Difference between revisions of "2013 Winter Project Week"
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| + | '''Summary: The 16th PROJECT EVENT was held January 7-11, 2013 in Salt Lake City. It recorded 80 registered attendees, who worked on 54 projects. These attendees represented 17 academic sites (Brigham and Women's Hospital, University of Utah, UNC Chapel Hill, UCLA, MIT, University of Alabama, UIowa, Queen University, Massachusetts General Hospital, WUSTL, Princess Margaret Hospital, Childrens Hospital Boston, NLM/NIH, University of Michigan, UCSD, Old Dominion, Memorial Sloan Kettering Cancer Center) and 4 companies (Kitware, Isomics, GE Research, Canon, Fraunhofer Mevis). The agenda and projects are detailed below.''' | ||
Project Week is a hands on activity -- programming using the open source [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC, NCIGT, and NAC calendars. It is held in the summer at MIT, typically the last week of June, and a shorter version is held in Salt Lake City in the winter, typically the second week of January. | Project Week is a hands on activity -- programming using the open source [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC, NCIGT, and NAC calendars. It is held in the summer at MIT, typically the last week of June, and a shorter version is held in Salt Lake City in the winter, typically the second week of January. | ||
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=Projects= | =Projects= | ||
| + | * [[2013_Project_Week_Template | Template for project pages]] | ||
==TBI== | ==TBI== | ||
| + | * [[4D DTI tractography in Slicer for TBI | Coregistration of structural and diffusion MRI towards 4D modeling of TBI]] (Bo Wang, Andrei Irimia, Micah Chambers, Jack Van Horn, Marcel Prastawa, Guido Gerig) | ||
| + | * [[Clinically oriented structural, connectomic and functional analysis of traumatic brain injury in 3D Slicer]] (Andrei Irimia, Bo Wang, Micah Chambers, Jack Van Horn, Marcel Prastawa, Guido Gerig) | ||
| + | * [[UKF Tractography in Slicer 4]] (Ryan Eckbo, Yogesh Rathi, Demian Wassermann, C.F Westin, Ron Kikinis) | ||
| + | * [[4D DTI analysis via longitudinal modeling of tract diffusivities]] (Anuja Sharma, Bo Wang, Andrei Irimia, Micah Chambers, Jack Van Horn, Marcel Prastawa, Guido Gerig) | ||
==Atrial Fibrillation== | ==Atrial Fibrillation== | ||
| − | * Scar Identification (LiangJia Zhu, Yi Gao, Josh Cates, Rob MacLeod, Allen Tannenbaum) | + | * [[2013_Project_Week:CARMA_Scar_Segmentation|Scar Identification (LiangJia Zhu, Yi Gao, Josh Cates, Rob MacLeod, Allen Tannenbaum)]] |
| + | * [[2013_Project_Week:CARMA_PV_Antrum_Cut|SLICER MODULE: PV Antrum Cut Filter (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)]] | ||
| + | * [[2013_Project_Week:CARMA_LA_Seg_Gopal|SLICER MODULE: Automated LA Segmentation by Gopal (Gopal Veni, Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)]] | ||
| + | * [[2013_Project_Week:CARMA_2D_Dilate|SLICER MODULE: 2D Dilate Filter (Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)]] | ||
| + | * [[2013_Project_Week:CARMA_PractialLASeg|SLICER WORKFLOW: Practical Manual LA Segmentation in Slicer (Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)]] | ||
| + | * [[2013_Project_Week:CARMA_Isolated_Connected_Filter|SLICER MODULE: Isolated Connected Image Filter (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)]] | ||
| + | * [[2013_Project_Week:CARMA_Connected_Threshold_Filter|SLICER MODULE: Connected Threshold Image Filter (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)]] | ||
| + | |||
| + | ==Slicer4 Extensions== | ||
| + | * [[2013_Project_Week:DTIExtension|Diffusion Tensor Images processing tools as Slicer4 extensions (Adrien Kaiser, Francois Budin, Martin Styner)]] | ||
| + | * [[2013_Project_Week:SPHARMExtension|SPHARM-PDM as Slicer4 extension (Beatriz Paniagua, Francois Budin, Martin Styner)]] | ||
==Huntington's Disease== | ==Huntington's Disease== | ||
* [[2013_Project_Week:QualityAssuranceModule|Quality assurance module enhancements]] (Dave Welch, Hans Johnson) | * [[2013_Project_Week:QualityAssuranceModule|Quality assurance module enhancements]] (Dave Welch, Hans Johnson) | ||
| − | * [[2013_Project_Week:PythonModules|Slicer interface to add Python modules to Slicer environment]] (Dave Welch) | + | * [[2013_Project_Week:PythonModules|Slicer interface to add Python modules to Slicer environment]] (Dave Welch, Hans Johnson, JC) |
| − | * [[2013_Project_Week:FastFiducialRegistrationModule|Fast fiducial registration module]] (Dave Welch) | + | <!-- * [[2013_Project_Week:FastFiducialRegistrationModule|Fast fiducial registration module]] (Dave Welch, Nicole Aucoin) --> |
| + | * [[2013_Project_Week:4DShapeAnalysis | 4D shape analysis: application to HD]] (James Fishbaugh, Marcel Prastawa, Hans Johnson, Guido Gerig) | ||
==Head and Neck Cancer== | ==Head and Neck Cancer== | ||
| + | * [[2013_Winter_Project_Week:MABS|Multi atlas-based segmentation]] (Sharp, Shusharina, Golland) | ||
| + | * [[2013_Winter_Project_Week:Hybrid_registration|Hybrid interactive-automatic registration]] (Shusharina, Sharp, Pieper) | ||
| + | * [[2013_Winter_Project_Week:PointSetRegistration|Constrained Point Set Registration]] (Kolesov, Karasev, Sharp, Tannenbaum) | ||
| + | * [[2013_Winter_Project_Week:InteractiveSegmentation|Interactive Segmentation and Supporting Utilities]] (Karasev, Kolesov, Tannenbaum) | ||
| − | == | + | ==Stroke== |
| − | * | + | * [[2013_Project_Week:WMH_Segmentation_for_Stroke|White Matter Hyperintensity Segmentation in Stroke (Adrian Dalca, Ramesh Sridharan, Polina Golland)]] |
| − | * | + | * [[2013_Project_Week:Imaging_Genetic_for_Stroke|Imaging Genetics for Stroke (Adrian Dalca, Kayhan Batmanghelich, Polina Golland)]] |
| − | |||
| − | |||
| − | == | + | ==Image-Guided Interventions== |
| − | * United SlicerIGT extension, repository, website (Tamas Ungi, Junichi Tokuda, Adam Rankin) | + | * [[2013_Project_Week:UnitedSlicerIGTExtension|United SlicerIGT extension, repository, website]] (Tamas Ungi, Junichi Tokuda, Adam Rankin) |
| − | * Mobile image overlay augmented reality needle guidance (Adam Rankin, Tamas Ungi) | + | * [[2013_Project_Week:MRIAblation|Thermal monitoring tools for MRI-guided laser ablation therapy of brain tumor]] (Laurent Chauvin, Noby Hata, Hatsuho Mamata, Alex Golby) |
| + | * [[2013_Project_Week:BRAINSFit_new_features|BRAINSFit in ITK4: extra functionality and testing for prostate MR registration (Andrey, Hans)]] | ||
| + | * [[2013_Project_Week:PkModeling_for_prostate_DCE_MRI|PkModeling for prostate DCE MRI (Jim, Andrey)]] | ||
| + | * [[2013_Winter_Project_Week_Gyne_Brachy|iGyne Needle Digitalization]] (Alireza Mehrtash, Csaba Pinter, Tina Kapur, Guillaume Pernelle, Jan Egger, Neha Agrawal, Antonio Damato) | ||
| + | * [[2013_Project_Week:AbdominalNavigationModule|Abdominal navigation module]] (Junichi Tokuda, Atsushi Yamada) | ||
| + | * [[2013_Project_Week:MobileImageOverlay|Mobile image overlay augmented reality needle guidance]] (Tamas Ungi, Adam Rankin) | ||
| + | * [[2013_Project_Week:US_IGT|Ultrasound Guidance for Neurosurgery]] (Matthew Toews, William Wells, Stephen Aylward, Tamas Ungi) | ||
==Radiation Therapy== | ==Radiation Therapy== | ||
| − | * SlicerRT: | + | * [[2013_Project_Week:DicomRtExport|SlicerRT: DICOM RT export]] (Kevin Wang, Greg Sharp, Csaba Pinter) |
| − | + | * [[2013_Project_Week:RtBeamGeometry|SlicerRT: Beam geometry widgets]] (Csaba Pinter, Greg Sharp) | |
| − | |||
| − | |||
| − | |||
| + | ==Medical Robotics== | ||
| + | * [[Configurable fiducial-based device to image registration]] (Junichi Tokuda, Nobuhiko Hata) | ||
| + | * [[2013_Project_Week:RobotizedUltrasoundProbeFor3DVolumeReconstruction| Robotized Ultrasound Probe For 3D Volume Reconstruction]] (Laurent Chauvin, Junichi Tokuda, Noby Hata) | ||
| + | * [[2013_Project_Week:AgileMedicalRobot | Agile medical robotics development with Slicer: Case study with MRI compatible robot(Taka Kato, Atsushi Yamada, Noby Hata, Kazuhumi Onuma)]] | ||
| + | * [[2013_Project_Week:InvestigatingRoleOfOpenSourceInTranslationalResearch | Investigating role of open source in translational research (Miki Kumekawa)]] | ||
==NA-MIC Kit Internals== | ==NA-MIC Kit Internals== | ||
| − | *[[2013_Project_Week:ITKv4Default|ITKv4 Default in Superbuild]] - [http://www.na-mic.org/Bug/search.php?project_id=3&sticky_issues=on&sortby=last_updated&dir=DESC&hide_status_id=80&tag_string=ITKv4 Issues] (Matt McCormick, Luis Ibanez, Hans Johnson, Jc | + | *[[2013_Project_Week:WebbasedAnatomicalTeachingFramework|Web-based anatomical teaching framework for mi2b2]] (Daniel Haehn, Steve Pieper, Sonia Pujol, Randy Gollub, Rudolph Pienaar, Ellen Grant) |
| + | *[[2013_Project_Week:ITKv4Default|ITKv4 Default in Superbuild]] - [http://www.na-mic.org/Bug/search.php?project_id=3&sticky_issues=on&sortby=last_updated&dir=DESC&hide_status_id=80&tag_string=ITKv4 Issues] (Matt McCormick, Luis Ibanez, Hans Johnson, Jc, Bill Lorensen, Bradley Lowekamp) | ||
*[[2013_Project_Week:MarkupsModule|Slicer4 Markups Module]] (Nicole Aucoin) | *[[2013_Project_Week:MarkupsModule|Slicer4 Markups Module]] (Nicole Aucoin) | ||
*[[2013_Project_Week:ColorHierarchies|Slicer4 Color Hierarchies]] (Nicole Aucoin) | *[[2013_Project_Week:ColorHierarchies|Slicer4 Color Hierarchies]] (Nicole Aucoin) | ||
| − | *[[2013_Project_Week:PatientHierarchy|Slicer4 Patient Hierarchy]] (Csaba Pinter, Andrey Fedorov | + | *[[2013_Project_Week:PatientHierarchy|Slicer4 Patient Hierarchy]] (Csaba Pinter, Andrey Fedorov, Nicole Aucoin, Steve Pieper) |
| − | *[[2013_Project_Week: | + | *[[2013_Project_Week:ScalarBar|Slicer4 Scalar bar improvements]] (Kevin Wang, Nicole Aucoin Csaba Pinter) |
| − | *[[2013_Project_Week:SelfTests|Slicer4 Self Test | + | *[[2013_Project_Week:CliMatlabInterface|Slicer4 CLI Matlab interface]] (Kevin Wang, Steve Pieper, Csaba Pinter) |
| − | *[[2013_Project_Week:SimplifyMRMLReference|Simplify MRML References]] - Issue [http://www.na-mic.org/Bug/view.php?id=2727 #2727] (Alex Yarmarkovich | + | *[[2013_Project_Week:SelfTests|Slicer4 Self Test and Sample Data Refactor]] (Steve Pieper, Jim Miller, Jc) |
| + | *[[2013_Project_Week:SpeedUp|Slicer4 Performance]] (Julien Finet) | ||
| + | *[[2013_Project_Week:SimplifyMRMLReference|Simplify MRML References]] - Issue [http://www.na-mic.org/Bug/view.php?id=2727 #2727] (Alex Yarmarkovich, Steve Pieper, Julien Finet ?, Jc ?) | ||
*[[2013_Project_Week:SlicerIPythonIntegration|Integration of IPython]] (Jc, Hans Johnson, Dave Welch, Steve Pieper, Matt McCormick) | *[[2013_Project_Week:SlicerIPythonIntegration|Integration of IPython]] (Jc, Hans Johnson, Dave Welch, Steve Pieper, Matt McCormick) | ||
| − | *[[2013_Project_Week:SlicerDebianPackage|Slicer Debian package]] (Jc, Dominique Belhachemi | + | *[[2013_Project_Week:SlicerDebianPackage|Slicer Debian package]] (Jc, Dominique Belhachemi, Greg Sharp) |
| − | *[[2013_Project_Week:SimplifyRendererMouseInteraction|Simplify renderer window mouse interaction]] - Mailing list [http://slicer-devel.65872.n3.nabble.com/Left-mouse-button-changes-window-level-Is-it-good-tt4026815.html thread] (Csaba | + | *[[2013_Project_Week:SimplifyRendererMouseInteraction|Simplify renderer window mouse interaction]] - Mailing list [http://slicer-devel.65872.n3.nabble.com/Left-mouse-button-changes-window-level-Is-it-good-tt4026815.html thread] (Csaba, Steve, Ron, Jc, Greg, Andriy) |
| − | *[[2013_Project_Week: | + | *[[2013_Project_Week:SteeredRegistration|Interactive Registration for Image Guided Therapy]] (Dirk Padfield, Jim Miller, Steve Pieper, Kunlin Cao) |
| − | *[[2013_Project_Week: | + | *[[2013_Project_Week:Threaded SimpleITK Modules|Threaded SimpleITK Modules]] (Brad Lowekamp, Steve Pieper) |
| + | *[[2013_Project_Week:Slicer Personal Cloud]] (Rui Li, Jim Miller) | ||
| + | *[[2013_Project_Week:XNATSlicer|XNATSlicer]] (Sunil Kumar, Dan Marcus, Steve Pieper, etc.) | ||
| + | *[[2013_Project_Week:PGP_Keysigning|PGP Keysigning]] (Matt McCormick, Luis Ibanez, Bradley Lowekamp) | ||
Latest revision as of 17:52, 2 April 2013
Home < 2013 Winter Project WeekBack to Project Events, Events
Back to Project Events, AHM_2013, Events
Summary: The 16th PROJECT EVENT was held January 7-11, 2013 in Salt Lake City. It recorded 80 registered attendees, who worked on 54 projects. These attendees represented 17 academic sites (Brigham and Women's Hospital, University of Utah, UNC Chapel Hill, UCLA, MIT, University of Alabama, UIowa, Queen University, Massachusetts General Hospital, WUSTL, Princess Margaret Hospital, Childrens Hospital Boston, NLM/NIH, University of Michigan, UCSD, Old Dominion, Memorial Sloan Kettering Cancer Center) and 4 companies (Kitware, Isomics, GE Research, Canon, Fraunhofer Mevis). The agenda and projects are detailed below.
Project Week is a hands on activity -- programming using the open source NA-MIC Kit, algorithm design, and clinical application -- that has become one of the major events in the NA-MIC, NCIGT, and NAC calendars. It is held in the summer at MIT, typically the last week of June, and a shorter version is held in Salt Lake City in the winter, typically the second week of January.
Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all na-mic members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. 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 NA-MIC coverage for all. Subsequent teleconferences 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 are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.
The event itself starts off with a short presentation by each project team, driven using their previously created description, and allows all participants to be acquainted with others who are doing similar work. In the rest of the week, about half the time is spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half is spent in project teams, doing hands-on programming, algorithm design, or clinical application of NA-MIC kit tools. The hands-on activities are done in 10-20 small teams of size 3-5, each with a mix of experts in NA-MIC kit software, algorithms, and clinical. To facilitate this work, a large room is setup with several tables, with internet and power access, and each team gathers on a table with their individual laptops, connects to the internet to download their software and data, and is able to work on their projects. On the last day of the event, a closing presentation session is held in which each project team presents a summary of what they accomplished during the week.
A summary of all past NA-MIC Project Events is available here.
Dates.Venue.Registration
Please click here for Dates, Venue, and Registration for this event.
AGENDA and Project List
Please:
Background and Preparation
A summary of all past NA-MIC Project Events is available here.
Please make sure that you are on the na-mic-project-week mailing list
Projects
TBI
- Coregistration of structural and diffusion MRI towards 4D modeling of TBI (Bo Wang, Andrei Irimia, Micah Chambers, Jack Van Horn, Marcel Prastawa, Guido Gerig)
- Clinically oriented structural, connectomic and functional analysis of traumatic brain injury in 3D Slicer (Andrei Irimia, Bo Wang, Micah Chambers, Jack Van Horn, Marcel Prastawa, Guido Gerig)
- UKF Tractography in Slicer 4 (Ryan Eckbo, Yogesh Rathi, Demian Wassermann, C.F Westin, Ron Kikinis)
- 4D DTI analysis via longitudinal modeling of tract diffusivities (Anuja Sharma, Bo Wang, Andrei Irimia, Micah Chambers, Jack Van Horn, Marcel Prastawa, Guido Gerig)
Atrial Fibrillation
- Scar Identification (LiangJia Zhu, Yi Gao, Josh Cates, Rob MacLeod, Allen Tannenbaum)
- SLICER MODULE: PV Antrum Cut Filter (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)
- SLICER MODULE: Automated LA Segmentation by Gopal (Gopal Veni, Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)
- SLICER MODULE: 2D Dilate Filter (Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)
- SLICER WORKFLOW: Practical Manual LA Segmentation in Slicer (Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)
- SLICER MODULE: Isolated Connected Image Filter (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)
- SLICER MODULE: Connected Threshold Image Filter (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)
Slicer4 Extensions
- Diffusion Tensor Images processing tools as Slicer4 extensions (Adrien Kaiser, Francois Budin, Martin Styner)
- SPHARM-PDM as Slicer4 extension (Beatriz Paniagua, Francois Budin, Martin Styner)
Huntington's Disease
- Quality assurance module enhancements (Dave Welch, Hans Johnson)
- Slicer interface to add Python modules to Slicer environment (Dave Welch, Hans Johnson, JC)
- 4D shape analysis: application to HD (James Fishbaugh, Marcel Prastawa, Hans Johnson, Guido Gerig)
Head and Neck Cancer
- Multi atlas-based segmentation (Sharp, Shusharina, Golland)
- Hybrid interactive-automatic registration (Shusharina, Sharp, Pieper)
- Constrained Point Set Registration (Kolesov, Karasev, Sharp, Tannenbaum)
- Interactive Segmentation and Supporting Utilities (Karasev, Kolesov, Tannenbaum)
Stroke
- White Matter Hyperintensity Segmentation in Stroke (Adrian Dalca, Ramesh Sridharan, Polina Golland)
- Imaging Genetics for Stroke (Adrian Dalca, Kayhan Batmanghelich, Polina Golland)
Image-Guided Interventions
- United SlicerIGT extension, repository, website (Tamas Ungi, Junichi Tokuda, Adam Rankin)
- Thermal monitoring tools for MRI-guided laser ablation therapy of brain tumor (Laurent Chauvin, Noby Hata, Hatsuho Mamata, Alex Golby)
- BRAINSFit in ITK4: extra functionality and testing for prostate MR registration (Andrey, Hans)
- PkModeling for prostate DCE MRI (Jim, Andrey)
- iGyne Needle Digitalization (Alireza Mehrtash, Csaba Pinter, Tina Kapur, Guillaume Pernelle, Jan Egger, Neha Agrawal, Antonio Damato)
- Abdominal navigation module (Junichi Tokuda, Atsushi Yamada)
- Mobile image overlay augmented reality needle guidance (Tamas Ungi, Adam Rankin)
- Ultrasound Guidance for Neurosurgery (Matthew Toews, William Wells, Stephen Aylward, Tamas Ungi)
Radiation Therapy
- SlicerRT: DICOM RT export (Kevin Wang, Greg Sharp, Csaba Pinter)
- SlicerRT: Beam geometry widgets (Csaba Pinter, Greg Sharp)
Medical Robotics
- Configurable fiducial-based device to image registration (Junichi Tokuda, Nobuhiko Hata)
- Robotized Ultrasound Probe For 3D Volume Reconstruction (Laurent Chauvin, Junichi Tokuda, Noby Hata)
- Agile medical robotics development with Slicer: Case study with MRI compatible robot(Taka Kato, Atsushi Yamada, Noby Hata, Kazuhumi Onuma)
- Investigating role of open source in translational research (Miki Kumekawa)
NA-MIC Kit Internals
- Web-based anatomical teaching framework for mi2b2 (Daniel Haehn, Steve Pieper, Sonia Pujol, Randy Gollub, Rudolph Pienaar, Ellen Grant)
- ITKv4 Default in Superbuild - Issues (Matt McCormick, Luis Ibanez, Hans Johnson, Jc, Bill Lorensen, Bradley Lowekamp)
- Slicer4 Markups Module (Nicole Aucoin)
- Slicer4 Color Hierarchies (Nicole Aucoin)
- Slicer4 Patient Hierarchy (Csaba Pinter, Andrey Fedorov, Nicole Aucoin, Steve Pieper)
- Slicer4 Scalar bar improvements (Kevin Wang, Nicole Aucoin Csaba Pinter)
- Slicer4 CLI Matlab interface (Kevin Wang, Steve Pieper, Csaba Pinter)
- Slicer4 Self Test and Sample Data Refactor (Steve Pieper, Jim Miller, Jc)
- Slicer4 Performance (Julien Finet)
- Simplify MRML References - Issue #2727 (Alex Yarmarkovich, Steve Pieper, Julien Finet ?, Jc ?)
- Integration of IPython (Jc, Hans Johnson, Dave Welch, Steve Pieper, Matt McCormick)
- Slicer Debian package (Jc, Dominique Belhachemi, Greg Sharp)
- Simplify renderer window mouse interaction - Mailing list thread (Csaba, Steve, Ron, Jc, Greg, Andriy)
- Interactive Registration for Image Guided Therapy (Dirk Padfield, Jim Miller, Steve Pieper, Kunlin Cao)
- Threaded SimpleITK Modules (Brad Lowekamp, Steve Pieper)
- 2013_Project_Week:Slicer Personal Cloud (Rui Li, Jim Miller)
- XNATSlicer (Sunil Kumar, Dan Marcus, Steve Pieper, etc.)
- PGP Keysigning (Matt McCormick, Luis Ibanez, Bradley Lowekamp)
