Difference between revisions of "2013 Summer Project Week"
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| − | + | __NOTOC__ | |
| + | Back to [[Events]] | ||
| + | |||
[[image:PW-MIT2013.png|300px]] | [[image:PW-MIT2013.png|300px]] | ||
| − | + | =Welcome to the web page for the 17th Project Week!= | |
| − | + | <gallery widths="800px" heights="300px" perrow="1" caption="Lunch in the Amphitheater at the Stata Building, June 20, 2013."> | |
| + | Image:Lunch at Project week IMG 0367.JPG|Shade was a popular commodity. | ||
| + | </gallery> | ||
| + | ==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 [[Project_Events#Past_Project_Weeks|summary]] of all past Project Events. | ||
| + | |||
| + | ==Logistics== | ||
| + | *Dates: June 17-21, 2013. | ||
| + | *Location: MIT, Cambridge, MA. | ||
==Agenda== | ==Agenda== | ||
| Line 52: | Line 63: | ||
|bgcolor="#ffffaa"|Lunch | |bgcolor="#ffffaa"|Lunch | ||
|bgcolor="#ffffaa"|Lunch | |bgcolor="#ffffaa"|Lunch | ||
| − | |bgcolor="#ffffaa"|Lunch | + | |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 | ||
|- | |- | ||
| Line 85: | Line 96: | ||
==Some Stats== | ==Some Stats== | ||
| − | + | 75 Projects, 104 Attendees. First time attendees 25. | |
===Huntington's Disease=== | ===Huntington's Disease=== | ||
| Line 94: | Line 105: | ||
* [[DWIConvert]] (Dave, Kent Williams) | * [[DWIConvert]] (Dave, Kent Williams) | ||
* [[Enhance and update SPL atlas]] (Dave, Hans) | * [[Enhance and update SPL atlas]] (Dave, Hans) | ||
| − | * [[Linear Mixed-effects shape model to explore Huntington's Disease Data]] (Manasi, Dave, Hans, Ross) | + | * [[Linear Mixed-effects shape model to explore Huntington's Disease Data]] (Manasi, Dave, Josh, Hans, Ross) |
<!-- If it applies, update the project count reported below and at the top of the page --> | <!-- If it applies, update the project count reported below and at the top of the page --> | ||
| Line 104: | Line 115: | ||
* [[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) | * [[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) | ||
* [[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) | * [[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) | ||
| − | |||
<!-- If it applies, update the project count reported below and at the top of the page --> | <!-- If it applies, update the project count reported below and at the top of the page --> | ||
| Line 110: | Line 120: | ||
===Atrial Fibrillation and Cardiac Image Analysis=== | ===Atrial Fibrillation and Cardiac Image Analysis=== | ||
| − | * [[2013_Summer_Project_Week:Fibrosis_analysis|Fibrosis distribution analysis]] (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, Josh Cates, Rob MacLeod, Sylvain Bouix, Ron Kikinis, Allen Tannenbaum) |
| + | * [[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) | ||
| Line 119: | Line 130: | ||
<!-- If it applies, update the project count reported below and at the top of the page --> | <!-- If it applies, update the project count reported below and at the top of the page --> | ||
| − | + | 8 projects | |
===Radiation Therapy=== | ===Radiation Therapy=== | ||
| Line 128: | Line 139: | ||
* [[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) | ||
* [[2013_Summer_Project_Week:Brachy_HDR_Ultrasound | Creating DICOM series from ultrasound for prostate HDR brachytherapy]] (Adam Rankin) | * [[2013_Summer_Project_Week:Brachy_HDR_Ultrasound | Creating DICOM series from ultrasound for prostate HDR brachytherapy]] (Adam Rankin) | ||
| − | * [[Analysis of different atlas-based segmentation techniques for parotid glands]] (Christian Wachinger, | + | * [[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) | * [[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) | ||
<!-- If it applies, update the project count reported below and at the top of the page --> | <!-- If it applies, update the project count reported below and at the top of the page --> | ||
| − | + | 10 projects | |
===IGT and Device Integration with Slicer=== | ===IGT and Device Integration with Slicer=== | ||
| Line 140: | Line 151: | ||
* [[2013_Summer_Project_Week:Ultrasound_Needle_Detection| Ultrasound Needle Detection]] (Alireza Mehrtash, Daniel Kostro, Matthew Toews, Tamas Ungi, William Wells, Tina Kapur) | * [[2013_Summer_Project_Week:Ultrasound_Needle_Detection| Ultrasound Needle Detection]] (Alireza Mehrtash, Daniel Kostro, Matthew Toews, Tamas Ungi, William Wells, Tina Kapur) | ||
* [[2013_Summer_Project_Week:Liver_Trajectory_Management| Liver Trajectory Management]] (Laurent Chauvin, Junichi Tokuda) | * [[2013_Summer_Project_Week:Liver_Trajectory_Management| Liver Trajectory Management]] (Laurent Chauvin, Junichi Tokuda) | ||
| − | |||
* [[2013_Summer_Project_Week:LabelMapStatistics| Label map statistics]] (Laurent Chauvin, Csaba Pinter) | * [[2013_Summer_Project_Week:LabelMapStatistics| Label map statistics]] (Laurent Chauvin, Csaba Pinter) | ||
* [[2013_Summer_Project_Week:PerkTutorExtension| Perk Tutor Extension]] (Matthew Holden, Tamas Ungi) | * [[2013_Summer_Project_Week:PerkTutorExtension| Perk Tutor Extension]] (Matthew Holden, Tamas Ungi) | ||
| Line 149: | Line 159: | ||
<!-- If it applies, update the project count reported below and at the top of the page --> | <!-- If it applies, update the project count reported below and at the top of the page --> | ||
| − | + | 11 projects | |
===Chronic Obstructive Pulmonary Disease=== | ===Chronic Obstructive Pulmonary Disease=== | ||
| − | * [[2013_Summer_Project_Week:Airway_Inspector_Porting | Porting Airway Inspector to Slicer 4]] (Raul San Jose, Demian Wassermann, Rola Harmouche) | + | * [[2013_Summer_Project_Week:Airway_Inspector_Porting | Porting Airway Inspector to Slicer 4]] (Raul San Jose, Demian Wassermann, Rola Harmouche, James Ross) |
| − | * [[2013_Summer_Project_Week:MRML_Infrastructure_Airway_Inspector | Airway Inspector: Slicer Extension and MRML Infrastructure]] (Demian Wassermann, Raul San Jose | + | * [[2013_Summer_Project_Week:MRML_Infrastructure_Airway_Inspector | Airway Inspector: Slicer Extension and MRML Infrastructure]] (Demian Wassermann, James, Ross, Rola Harmouche, Raul San Jose) |
* [[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) | * [[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) | ||
| Line 160: | Line 170: | ||
=== '''Additional Collaborations'''=== | === '''Additional Collaborations'''=== | ||
| + | * [[2013_Summer_Project_Week:VicomTech| VicomTech visit: Imaging solutions and Slicer use]] (Ivan Macia) | ||
* [[2013_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis) | * [[2013_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis) | ||
* [[2013_Summer_Project_Week: Computer Assisted Surgery| Computer Assisted Reconstruction of Complex Bone Fractures]] (Karl Fritscher, Peter Karasev, Ivan Kolesov, Allen Tannenbaum, Ron Kikinis) | * [[2013_Summer_Project_Week: Computer Assisted Surgery| Computer Assisted Reconstruction of Complex Bone Fractures]] (Karl Fritscher, Peter Karasev, Ivan Kolesov, Allen Tannenbaum, Ron Kikinis) | ||
| Line 168: | Line 179: | ||
* [[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: Individualized Neuroimaging Content Analysis using 3D Slicer in Alzheimer's Disease | + | * [[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:CMFReg | Cranio-Maxillofacial Registration]] (Vinicius Boen) | + | * [[2013_Summer_Project_Week:CMFReg | Cranio-Maxillofacial Registration]] (Francois Budin, Vinicius Boen) |
* [[2013_Summer_Project_Week:DTIPipelineExtensions | DTI Analysis Pipeline as Slicer4 Extensions]] (Francois Budin) | * [[2013_Summer_Project_Week:DTIPipelineExtensions | DTI Analysis Pipeline as Slicer4 Extensions]] (Francois Budin) | ||
| − | *[[2013_Project_Week:WebbasedAnatomicalTeachingFrameworkSummer2013|Web-based anatomical teaching framework]] (Lilla Zollei | + | *[[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: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: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: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: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: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) | * [[2013_Summer_Project_Week:WMQL Integration in Slicer|White Matter Query Language (WMQL) Integration in Slicer]] (Demian Wassermann, Carl-Fredrik Westin) | ||
| − | * [[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, | + | * [[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) | ||
<!-- If it applies, update the project count reported below and at the top of the page --> | <!-- If it applies, update the project count reported below and at the top of the page --> | ||
| − | + | 20 projects | |
==='''Infrastructure'''=== | ==='''Infrastructure'''=== | ||
* [[2013_Summer_Project_Week:MarkupsModuleSummer2013| Markups/Annotations rewrite]] (Nicole Aucoin, Ron Kikinis) | * [[2013_Summer_Project_Week:MarkupsModuleSummer2013| Markups/Annotations rewrite]] (Nicole Aucoin, Ron Kikinis) | ||
* [[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) | ||
| + | * [[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) | ||
* [[2013_Summer_Project_Week:CLI_Improvements | CLI Improvements (hierarchy nodes, related nodes, roles)]] (Andras Lasso, Csaba Pinter, Jc, Steve, Jim) | * [[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) | * [[2013_Summer_Project_Week:Sample_Data | Sample Data]] (Steve Pieper, Jim Miller, Bill Lorensen, Jc) | ||
* [[ITK -VTK wrapper]] (Paolo Zaffino, Greg Sharp, Steve Pieper) | * [[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_Summer_Project_Week:SimpleITK_GUI| Common Usage GUI for SimpleITK]] (Brad Lowekamp, Hans Johnson, | + | * [[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) | * [[2013_Summer_Project_Week:Extension_dependencies| Extension dependencies]] (Jc, Adam Rankin) | ||
| − | * [[2013_Summer_Project_Week:Parameter_heirarchy| Parameter (time) Hierarchy]] (Adam Rankin) | + | * [[2013_Summer_Project_Week:Parameter_heirarchy| Parameter (time) Hierarchy]] (Adam Rankin, Andras Lasso, Steve Pieper) |
| − | * [[2013_Summer_Project_Week:ITK_Shared_IO_Libraries| ITK Shared I/O Libraries]] (Brad Lowekamp) | + | * [[2013_Summer_Project_Week:ITK_Shared_IO_Libraries| ITK Shared I/O Libraries]] (Jim,Brad Lowekamp, Jc) |
* [[2013_Summer_Project_Week:Python_Embedding| Python Embedding Library]] (Rui, Jim, Jc, Steve) | * [[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) | ||
<!-- If it applies, update the project count reported below and at the top of the page --> | <!-- If it applies, update the project count reported below and at the top of the page --> | ||
| − | + | 12 projects | |
== '''Background''' == | == '''Background''' == | ||
| Line 209: | 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 | + | 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. |
| − | + | 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 235: | 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 [ | + | ## 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 242: | 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.]) | ||
| − | #Parth Amin | + | # Parth Amin :: Wentworth Institute of Technology :: aminp at wit.edu |
| − | #Charles Anderson | + | # Charles Anderson :: Brigham and Women's Hospital :: canderson26 at partners.org |
| − | #Peter Anderson | + | # Peter Anderson :: Retired :: traneus at verizon.net |
| − | #Nicole Aucoin | + | # Nicole Aucoin :: Brigham and Women's Hospital :: nicole at bwh.harvard.edu |
| − | + | # Kayhan Batmanghelich :: Massachusetts Institute of Technology :: kayhan at csail.mit.edu | |
| − | #Kayhan Batmanghelich | + | # Salma Bengali :: University of Utah :: salma.bengali at carma.utah.edu |
| − | #Salma Bengali | + | # Anthony Blumfield :: Radnostics :: Anthony.Blumfield at Radnostics.com |
| − | #Anthony Blumfield | + | # Vinicius Boen :: University of Michigan :: vboen at umich.edu |
| − | #Vinicius Boen | + | # Taylor Braun-Jones :: General Electric :: taylor.braun-jones at ge.com |
| − | #Matthew Brennan | + | # Matthew Brennan :: Massachusetts Institute of Technology :: brennanm at mit.edu |
| − | #Francois Budin | + | # Francois Budin :: University of North Carolina :: fbudin at unc.edu |
| − | #Ivan Buzurovic | + | # Ivan Buzurovic :: Brigham and Women's Hospital :: ibuzurovic at lroc.harvard.edu |
| − | # | + | # Juan Carlos Avila-Vilchis :: jc.avila.vilchis at hotmail.com |
| − | #Micah Chambers | + | # Joshua Cates :: University of Utah :: cates at sci.utah.edu |
| − | #Laurent Chauvin | + | # Micah Chambers :: UCLA :: micahcc at ucla.edu |
| − | #Marine Clogenson | + | # Laurent Chauvin :: Brigham and Women's Hospital :: lchauvin at bwh.harvard.edu |
| − | + | # Marine Clogenson :: Ecole Polytechnique Federale de Lausanne :: marine.clogenson at epfl.ch | |
| − | #Matthew D'Artista | + | # Matthew D'Artista :: Brigham and Women's Hospital :: mdartista7 at gmail.com |
| − | #Manasi Datar | + | # Adrian Dalca :: Massachusetts Institute of Technology :: adalca at MIT.EDU |
| − | #Sneha Durgapal | + | # Manasi Datar :: University of Utah :: datar at sci.utah.edu |
| − | + | # Sneha Durgapal :: Brigham and Women's Hospital :: durgapalsneha at gmail.com | |
| − | #Andriy Fedorov | + | # Andriy Fedorov :: Brigham and Women's Hospital :: fedorov at bwh.harvard.edu |
| − | #Jean-Christophe Fillion-Robin | + | # Jean-Christophe Fillion-Robin :: Kitware, Inc. :: jchris.fillionr at kitware.com |
| − | #Gregory Fischer | + | # Gregory Fischer :: Worcester Polytechnic Institute :: gfischer at wpi.edu |
| − | #Barton Fiske | + | # Barton Fiske :: zSpace :: bfiske at zspace.com |
| − | #Matthew Flynn | + | # Matthew Flynn :: Wentworth Institute of Technology :: flynnm3 at wit.edu |
| − | #Karl Fritscher | + | # Karl Fritscher :: Massachusetts General Hospital :: kfritscher at gmail.com |
| − | #Yi Gao | + | # Yi Gao :: University of Alabama at Birmingham :: gaoyi.cn at gmail.com |
| − | #Maria Gonzalez-Puente | + | # Alexandra Golby :: Brigham and Women's Hospital :: agolby at partners.org |
| − | #Dan Groszmann | + | # Maria Gonzalez-Puente :: Wentworth Institute of Technology :: gonzalezpuentem at wit.edu |
| − | #Daniel Haehn | + | # Dan Groszmann :: General Electric :: daniel.groszmann at ge.com |
| − | #Michael Halle | + | # Daniel Haehn :: Boston Children's Hospital :: daniel.haehn at childrens.harvard.edu |
| − | #Rola Harmouche | + | # Michael Halle :: Brigham and Women's Hospital :: mhalle at bwh.harvard.edu |
| − | #Amanda Hartung | + | # Rola Harmouche :: Brigham and Women's Hospital :: rharmo at bwh.harvard.edu |
| − | #Nobuhiko Hata | + | # Amanda Hartung :: Rochester Institute of Technology :: amh1646 at rit.edu |
| − | #Nicholas Herlambang | + | # Nobuhiko Hata :: Brigham and Women's Hospital :: hata at bwh.harvard.edu |
| − | #Matthew Holden | + | # Nicholas Herlambang :: AZE Technology, Inc. :: nicholas.herlambang at azetech.com |
| − | #Andrei Irimia | + | # Matthew Holden :: Queen's University :: mholden8 at cs.queensu.ca |
| − | #Jayender Jagadeesan | + | # Andrei Irimia :: UCLA :: andrei.irimia at loni.ucla.edu |
| − | #Hans Johnson | + | # Jayender Jagadeesan :: Brigham and Women's Hospital :: jayender at bwh.harvard.edu |
| − | #Tina Kapur | + | # Sylvain Jaume :: Wentworth Institute of Technology :: jaumes at wit.edu |
| − | #Alex Kikinis | + | # Daniel Jimenez :: Texas A&M University :: daniel.jimenez at gmail.com |
| − | #Ron Kikinis | + | # Hans Johnson :: University of Iowa :: hans-johnson at uiowa.edu |
| − | #Nils Klarlund | + | # Tina Kapur :: Brigham and Women's Hospital :: tkapur at bwh.harvard.edu |
| − | #Daniel Kostro | + | # Alex Kikinis :: Brigham and Women's Hospital :: alexkikinis at gmail.com |
| − | #Andras Lasso | + | # Ron Kikinis :: Brigham and Women's Hospital :: kikinis at bwh.harvard.edu |
| − | #Rui Li | + | # Nils Klarlund :: IEEE :: klarlund at ieee.org |
| − | #Xu Li | + | # Daniel Kostro :: Brigham and Women's Hospital :: dkostro at bwh.harvard.edu |
| − | #Lichen Liang | + | # Andras Lasso :: Queen's University :: lasso at cs.queensu.ca |
| − | #Sidong Liu | + | # Rui Li :: General Electric :: li.rui at ge.com |
| − | # | + | # Xu Li :: Brigham and Women's Hospital :: lixu0103 at gmail.com |
| − | #Bradley Lowekamp | + | # Lichen Liang :: Massachusetts General Hospital :: lichenl at nmr.mgh.harvard.edu |
| − | #Athena Lyons | + | # Sidong Liu :: University of Sydney :: sliu7418 at uni.sydney.edu.au |
| − | #Nikos Makris | + | # Bill Lorensen :: Bill's Basement :: bill.lorensen at gmail.com |
| − | #Katie Mastrogiacomo | + | # Bradley Lowekamp :: Medical Science & Computing Inc. :: bradley.lowekamp at nih.gov |
| − | #Alireza Mehrtash | + | # Athena Lyons :: University of Western Australia :: 20359511 at student.uwa.edu.au |
| − | #Hans Meine | + | # Nikos Makris :: Massachusetts General Hospital :: nikos at nmr.mgh.harvard.edu |
| − | # | + | # Katie Mastrogiacomo :: Brigham and Women's Hospital :: kmast at bwh.harvard.edu |
| − | # | + | # Alireza Mehrtash :: Brigham and Women's Hospital :: mehrtash at bwh.harvard.edu |
| − | #Arie Nakhmani | + | # Hans Meine :: Fraunhofer MEVIS, Bremen :: hans.meine at mevis.fraunhofer.de |
| − | #Isaiah Norton | + | # James Miller :: General Electric :: millerjv at ge.com |
| − | #Lauren O'Donnell | + | # Luiz Otavio Murta :: University of Sao Paulo :: lomurta at gmail.com |
| − | #Dirk Padfield | + | # Arie Nakhmani :: University of Alabama at Birmingham :: anry at uab.edu |
| − | #Jian Pan | + | # Isaiah Norton :: Brigham and Women's Hospital :: inorton at bwh.harvard.edu |
| − | #George Papadimitriou | + | # Lauren O'Donnell :: Brigham and Women's Hospital :: odonnell at bwh.harvard.edu |
| − | #Nirav Patel | + | # Dirk Padfield :: General Electric :: padfield at research.ge.com |
| − | #Tobias Penzkofer | + | # Jian Pan :: University of Technology, China :: pj at zjut.edu.cn |
| − | #Rudolph Pienaar | + | # George Papadimitriou :: Massachusetts General Hospital :: georgep at nmr.mgh.harvard.edu |
| − | #Steve Pieper, | + | # Nirav Patel :: Worcester Polytechnic Institute :: napatel at wpi.edu |
| − | #Csaba Pinter | + | # Tobias Penzkofer :: Brigham and Women's Hospital :: pt at bwh.harvard.edu |
| − | #Sonia Pujol | + | # Rudolph Pienaar :: Boston Children's Hospital :: Rudolph.Pienaar at childrens.harvard.edu |
| − | #Adam Rankin | + | # Steve Pieper :: Isomics, Inc. :: pieper at isomics.com |
| − | #Nathaniel Reynolds | + | # Csaba Pinter :: Queen's University :: pinter at cs.queensu.ca |
| − | #Raul San Jose | + | # William Plishker :: IGI Technologies :: will at igitechnologies.com |
| − | #Peter Savadjiev | + | # Sonia Pujol :: Brigham and Women's Hospital :: spujol at bwh.harvard.edu |
| − | #Anuja Sharma | + | # Adam Rankin :: Queen's University :: rankin at cs.queensu.ca |
| − | # | + | # Nathaniel Reynolds :: Massachusetts General Hospital :: reynolds at nmr.mgh.harvard.edu |
| − | #Nadya Shusharina | + | # Raul San Jose Estepar :: Brigham and Women's Hospital :: rjosest at bwh.harvard.edu |
| − | #Sebastian Tauscher | + | # Peter Savadjiev :: Brigham and Women's Hospital :: petersv at bwh.harvard.edu |
| − | #Clare Tempany | + | # Tobias Schroeder :: General Electric :: tobias.schroeder at ge.com |
| − | + | # Anuja Sharma :: University of Utah :: anuja at cs.utah.edu | |
| − | #Gaurie Tilak | + | # Gregory Sharp :: Massachusetts General Hospital :: gcsharp at partners.org |
| − | #Matthew Toews | + | # Nadya Shusharina :: Massachusetts General Hospital :: nshusharina at partners.org |
| − | #Junichi Tokuda | + | # Sebastian Tauscher :: Leibniz Universität Hannover :: sebastian.tauscher at imes.uni-hannover.de |
| − | #Tamas Ungi | + | # Clare Tempany :: Brigham and Women's Hospital :: ctempanyafdhal at partners.org |
| − | #Adriana Vilchis González | + | # Gaurie Tilak :: Brigham and Women's Hospital :: gaurie_tilak at hms.harvard.edu |
| − | #Kirby Vosburgh | + | # Matthew Toews :: Brigham and Women's Hospital :: mt at bwh.harvard.edu |
| − | #Christian Wachinger | + | # Junichi Tokuda :: Brigham and Women's Hospital :: tokuda at bwh.harvard.edu |
| − | #Bo Wang | + | # Tamas Ungi :: Queen's University :: ungi at cs.queensu.ca |
| − | #Demian Wassermann | + | # Adriana Vilchis González :: Universidad Autonoma del Estado de Mexico :: hvigady at hotmail.com |
| − | #David Welch | + | # 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 |
| − | #Kitaro Yoshimitsu | + | # Demian Wassermann :: Brigham and Women's Hospital :: demian at bwh.harvard.edu |
| − | #Yang Yu | + | # David Welch :: University of Iowa :: david-welch at uiowa.edu |
| − | #Paolo Zaffino | + | # Sandy Wells :: Brigham and Women's Hospital :: sw at bwh.harvard.edu |
| − | #Lilla Zollei | + | # 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 WeekBack to Events
Welcome to the web page for the 17th Project Week!
- Lunch in the Amphitheater at the Stata Building, June 20, 2013.
Shade was a popular commodity.
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) |
9:30-11pm: Breakout Session: Slicer and SimpleITK (Hans Johnson, Brad Lowekamp) |
9:30-10:30am Tutorial Contest Presentations |
10am-12pm: Project Progress Updates | |
| 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
|
1-3pm: NA-MIC Renewal PIs Closed Door Session with Ron |
---------------------------------------- 3-5:30pm: Breakout Session: Radiation Therapy (Greg, Csaba) |
||
| 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
- Learn and Apply FiberBundleLabelSelect for Huntington's Disease Data (Hans, Demian)
- Investigate Potential Tensor Computation Improvement via Positive Semi-Definite (PSD) Tensor Estimation (Hans)
- Single Precision Registration (Hans, Brad Lowekamp, Dave, Ali Ghayoor)
- Dynamically Configurable Quality Assurance Module for Large Huntington's Disease Database Frontend (Dave)
- DWIConvert (Dave, Kent Williams)
- Enhance and update SPL atlas (Dave, Hans)
- Linear Mixed-effects shape model to explore Huntington's Disease Data (Manasi, Dave, Josh, Hans, Ross)
7 projects
Traumatic Brain Injury
- 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)
- 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)
- 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)
- 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)
5 projects
Atrial Fibrillation and Cardiac Image Analysis
- Fibrosis distribution analysis (Yi Gao, LiangJia Zhu, Josh Cates, Rob MacLeod, Sylvain Bouix, Ron Kikinis, Allen Tannenbaum)
- Segmentation Aided Registration (Yi Gao, LiangJia Zhu, Josh Cates, Rob MacLeod, Sylvain Bouix, Ron Kikinis, Allen Tannenbaum)
- Cardiac MRI Toolkit LA segmentation and enhancement quantification workflow wizard (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
- Cardiac MRI Toolkit Documentation Project (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
- LA model visualization (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)
- Cardiac MRI Toolkit: Automatic LA Segmentation with Graph Cuts Module (Salma Bengali, Alan Morris, Josh Cates, Gopal, Ross Whitaker, Rob MacLeod)
- Medical Volume Segmentation Using Sobolev Active Contours (Arie Nakhmani, Yi Gao, LiangJia Zhu, Rob MacLeod, Josh Cates, Ron Kikinis, Allen Tannenbaum)
- Left Ventricle Motion Analysis using Tagged MRI (Yang Yu, Shaoting Zhang, Dimitris Metaxas)
8 projects
Radiation Therapy
- Landmark Registration (Steve, Nadya, Greg, Paolo, Erol)
- SlicerRT: Dicom-RT Export (Greg Sharp, Kevin Wang, Csaba Pinter)
- Proton dose calculation (Greg Sharp, Kevin Wang, Maxime Desplanques)
- Deformable registration validation toolkit (Greg Sharp, Kevin Wang, Andrey Fedorov)
- Deformable transform handling in Transforms module (Csaba Pinter, Alex Yarmarkovich, Andras Lasso)
- Creating DICOM series from ultrasound for prostate HDR brachytherapy (Adam Rankin)
- Analysis of different atlas-based segmentation techniques for parotid glands (Karl Fritscher, Christian Wachinger, Greg Sharp, Matthew Brennan)
- DICOM communication between Slicer and Oncentra Prostate radiation therapy planning system (Andrey Fedorov, Csaba Pinter, Emily Neubauer-Sugar, Alireza Mehrtash)
10 projects
IGT and Device Integration with Slicer
- Tract Atlas and Clustering for Neurosurgery (Lauren O'Donnell)
- SlicerIGT extension (Tamas Ungi, Junichi Tokuda, Laurent Chauvin)
- Ultrasound Calibration (Matthew Toews, Daniel Kostro, William Wells, Stephen Aylward, Isaiah Norton, Tamas Ungi)
- Ultrasound Needle Detection (Alireza Mehrtash, Daniel Kostro, Matthew Toews, Tamas Ungi, William Wells, Tina Kapur)
- Liver Trajectory Management (Laurent Chauvin, Junichi Tokuda)
- Label map statistics (Laurent Chauvin, Csaba Pinter)
- Perk Tutor Extension (Matthew Holden, Tamas Ungi)
- Open-source electromagnetic trackers using OpenIGTLink (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
- Segmentation of Prostate Gland from 3D US for Prostate Interventions (Xu Li, Andriy Fedorov, Tina Kapur, William Wells)
- 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)
- MRI-guided robotic prostate interventinos (Junichi Tokuda, Greg Fischer, Nirav Patel, Nobuhiko Hata, Clare Tempnay)
11 projects
Chronic Obstructive Pulmonary Disease
- Porting Airway Inspector to Slicer 4 (Raul San Jose, Demian Wassermann, Rola Harmouche, James Ross)
- Airway Inspector: Slicer Extension and MRML Infrastructure (Demian Wassermann, James, Ross, Rola Harmouche, Raul San Jose)
- Integration of Nipype with CLI modules in the Chest Imaging Platform Library (Rola Harmouche,Demian Wassermann, Raul San Jose)
3 projects
Additional Collaborations
- VicomTech visit: Imaging solutions and Slicer use (Ivan Macia)
- Spine Segmentation & Osteoporosis Detection In CT Imaging Studies (Anthony Blumfield, Ron Kikinis)
- Computer Assisted Reconstruction of Complex Bone Fractures (Karl Fritscher, Peter Karasev, Ivan Kolesov, Allen Tannenbaum, Ron Kikinis)
- XNAT 3D Viewer (Amanda Hartung, Steve Pieper, Daniel Haehn)
- Interface for the integration of a KUKA robot using OpenIGTLink (Sebastian Tauscher, Thomas Neff, Junichi Tokuda, Nobuhiko Hata)
- Application of Statistical Shape Modeling to Robot Assisted Spine Surgery (Marine Clogenson)
- Robot Control (A.Vilchis, J-C. Avila-Vilchis, S.Pujol)
- Identification of MRI Blurring in Temporal Lobe Epilepsy Surgery (Luiz Murta)
- Is Neurosurgical Rigid Registration Really Rigid? (Athena)
- Individualized Neuroimaging Content Analysis using 3D Slicer in Alzheimer's Disease (Sidong Liu, Weidong Cai, Sonia Pujol, Ron Kikinis)
- Cranio-Maxillofacial Registration (Francois Budin, Vinicius Boen)
- DTI Analysis Pipeline as Slicer4 Extensions (Francois Budin)
- Web-based anatomical teaching framework (Nathaniel Reynolds, Lilla Zollei, Daniel Haehn, Nicolas Rannou, Steve Pieper, Rudolph Pienaar)
- 3D Slicer based Biomedical image computing teaching modules (A. Vilchis, J-C. Avila-Vilchis, S. Pujol)
- Analyzing Breast Tumor Heterogeneity Using 3D Slicer (Sneha Durgapal, Jayender Jagadeesan, Tobias Penzkofer, Vivek Narayan)
- WMH Segmentation for Stroke (Adrian Dalca, Ramesh Sridharan, Kayhan Batmanghelich, Polina Golland)
- White Matter Query Language (WMQL) Integration in Slicer (Demian Wassermann, Carl-Fredrik Westin)
- Documentation for Slicer 4.2 Data Loading and 3D Visualization (Parth Amin WIT, Matt Flynn WIT, Sonia Pujol, BWH, Sylvain Jaume, WIT)
- 3D Printing of a Prostate Slicer (Maria Gonzalez-Puente WIT, Andriy Fedorov, BWH, Sylvain Jaume, WIT)
- Integration in Slicer of white matter geometry tools (Peter Savadjiev, Carl-Fredrik Westin)
20 projects
Infrastructure
- Markups/Annotations rewrite (Nicole Aucoin, Ron Kikinis)
- Patient hierarchy (Csaba Pinter, Andras Lasso, Steve Pieper)
- Common resampling and conversion utility functions in Slicer (Csaba Pinter, Steve Pieper, Hans, Kevin Wang)
- CLI module implementation in Matlab - without building Slicer or Matlab MEX files (Andras Lasso, Jc)
- CLI Improvements (hierarchy nodes, related nodes, roles) (Andras Lasso, Csaba Pinter, Jc, Steve, Jim)
- Sample Data (Steve Pieper, Jim Miller, Bill Lorensen, Jc)
- ITK -VTK wrapper (Paolo Zaffino, Greg Sharp, Steve Pieper)
- Integrating CTK CLI modules into MeVisLab (Hans Meine, Steve, Jc)
- Common Usage GUI for SimpleITK (Dave Welch, Brad Lowekamp, Hans Johnson, Steve)
- Extension dependencies (Jc, Adam Rankin)
- Parameter (time) Hierarchy (Adam Rankin, Andras Lasso, Steve Pieper)
- ITK Shared I/O Libraries (Jim,Brad Lowekamp, Jc)
- Python Embedding Library (Rui, Jim, Jc, Steve)
- Masked FFT Normalized Correlation Overlay (Dirk, Hans, Brad)
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
- Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
- The NA-MIC engineering team will be discussing 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!
- By 3pm ET on Thursday May 8, all participants to add a one line title of their project to #Projects
- 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.
- By 3pm on June 13: Create a directory for each project on the NAMIC Sandbox (Matt)
- Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
- Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
- 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)
- 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.
- See the Developer Section of slicer.org for information.
- 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.)
- Parth Amin :: Wentworth Institute of Technology :: aminp at wit.edu
- Charles Anderson :: Brigham and Women's Hospital :: canderson26 at partners.org
- Peter Anderson :: Retired :: traneus at verizon.net
- Nicole Aucoin :: Brigham and Women's Hospital :: nicole at bwh.harvard.edu
- Kayhan Batmanghelich :: Massachusetts Institute of Technology :: kayhan at csail.mit.edu
- Salma Bengali :: University of Utah :: salma.bengali at carma.utah.edu
- Anthony Blumfield :: Radnostics :: Anthony.Blumfield at Radnostics.com
- Vinicius Boen :: University of Michigan :: vboen at umich.edu
- Taylor Braun-Jones :: General Electric :: taylor.braun-jones at ge.com
- Matthew Brennan :: Massachusetts Institute of Technology :: brennanm at mit.edu
- Francois Budin :: University of North Carolina :: fbudin at unc.edu
- Ivan Buzurovic :: Brigham and Women's Hospital :: ibuzurovic at lroc.harvard.edu
- Juan Carlos Avila-Vilchis :: jc.avila.vilchis at hotmail.com
- Joshua Cates :: University of Utah :: cates at sci.utah.edu
- Micah Chambers :: UCLA :: micahcc at ucla.edu
- Laurent Chauvin :: Brigham and Women's Hospital :: lchauvin at bwh.harvard.edu
- Marine Clogenson :: Ecole Polytechnique Federale de Lausanne :: marine.clogenson at epfl.ch
- Matthew D'Artista :: Brigham and Women's Hospital :: mdartista7 at gmail.com
- Adrian Dalca :: Massachusetts Institute of Technology :: adalca at MIT.EDU
- Manasi Datar :: University of Utah :: datar at sci.utah.edu
- Sneha Durgapal :: Brigham and Women's Hospital :: durgapalsneha at gmail.com
- Andriy Fedorov :: Brigham and Women's Hospital :: fedorov at bwh.harvard.edu
- Jean-Christophe Fillion-Robin :: Kitware, Inc. :: jchris.fillionr at kitware.com
- Gregory Fischer :: Worcester Polytechnic Institute :: gfischer at wpi.edu
- Barton Fiske :: zSpace :: bfiske at zspace.com
- Matthew Flynn :: Wentworth Institute of Technology :: flynnm3 at wit.edu
- Karl Fritscher :: Massachusetts General Hospital :: kfritscher at gmail.com
- Yi Gao :: University of Alabama at Birmingham :: gaoyi.cn at gmail.com
- Alexandra Golby :: Brigham and Women's Hospital :: agolby at partners.org
- Maria Gonzalez-Puente :: Wentworth Institute of Technology :: gonzalezpuentem at wit.edu
- Dan Groszmann :: General Electric :: daniel.groszmann at ge.com
- Daniel Haehn :: Boston Children's Hospital :: daniel.haehn at childrens.harvard.edu
- Michael Halle :: Brigham and Women's Hospital :: mhalle at bwh.harvard.edu
- Rola Harmouche :: Brigham and Women's Hospital :: rharmo at bwh.harvard.edu
- Amanda Hartung :: Rochester Institute of Technology :: amh1646 at rit.edu
- Nobuhiko Hata :: Brigham and Women's Hospital :: hata at bwh.harvard.edu
- Nicholas Herlambang :: AZE Technology, Inc. :: nicholas.herlambang at azetech.com
- Matthew Holden :: Queen's University :: mholden8 at cs.queensu.ca
- Andrei Irimia :: UCLA :: andrei.irimia at loni.ucla.edu
- Jayender Jagadeesan :: Brigham and Women's Hospital :: jayender at bwh.harvard.edu
- Sylvain Jaume :: Wentworth Institute of Technology :: jaumes at wit.edu
- Daniel Jimenez :: Texas A&M University :: daniel.jimenez at gmail.com
- Hans Johnson :: University of Iowa :: hans-johnson at uiowa.edu
- Tina Kapur :: Brigham and Women's Hospital :: tkapur at bwh.harvard.edu
- Alex Kikinis :: Brigham and Women's Hospital :: alexkikinis at gmail.com
- Ron Kikinis :: Brigham and Women's Hospital :: kikinis at bwh.harvard.edu
- Nils Klarlund :: IEEE :: klarlund at ieee.org
- Daniel Kostro :: Brigham and Women's Hospital :: dkostro at bwh.harvard.edu
- Andras Lasso :: Queen's University :: lasso at cs.queensu.ca
- Rui Li :: General Electric :: li.rui at ge.com
- Xu Li :: Brigham and Women's Hospital :: lixu0103 at gmail.com
- Lichen Liang :: Massachusetts General Hospital :: lichenl at nmr.mgh.harvard.edu
- Sidong Liu :: University of Sydney :: sliu7418 at uni.sydney.edu.au
- Bill Lorensen :: Bill's Basement :: bill.lorensen at gmail.com
- Bradley Lowekamp :: Medical Science & Computing Inc. :: bradley.lowekamp at nih.gov
- Athena Lyons :: University of Western Australia :: 20359511 at student.uwa.edu.au
- Nikos Makris :: Massachusetts General Hospital :: nikos at nmr.mgh.harvard.edu
- Katie Mastrogiacomo :: Brigham and Women's Hospital :: kmast at bwh.harvard.edu
- Alireza Mehrtash :: Brigham and Women's Hospital :: mehrtash at bwh.harvard.edu
- Hans Meine :: Fraunhofer MEVIS, Bremen :: hans.meine at mevis.fraunhofer.de
- James Miller :: General Electric :: millerjv at ge.com
- Luiz Otavio Murta :: University of Sao Paulo :: lomurta at gmail.com
- Arie Nakhmani :: University of Alabama at Birmingham :: anry at uab.edu
- Isaiah Norton :: Brigham and Women's Hospital :: inorton at bwh.harvard.edu
- Lauren O'Donnell :: Brigham and Women's Hospital :: odonnell at bwh.harvard.edu
- Dirk Padfield :: General Electric :: padfield at research.ge.com
- Jian Pan :: University of Technology, China :: pj at zjut.edu.cn
- George Papadimitriou :: Massachusetts General Hospital :: georgep at nmr.mgh.harvard.edu
- Nirav Patel :: Worcester Polytechnic Institute :: napatel at wpi.edu
- Tobias Penzkofer :: Brigham and Women's Hospital :: pt at bwh.harvard.edu
- Rudolph Pienaar :: Boston Children's Hospital :: Rudolph.Pienaar at childrens.harvard.edu
- Steve Pieper :: Isomics, Inc. :: pieper at isomics.com
- 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
