in Outdoor Amphitheather! Lunch boxes; Adjourn by 1:30pm
1pm-5:30pm 1-1:05pm: Ron Kikinis: Welcome

Grier Rooms
----------------------------------------
1:05-3:30pm: Project Introductions (all Project Leads) Grier Rooms
----------------------------------------
3:30-4:30pm Slicer4 Extensions (Jean-Christophe Fillion-Robin)
Grier Room (Left)

1-3pm: NA-MIC Renewal
PIs
Closed Door Session with Ron

32-262


----------------------------------------
3-5:30pm: Breakout Session:
Radiation Therapy (Greg, Csaba)

32-D407

5:30pm Adjourn for the day Adjourn for the day Adjourn for the day Adjourn for the day

Projects

Please use this template to create wiki pages for your project. Then link the page here with a list of key personnel.


Some Stats

75 Projects, 104 Attendees. First time attendees 25.

Huntington's Disease

7 projects

Traumatic Brain Injury

5 projects

Atrial Fibrillation and Cardiac Image Analysis

8 projects

Radiation Therapy

10 projects

IGT and Device Integration with Slicer

11 projects

Chronic Obstructive Pulmonary Disease

3 projects

Additional Collaborations

20 projects

Infrastructure

12 projects

Background

We are pleased to announce the 17th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the 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. If you would like to learn more about this event, please click here to join our mailing list.


Active preparation begins on Thursday, April 25th 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 40-50 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 NA-MIC, NCIGT, NAC, Harvard Catalyst, CIMIT, and OCAIRO. 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 Women's 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.

Please make sure that you are on the NA-MIC Project Week mailing list.


Logistics

  • Dates: June 17-21, 2013.
  • Location: Stata Center / RLE MIT.
  • REGISTRATION: http://www.regonline.com/namic2013summerprojweek. Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
  • Registration Fee: $300.
  • Hotel: Similar to previous years, no rooms have been blocked in a particular hotel.
  • Room sharing: If interested, add your name to the list before May 27th. See here

Preparation

  1. Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
  2. The NA-MIC engineering team will be discussing projects in a their weekly teleconferences. Participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
  3. By 3pm ET on Thursday May 8, all participants to add a one line title of their project to #Projects
  4. By 3pm ET on Thursday June 6, all project leads to complete 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.
  5. By 3pm on June 13: Create a directory for each project on the NAMIC Sandbox (Matt)
    1. 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)
    2. 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.)
    3. Where possible, 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. (Matt)
  6. 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...
  7. People doing Slicer related projects should come to project week with slicer built on your laptop.
    1. See the Developer Section of slicer.org for information.
    2. Projects to develop extension modules should be built against the latest Slicer4 trunk.

Registrants

Do not add your name to this list - it is maintained by the organizers based on your paid registration. (Please click here to register.)

  1. Parth Amin :: Wentworth Institute of Technology :: aminp at wit.edu
  2. Charles Anderson :: Brigham and Women's Hospital :: canderson26 at partners.org
  3. Peter Anderson :: Retired :: traneus at verizon.net
  4. Nicole Aucoin :: Brigham and Women's Hospital :: nicole at bwh.harvard.edu
  5. Kayhan Batmanghelich :: Massachusetts Institute of Technology :: kayhan at csail.mit.edu
  6. Salma Bengali :: University of Utah :: salma.bengali at carma.utah.edu
  7. Anthony Blumfield :: Radnostics :: Anthony.Blumfield at Radnostics.com
  8. Vinicius Boen :: University of Michigan :: vboen at umich.edu
  9. Taylor Braun-Jones :: General Electric :: taylor.braun-jones at ge.com
  10. Matthew Brennan :: Massachusetts Institute of Technology :: brennanm at mit.edu
  11. Francois Budin :: University of North Carolina :: fbudin at unc.edu
  12. Ivan Buzurovic :: Brigham and Women's Hospital :: ibuzurovic at lroc.harvard.edu
  13. Juan Carlos Avila-Vilchis :: jc.avila.vilchis at hotmail.com
  14. Joshua Cates :: University of Utah :: cates at sci.utah.edu
  15. Micah Chambers :: UCLA :: micahcc at ucla.edu
  16. Laurent Chauvin :: Brigham and Women's Hospital :: lchauvin at bwh.harvard.edu
  17. Marine Clogenson :: Ecole Polytechnique Federale de Lausanne :: marine.clogenson at epfl.ch
  18. Matthew D'Artista :: Brigham and Women's Hospital :: mdartista7 at gmail.com
  19. Adrian Dalca :: Massachusetts Institute of Technology :: adalca at MIT.EDU
  20. Manasi Datar :: University of Utah :: datar at sci.utah.edu
  21. Sneha Durgapal :: Brigham and Women's Hospital :: durgapalsneha at gmail.com
  22. Andriy Fedorov :: Brigham and Women's Hospital :: fedorov at bwh.harvard.edu
  23. Jean-Christophe Fillion-Robin :: Kitware, Inc. :: jchris.fillionr at kitware.com
  24. Gregory Fischer :: Worcester Polytechnic Institute :: gfischer at wpi.edu
  25. Barton Fiske :: zSpace :: bfiske at zspace.com
  26. Matthew Flynn :: Wentworth Institute of Technology :: flynnm3 at wit.edu
  27. Karl Fritscher :: Massachusetts General Hospital :: kfritscher at gmail.com
  28. Yi Gao :: University of Alabama at Birmingham :: gaoyi.cn at gmail.com
  29. Alexandra Golby :: Brigham and Women's Hospital :: agolby at partners.org
  30. Maria Gonzalez-Puente :: Wentworth Institute of Technology :: gonzalezpuentem at wit.edu
  31. Dan Groszmann :: General Electric :: daniel.groszmann at ge.com
  32. Daniel Haehn :: Boston Children's Hospital :: daniel.haehn at childrens.harvard.edu
  33. Michael Halle :: Brigham and Women's Hospital :: mhalle at bwh.harvard.edu
  34. Rola Harmouche :: Brigham and Women's Hospital :: rharmo at bwh.harvard.edu
  35. Amanda Hartung :: Rochester Institute of Technology :: amh1646 at rit.edu
  36. Nobuhiko Hata :: Brigham and Women's Hospital :: hata at bwh.harvard.edu
  37. Nicholas Herlambang :: AZE Technology, Inc. :: nicholas.herlambang at azetech.com
  38. Matthew Holden :: Queen's University :: mholden8 at cs.queensu.ca
  39. Andrei Irimia :: UCLA :: andrei.irimia at loni.ucla.edu
  40. Jayender Jagadeesan :: Brigham and Women's Hospital :: jayender at bwh.harvard.edu
  41. Sylvain Jaume :: Wentworth Institute of Technology :: jaumes at wit.edu
  42. Daniel Jimenez :: Texas A&M University :: daniel.jimenez at gmail.com
  43. Hans Johnson :: University of Iowa :: hans-johnson at uiowa.edu
  44. Tina Kapur :: Brigham and Women's Hospital :: tkapur at bwh.harvard.edu
  45. Alex Kikinis :: Brigham and Women's Hospital :: alexkikinis at gmail.com
  46. Ron Kikinis :: Brigham and Women's Hospital :: kikinis at bwh.harvard.edu
  47. Nils Klarlund :: IEEE :: klarlund at ieee.org
  48. Daniel Kostro :: Brigham and Women's Hospital :: dkostro at bwh.harvard.edu
  49. Andras Lasso :: Queen's University :: lasso at cs.queensu.ca
  50. Rui Li :: General Electric :: li.rui at ge.com
  51. Xu Li :: Brigham and Women's Hospital :: lixu0103 at gmail.com
  52. Lichen Liang :: Massachusetts General Hospital :: lichenl at nmr.mgh.harvard.edu
  53. Sidong Liu :: University of Sydney :: sliu7418 at uni.sydney.edu.au
  54. Bill Lorensen :: Bill's Basement :: bill.lorensen at gmail.com
  55. Bradley Lowekamp :: Medical Science & Computing Inc. :: bradley.lowekamp at nih.gov
  56. Athena Lyons :: University of Western Australia :: 20359511 at student.uwa.edu.au
  57. Nikos Makris :: Massachusetts General Hospital :: nikos at nmr.mgh.harvard.edu
  58. Katie Mastrogiacomo :: Brigham and Women's Hospital :: kmast at bwh.harvard.edu
  59. Alireza Mehrtash :: Brigham and Women's Hospital :: mehrtash at bwh.harvard.edu
  60. Hans Meine :: Fraunhofer MEVIS, Bremen :: hans.meine at mevis.fraunhofer.de
  61. James Miller :: General Electric :: millerjv at ge.com
  62. Luiz Otavio Murta :: University of Sao Paulo :: lomurta at gmail.com
  63. Arie Nakhmani :: University of Alabama at Birmingham :: anry at uab.edu
  64. Isaiah Norton :: Brigham and Women's Hospital :: inorton at bwh.harvard.edu
  65. Lauren O'Donnell :: Brigham and Women's Hospital :: odonnell at bwh.harvard.edu
  66. Dirk Padfield :: General Electric :: padfield at research.ge.com
  67. Jian Pan :: University of Technology, China :: pj at zjut.edu.cn
  68. George Papadimitriou :: Massachusetts General Hospital :: georgep at nmr.mgh.harvard.edu
  69. Nirav Patel :: Worcester Polytechnic Institute :: napatel at wpi.edu
  70. Tobias Penzkofer :: Brigham and Women's Hospital :: pt at bwh.harvard.edu
  71. Rudolph Pienaar :: Boston Children's Hospital :: Rudolph.Pienaar at childrens.harvard.edu
  72. Steve Pieper :: Isomics, Inc. :: pieper at isomics.com
  73. Csaba Pinter :: Queen's University :: pinter at cs.queensu.ca
  74. William Plishker :: IGI Technologies :: will at igitechnologies.com
  75. Sonia Pujol :: Brigham and Women's Hospital :: spujol at bwh.harvard.edu
  76. Adam Rankin :: Queen's University :: rankin at cs.queensu.ca
  77. Nathaniel Reynolds :: Massachusetts General Hospital :: reynolds at nmr.mgh.harvard.edu
  78. Raul San Jose Estepar :: Brigham and Women's Hospital :: rjosest at bwh.harvard.edu
  79. Peter Savadjiev :: Brigham and Women's Hospital :: petersv at bwh.harvard.edu
  80. Tobias Schroeder :: General Electric :: tobias.schroeder at ge.com
  81. Anuja Sharma :: University of Utah :: anuja at cs.utah.edu
  82. Gregory Sharp :: Massachusetts General Hospital :: gcsharp at partners.org
  83. Nadya Shusharina :: Massachusetts General Hospital :: nshusharina at partners.org
  84. Sebastian Tauscher :: Leibniz Universität Hannover :: sebastian.tauscher at imes.uni-hannover.de
  85. Clare Tempany :: Brigham and Women's Hospital :: ctempanyafdhal at partners.org
  86. Gaurie Tilak :: Brigham and Women's Hospital :: gaurie_tilak at hms.harvard.edu
  87. Matthew Toews :: Brigham and Women's Hospital :: mt at bwh.harvard.edu
  88. Junichi Tokuda :: Brigham and Women's Hospital :: tokuda at bwh.harvard.edu
  89. Tamas Ungi :: Queen's University :: ungi at cs.queensu.ca
  90. Adriana Vilchis González :: Universidad Autonoma del Estado de Mexico :: hvigady at hotmail.com
  91. Cyrill von Tiesenhausen :: KUKA Laboratories :: cyrill.tiesenhausen at kuka.com
  92. Kirby Vosburgh :: Brigham and Women's Hospital :: kirby at bwh.harvard.edu
  93. Christian Wachinger :: Massachusetts Institute of Technology :: wachinge at mit.edu
  94. Bo Wang :: University of Utah :: bowang at sci.utah.edu
  95. Demian Wassermann :: Brigham and Women's Hospital :: demian at bwh.harvard.edu
  96. David Welch :: University of Iowa :: david-welch at uiowa.edu
  97. Sandy Wells :: Brigham and Women's Hospital :: sw at bwh.harvard.edu
  98. Jason White :: Brigham and Women's Hospital :: white at bwh.harvard.edu
  99. Alexander Yarmarkovich :: Isomics, Inc. :: alexy at bwh.harvard.edu
  100. Kitaro Yoshimitsu :: Brigham and Women's Hospital :: kitarof1 at bwh.harvard.edu
  101. Yang Yu :: Rutgers University :: yyu at cs.rutgers.edu
  102. Paolo Zaffino :: Magna Græcia University of Catanzaro :: p.zaffino at unicz.it
  103. Luping Fang Zhejiang :: University of Technology, China :: flp at zjut.edu.cn
  104. Lilla Zollei :: Massachusetts General Hospital :: lzollei at nmr.mgh.harvard.edu