NAMIC Wiki - User contributions [en]

2014 Winter Project Week

2013-12-18T19:00:40Z

Gveni: /* Atrial Fibrillation */

Back to [[Project Events]], [[AHM_2014]], [[Events]]

__NOTOC__
[[image:PW-SLC2014.png|300px]]

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.

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 [[Project_Events#Past|here]].
= Dates.Venue.Registration =

Please [[AHM_2014#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

= [[AHM_2014#Agenda|'''AGENDA''']] and Project List=

Please:
* [[AHM_2014#Agenda|'''Click here for the agenda for AHM 2014 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

=Background and Preparation=

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]

=Projects=
* [[2014_Project_Week_Template | Template for project pages]]

==TBI==
*[[2014_Project_Week:TBIatrophy|Multimodal neuroimaging for the quantification of brain atrophy at six months following severe traumatic brain injury]] (Andrei Irimia, SY Matthew Goh, Carinna M. Torgerson, John D. Van Horn)
*[[2014_Project_Week:TBIdemyelination|Systematic evaluation of axonal demyelination subsequent to traumatic brain injury using structural T1- and T2-weighted magnetic resonance imaging]] (Andrei Irimia, SY Matthew Goh, Carinna M. Torgerson, John D. Van Horn)
*[[2014_Project_Week:BrainAging|Mapping the effect of traumatic brain injury upon white matter connections in the human brain using 3D Slicer]] (Andrei Irimia, John D. Van Horn)
*[[2014_Project_Week:LongitudinalDTI|Patient-specific longitudinal DTI analysis in traumatic brain injury]] (Anuja Sharma, Andrei Irimia, Bo Wang, John D. Van Horn, Martin Styner, Guido gerig)
*[[2014_Project_Week:TBISegmentation|Testing the interactive segmentation algorithm for traumatic brain injury]] (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)

==Atrial Fibrillation==
*[[2014_Project_Week:GraphCutsLASegmentation|LA Segmentation via Graph Cuts]] (Josh, Salma, Gopal)
*[[2014_Project_Week:MRAFusionRegistration|DEMRI LA Segmentation via Image Fusion (MRA)]] (Josh, Salma, Alan)
*[[2014_Project_Week:LAFibrosisVisualizationModule|LA Fibrosis / Scar Visualization]] (Josh, Salma, Alan)
*[[2014_Project_Week:CARMADocumentation|CARMA Extension Documentation Project]] (Josh, Salma)
*[[2014_Project_Week:GraphCutsLASegmentationModule|LA Segmentation module using multi-column Graph Cuts]] (Gopal, Salma, Josh, Rob, Ross)

==Slicer4 Extensions==
*[[2014_Project_Week:ShapePopulationViewer|Surface Visualization - ShapePopulationViewer]] (Alexis Girault, Francois Budin, Beatriz Panaigua, Martin Styner)

==Huntington's Disease==
*[[2014_Project_Week:DWIDispersion|DWI Dispersion]] (Hans, CF)
*[[2014_Project_Week:DTIAnalysis|DTI Compressed Sensing?]] (Hans, CF)
*[[2014_Project_Week:Modules scripting|Slicer module scripting?]] (Dave)
*[[2014_Project_Week:DWIConverter|DWIConverter?]] (Hans, Kent)
*Slicer Based Surface Template Estimation (Saurabh JHU, Steve Pieper, Hans Johnson, Josh Cates)
*[[2014_Project_Week:HD_4DShapes|4D shape analysis: application to HD ]] (James Fishbaugh,Hans Johnson, Guido Gerig)
*[[2014_Project_Week:Shape_Registration_and_Regression|Shape registration and regression in Slicer4 ]] (James Fishbaugh,Hans Johnson, Guido Gerig)

==Head and Neck Cancer==
*[[2014_Project_Week:DIR_validation|DIR Validation]] (Nadya and Greg)
*[[2014_Project_Week:Hybrid_bspline|Hybrid B Spline]] (Nadya, Greg, Steve)
*[[2014_Project_Week:KSlice|Interactive Segmentation]] (Ivan, Nadya, Greg, Allen)

==Stroke==

*[[2014_Project_Week:Multi-Tissue_Stroke_Segmentation|Multi-Tissue Stroke Segmentation]] (Ramesh, Polina B., Polina G.)

==Image-Guided Interventions==

==Radiation Therapy==
*[[2014_Project_Week:DICOM_RT|DICOM RT Export]] (Greg, Kevin Wang, others)
*[[2014_Project_Week:DICOM_SRO|DICOM Spatial Registration Export]] (Greg, Kevin Wang, others)
*[[2014_Project_Week:Registration_Evaluation|Interactive Registration and Evaluation]] (Kevin Wang, Greg, others)

==Medical Robotics==
==[http://qiicr.org QIICR]==

*[[2014_Project_Week:4D_NIfTI_Multivolume|4D NIfTI Multivolume Support]] (Jayashree, Andrey, Jim, John)
*[[2014_Project_Week:RT_FormatConversions|RT and ITK Format Conversions]] (Jayashree, Andras, Csaba. John)
*[[2014_Project_Week:BatchConvertDICOM|Python Scripting Slicer DICOM read/write to convert segmentation objects]] (Jayashree, Andrey, Alireza, Steve, Jc, Hans, John)
*[[2014_Project_Week:PkModeling_user_tool|User module for DCE modeling]] (Andrey, Jayashree, Jim, Alireza, Steve, Ron)
*[[2014_Project_Week:DICOM_enhanced_multiframe|DICOM enhanced multiframe object support]] (Andrey, Alireza, David Clunie, Jayashree, Steve, Reinhard, Jim)

==TMJ-OA==

==Infrastructure==
*[[2014_Project_Week:SlicerSpeedUp|Slicer speed up]] (Jc, Andras Lasso, Steve Pieper)
*[[2014_Project_Week:MRMLSceneSpeedUp|MRML Scene speed up]] (Jc, Andras Lasso)
*[[2014_Project_Week:SlicerIPythonIntegration|Integration of IPython]] (Jc, Steve Pieper)
*[[2014_Project_Week:MultidimensionalDataSupport|Multidimensional data support]] (Andras Lasso, Andriy Fedorov, Steve Pieper, JC, Kevin Wang)
*CLI - Resources? Conditionals? Autonaming? Provenance? CTK unification? (Jim Miller)
*[[2014_Project_Week:MarkupsModule|Markups Module]] (Nicole Aucoin)
* [[2014_Winter_Project_Week:Steered Registration|Steered Registration]] (Steve, Greg, Kevin, Vinicius, Marcel)
* [[2014_Winter_Project_Week:MRB Extension Dependencies|MRB Extension Dependencies]] (Steve, Jc, Jim, Nicole, Alex)
* [[2014_Winter_Project_Week:SubjectHierarchy|Subject Hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper, Jc, Jayashree, John, Alireza, Andrey)
* [[2014_Winter_Project_Week:IntegrationOfContourObject|Integration of Contour object]] (Csaba Pinter, Andras Lasso, Steve Pieper, ???)
* [[2014_Winter_Project_Week:NonLinearTransforms|Integration non-linear transforms]] (Alex Yarmarkovich, Csaba Pinter, Andras Lasso, Steve Pieper, ???)

2014 Project Week:GraphCutsLASegmentationModule

2013-12-18T18:59:54Z

Gveni: /* Key Investigators */

[[File:LAsegment GraphCut.png]]
==Key Investigators==

Gopalkrishna Veni (SCI Institute, University of Utah)

Salma Bengali (CARMA center, University of Utah)

Josh Cates (CARMA center, University of Utah)

Rob Macleod (CARMA center, SCI Institute, University of Utah)

Ross Whitaker(SCI Institute, University of Utah)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a Slicer module that automatically segments the left atrial wall from a given LGE-MRI image.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Involves Bayesian formulation with Markov random field prior within a nested-layer 3D mesh which leads to surface-net problem [Veni ''et al'', IPMI 2013].
* Solved by using VCEnet strategy and graph-cuts [Wu and Chen, 2002].
* Uses training strategy in order to generate model shapes as well as to compute costs at each mesh point.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Module is now available in the Slicer. It could be downloaded from: https://github.com/carma-center/carma_slicer_extension/
* The online documentation on its usage is available at: https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/AutomatedLASegmentation
* Model data could be downloaded from: http://slicer.kitware.com/midas3/folder/1550

</div>
</div>

2014 Project Week:GraphCutsLASegmentationModule

2013-12-18T18:55:15Z

Gveni:

[[File:LAsegment GraphCut.png]]
==Key Investigators==

Gopalkrishna Veni (SCI Institute, University of Utah)

Salma Bengali (CARMA center, University of Utah)

Josh Cates (CARMA center, University of Utah)

Ross Whitaker(SCI Institute, University of Utah)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a Slicer module that automatically segments the left atrial wall from a given LGE-MRI image.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Involves Bayesian formulation with Markov random field prior within a nested-layer 3D mesh which leads to surface-net problem [Veni ''et al'', IPMI 2013].
* Solved by using VCEnet strategy and graph-cuts [Wu and Chen, 2002].
* Uses training strategy in order to generate model shapes as well as to compute costs at each mesh point.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Module is now available in the Slicer. It could be downloaded from: https://github.com/carma-center/carma_slicer_extension/
* The online documentation on its usage is available at: https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/AutomatedLASegmentation
* Model data could be downloaded from: http://slicer.kitware.com/midas3/folder/1550

</div>
</div>

File:LAsegment GraphCut.png

2013-12-18T18:53:36Z

Gveni:

2014 Project Week:GraphCutsLASegmentationModule

2013-12-18T18:39:34Z

Gveni: /* Project Description */

==Key Investigators==

Gopalkrishna Veni (SCI Institute, University of Utah)

Salma Bengali (CARMA center, University of Utah)

Josh Cates (CARMA center, University of Utah)

Ross Whitaker(SCI Institute, University of Utah)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Develop a Slicer module that automatically segments the left atrial wall from a given LGE-MRI image.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Involves Bayesian formulation with Markov random field prior within a nested-layer 3D mesh which leads to surface-net problem [Veni ''et al'', IPMI 2013].
* Solved by using VCEnet strategy and graph-cuts [Wu and Chen, 2002].
* Uses training strategy in order to generate model shapes as well as to compute costs at each mesh point.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Module is now available in the Slicer. It could be downloaded from: https://github.com/carma-center/carma_slicer_extension/
* The online documentation on its usage is available at: https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/AutomatedLASegmentation
* Model data could be downloaded from: http://slicer.kitware.com/midas3/folder/1550

</div>
</div>

2014 Project Week:GraphCutsLASegmentationModule

2013-12-18T18:29:47Z

Gveni: /* Project Description */

DBP Utah Atrial Fibrillation 2014

2013-12-18T18:01:48Z

Gveni:

[[AHM_2014#Agenda|Back to AHM_2014 Agenda]]

*Time: 2-3pm
*Goal: Get together with your partners from algorithm and engineering to make plans for the upcoming year.
**Create Slicer modules
**Create Slicer extensions
**Create Slicer workflows
*DBP PI: Rob MacLeod
*Algorithms as extensions in Slicer: Ross Whitaker, Allen Tannenbaum
**Left atrial scar segmenter (Liangjia Zhu, Yi Gao, Josh Cates, Alan Morris, Danny Perry, Greg Gardner, Rob MacLeod, Allen Tannenbaum)
**Left atrium segmenter (Liangjia Zhu, Yi Gao, Josh Cates, Alan Morris, Danny Perry, Greg Gardner, Rob MacLeod, Allen Tannenbaum)
**Fibrosis distribution analysis (Yi Gao, Liangjia Zhu, Josh Cates, Alan Morris, Danny Perry, Greg Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
**Grow cut, level set integration for interactive segmentation (Ivan Kolesov, Liangjia Zhu, Yi Gao, Peter Karasev, Allen Tannenbaum)
**Left atrial wall segmentation using multi-column graph-cuts (Gopal Veni, Salma Bengali, Josh Cates, Rob Macleod, Ross Whitaker)
*Engineering: workflows in collaboration with DBP: Jim Miller

2014 Project Week:GraphCutsLASegmentationModule

2013-12-18T07:04:03Z

Gveni: /* Key Investigators */

2014 Project Week:GraphCutsLASegmentationModule

2013-12-18T07:00:07Z

Gveni: Created page with '==Key Investigators== Gopalkrishna Veni (SCI Institute, University of Utah) Salma Bengali (CARMA center, University of Utah) Josh Cates (CARMA center, University of Utah) Ros…'

2014 Winter Project Week

2013-12-18T06:56:46Z

Gveni: /* Atrial Fibrillation */

Back to [[Project Events]], [[AHM_2014]], [[Events]]

__NOTOC__
[[image:PW-SLC2014.png|300px]]

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.

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 [[Project_Events#Past|here]].
= Dates.Venue.Registration =

Please [[AHM_2014#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

= [[AHM_2014#Agenda|'''AGENDA''']] and Project List=

Please:
* [[AHM_2014#Agenda|'''Click here for the agenda for AHM 2014 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

=Background and Preparation=

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]

=Projects=
* [[2014_Project_Week_Template | Template for project pages]]

==TBI==
*[[2014_Project_Week:TBIatrophy|Multimodal neuroimaging for the quantification of brain atrophy at six months following severe traumatic brain injury]] (Andrei Irimia, SY Matthew Goh, Carinna M. Torgerson, John D. Van Horn)
*[[2014_Project_Week:TBIdemyelination|Systematic evaluation of axonal demyelination subsequent to traumatic brain injury using structural T1- and T2-weighted magnetic resonance imaging]] (Andrei Irimia, SY Matthew Goh, Carinna M. Torgerson, John D. Van Horn)
*[[2014_Project_Week:BrainAging|Mapping the effect of traumatic brain injury upon white matter connections in the human brain using 3D Slicer]] (Andrei Irimia, John D. Van Horn)
*[[2014_Project_Week:LongitudinalDTI|Patient-specific longitudinal DTI analysis in traumatic brain injury]] (Anuja Sharma, Andrei Irimia, Bo Wang, John D. Van Horn, Martin Styner, Guido gerig)
*[[2014_Project_Week:TBISegmentation|Testing the interactive segmentation algorithm for traumatic brain injury]] (Bo Wang, Marcel Prastawa, Andrei Irimia, John D. Van Horn, Guido Gerig)

==Atrial Fibrillation==
*[[2014_Project_Week:GraphCutsLASegmentation|LA Segmentation via Graph Cuts]] (Josh, Salma, Gopal)
*[[2014_Project_Week:MRAFusionRegistration|DEMRI LA Segmentation via Image Fusion (MRA)]] (Josh, Salma, Alan)
*[[2014_Project_Week:LAFibrosisVisualizationModule|LA Fibrosis / Scar Visualization]] (Josh, Salma, Alan)
*[[2014_Project_Week:CARMADocumentation|CARMA Extension Documentation Project]] (Josh, Salma)
*[[2014_Project_Week:GraphCutsLASegmentationModule|LA Segmentation module using multi-column Graph Cuts]] (Gopal, Salma, Josh, Ross)

==Huntington's Disease==
*[[2014_Project_Week:DWIDispersion|DWI Dispersion]] (Hans, CF)
*[[2014_Project_Week:DTIAnalysis|DTI Compressed Sensing?]] (Hans, CF)
*[[2014_Project_Week:Modules scripting|Slicer module scripting?]] (Dave)
*[[2014_Project_Week:DWIConverter|DWIConverter?]] (Hans, Kent)
*Slicer Based Surface Template Estimation (Saurabh JHU, Steve Pieper, Hans Johnson, Josh Cates)
*[[2014_Project_Week:HD_4DShapes|4D shape analysis: application to HD ]] (James Fishbaugh,Hans Johnson, Guido Gerig)
*[[2014_Project_Week:Shape_Registration_and_Regression|Shape registration and regression in Slicer4 ]] (James Fishbaugh,Hans Johnson, Guido Gerig)

==Head and Neck Cancer==
*[[2014_Project_Week:DIR_validation|DIR Validation]] (Nadya and Greg)
*[[2014_Project_Week:Hybrid_bspline|Hybrid B Spline]] (Nadya, Greg, Steve)
*[[2014_Project_Week:KSlice|Interactive Segmentation]] (Ivan, Nadya, Greg, Allen)

==Stroke==

*[[2014_Project_Week:Multi-Tissue_Stroke_Segmentation|Multi-Tissue Stroke Segmentation]] (Ramesh, Polina B., Polina G.)

==Image-Guided Interventions==

==Radiation Therapy==
*[[2014_Project_Week:DICOM_RT|DICOM RT Export]] (Greg, Kevin Wang, others)
*[[2014_Project_Week:DICOM_SRO|DICOM Spatial Registration Export]] (Greg, Kevin Wang, others)
*[[2014_Project_Week:Registration_Evaluation|Interactive Registration and Evaluation]] (Kevin Wang, Greg, others)

==Medical Robotics==
==[http://qiicr.org QIICR]==

*[[2014_Project_Week:4D_NIfTI_Multivolume|4D NIfTI Multivolume Support]] (Jayashree, Andrey, Jim, John)
*[[2014_Project_Week:RT_FormatConversions|RT and ITK Format Conversions]] (Jayashree, Andras, Csaba. John)
*[[2014_Project_Week:BatchConvertDICOM|Python Scripting Slicer DICOM read/write to convert segmentation objects]] (Jayashree, Andrey, Alireza, Steve, Jc, Hans, John)
*[[2014_Project_Week:PkModeling_user_tool|User module for DCE modeling]] (Andrey, Jayashree, Jim, Alireza, Steve, Ron)
*[[2014_Project_Week:DICOM_enhanced_multiframe|DICOM enhanced multiframe object support]] (Andrey, Alireza, David Clunie, Jayashree, Steve, Reinhard, Jim)

==TMJ-OA==

==Infrastructure==
*[[2014_Project_Week:SlicerSpeedUp|Slicer speed up]] (Jc, Andras Lasso, Steve Pieper)
*[[2014_Project_Week:MRMLSceneSpeedUp|MRML Scene speed up]] (Jc, Andras Lasso)
*[[2014_Project_Week:SlicerIPythonIntegration|Integration of IPython]] (Jc, Steve Pieper)
*[[2014_Project_Week:MultidimensionalDataSupport|Multidimensional data support]] (Andras Lasso, Andriy Fedorov, Steve Pieper, JC, Kevin Wang)
*CLI - Resources? Conditionals? Autonaming? Provenance? CTK unification? (Jim Miller)
*[[2014_Project_Week:MarkupsModule|Markups Module]] (Nicole Aucoin)
* [[2014_Winter_Project_Week:Steered Registration|Steered Registration]] (Steve, Greg, Kevin, Vinicius, Marcel)
* [[2014_Winter_Project_Week:MRB Extension Dependencies|MRB Extension Dependencies]] (Steve, Jc, Jim, Nicole, Alex)
* [[2014_Winter_Project_Week:SubjectHierarchy|Subject Hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper, Jc, Jayashree, John, Alireza, Andrey)
* [[2014_Winter_Project_Week:IntegrationOfContourObject|Integration of Contour object]] (Csaba Pinter, Andras Lasso, Steve Pieper, ???)
* [[2014_Winter_Project_Week:NonLinearTransforms|Integration non-linear transforms]] (Alex Yarmarkovich, Csaba Pinter, Andras Lasso, Steve Pieper, ???)

DBP Utah Atrial Fibrillation 2014

2013-12-18T06:49:13Z

Gveni:

[[AHM_2014#Agenda|Back to AHM_2014 Agenda]]

*Time: 2-3pm
*Goal: Get together with your partners from algorithm and engineering to make plans for the upcoming year.
**Create Slicer modules
**Create Slicer extensions
**Create Slicer workflows
*DBP PI: Rob MacLeod
*Algorithms as extensions in Slicer: Ross Whitaker, Allen Tannenbaum
**Left atrial scar segmenter (Liangjia Zhu, Yi Gao, Josh Cates, Alan Morris, Danny Perry, Greg Gardner, Rob MacLeod, Allen Tannenbaum)
**Left atrium segmenter (Liangjia Zhu, Yi Gao, Josh Cates, Alan Morris, Danny Perry, Greg Gardner, Rob MacLeod, Allen Tannenbaum)
**Fibrosis distribution analysis (Yi Gao, Liangjia Zhu, Josh Cates, Alan Morris, Danny Perry, Greg Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
**Grow cut, level set integration for interactive segmentation (Ivan Kolesov, Liangjia Zhu, Yi Gao, Peter Karasev, Allen Tannenbaum)
**Left atrial wall segmentation using multi-column graph-cuts (Gopal Veni, Salma Bengali, Josh Cates, Ross Whitaker)
*Engineering: workflows in collaboration with DBP: Jim Miller

2013 Project Week:CARMA LA Seg Gopal

2013-01-11T06:25:49Z

Gveni: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
Gopal Veni, Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod, Ross Whitaker

[[File:CARMA_GopalLASeg.png‎|thumb|center|Image Here]]

The goal of this project is to begin Slicer implementation and testing of Gopal and Ross' segmentation method: "Left atrial wall segmentation using intensity profile based feature detector and optimal graph-cuts." Our objective is to implement this method in Slicer. There are several fairly involved steps for the entire segmentation process, including
# An LA shape model building phase
# User input to identify the center of a region of interest
# Computation of the segmentation, given a new LGE-MRI image
# Surface reconstruction of the output point set and (optionally) scan-conversion of the surface mesh to a binary segmentation volume.

For the Winter Project Week, our team will focus on steps 2-3 of this pipeline, with the goal of implementing a command-line module to perform the processing. Step 1 of the process will be implemented in a future planned Slicer module, but for now we will use an existing model built from the the CARMA LA shape database (available through the Data section of the CARMA DBP Wiki page).

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
Our Project Week objective is to produce a preliminary version of the segmentation computation outlined in steps 2-3 above.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
We plan to implement this algorithm as a Slicer command-line module. Gopal has existing C++ code, but this code relies upon a 3rd party LGPL library for the Graph Cut algorithm. We will need to identify an alternative to this 3rd party code. Several other NAMIC partners have past projects requiring Graph Cuts, so there may be a solution available. We will investigate.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
Discussed with Jim and Jc on the possibilities of handling/embeding the model-based-data while the module is being uploaded.
Module written but needs to be integrated into the Slicer. Currently, dealing with some slicer build based errors. Once sorted, the module should be ready to check-in.
</div>
</div>

2013 Project Week:CARMA LA Seg Gopal

2013-01-11T06:04:36Z

Gveni: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
Gopal Veni, Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod, Ross Whitaker

[[File:CARMA_GopalLASeg.png‎|thumb|center|Image Here]]

The goal of this project is to begin Slicer implementation and testing of Gopal and Ross' segmentation method: "Left atrial wall segmentation using intensity profile based feature detector and optimal graph-cuts." Our objective is to implement this method in Slicer. There are several fairly involved steps for the entire segmentation process, including
# An LA shape model building phase
# User input to identify the center of a region of interest
# Computation of the segmentation, given a new LGE-MRI image
# Surface reconstruction of the output point set and (optionally) scan-conversion of the surface mesh to a binary segmentation volume.

For the Winter Project Week, our team will focus on steps 2-3 of this pipeline, with the goal of implementing a command-line module to perform the processing. Step 1 of the process will be implemented in a future planned Slicer module, but for now we will use an existing model built from the the CARMA LA shape database (available through the Data section of the CARMA DBP Wiki page).

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
Our Project Week objective is to produce a preliminary version of the segmentation computation outlined in steps 2-3 above.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
We plan to implement this algorithm as a Slicer command-line module. Gopal has existing C++ code, but this code relies upon a 3rd party LGPL library for the Graph Cut algorithm. We will need to identify an alternative to this 3rd party code. Several other NAMIC partners have past projects requiring Graph Cuts, so there may be a solution available. We will investigate.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
Discussed with Jim and Jc on how to handle/embed the model based data while the module being uploaded.
Module written but needs to integrated into the Slicer. Currently, dealing with some slicer build based errors. Once sorted, the module should be ready to check-in.
</div>
</div>

2012 Summer Project Week

2012-05-05T20:17:47Z

Gveni: /* Atrial Fibrillation */

Back to [[Events]]

[[image:PW-MIT2012.png|200px]]

*'''Dates:''' June 18-22, 2012
*'''Location:''' MIT

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 18
!style="width:18%" |Tuesday, June 19
!style="width:18%" |Wednesday, June 20
!style="width:18%" |Thursday, June 21
!style="width:18%" |Friday, June 22
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-10am:''' Slicer4 (Jean-Christophe Fillion-Robin)
'''10-11am''' Slicer4 Breakout (Continued) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> )<br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>'''10:30am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> <br>
<br>[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:15pm''' Slicer4 Developers Session (Pieper) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
<br>---<br>
'''4:15-5:00pm''' Slicer4 Developer Session Continued <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>---<br>
'''4:15-5:00pm''' Breakout Session: TBD <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Right)]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> TBD
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[2012_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' Breakout Session:TBD
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2012|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''2-4pm: <font color="#4020ff">Core and Site PIs meeting with Ron:'''</font><br>
<br>Star Room
|'''1-4pm: <font color="#4020ff">Breakout Session:'''</font><br>
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

This is where the list of projects goes...

Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template THIS TEMPLATE] to create project pages for this event.

==='''Neurosurgery, Brain and Spine, Traumatic Brain Injury'''===

# [[2012_Summer_Project_Week:Early_Dementia_Diagnostic |Early Dementia Diagnostic Tools]] (Marcel Koek, Sonia Pujol)
# Intraoperative White Matter Tract Detection Module (Lauren O'Donnell, Isaiah Norton)

==='''Radiation Therapy'''===

#Dose Calculation for Interstitial Brachytherapy (Tina Kapur, Greg Sharp)
#[[2012_Summer_Project_Week:Overlapping_structures|Overlapping structures]] (Greg Sharp, Steve Pieper)
#[[2012_Summer_Project_Week:Atlas_based_segmentation_for_head_and_neck|Atlas-based segmentation for head and neck]] (Greg Sharp, Nadya Shusharina, James Shackleford, Polina Golland)

==='''Huntington's Disease'''===
#
#

==='''Atrial Fibrillation'''===
# Model-based segmentation of left Atrium using Graph-cuts (Gopal Veni, Ross Whitaker)
#

==='''Device Integration with Slicer and General Image Guided Therapy'''===
# [[2012_Summer_Project_Week:iGyne|iGyne for Gyne Brachytherapy]] (Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper)

==='''General Segmentation'''===
#
#
==='''General Registration'''===
# Interactive registration (Kunlin)
# [[2012_Summer_Project_Week:NiftyReg|NiftyReg integration]] (Marc Modat, Sonia Pujol)

==='''General Diffusion Tractography'''===
#
#

==='''Vessels'''===
#
#
==='''Infrastructure'''===

# [[2012_Summer_Project_Week:SelfTesting|Built-In Self-Testing (BIST) for Slicer]] (Steve, Julien, Jc, Sonia)
# Annotation module redesign (Nicole)
# Multivolume, nrrd, .... (Andriy, Jim)
# Python CLI modules (Demian, JC, Julien)
# Charting (Jim)
# ITKv4
# SimpleITK
# GPU Editor Effects
# XTK/WebGL Exporter (Daniel, Nicolas - Children's Hospital Boston)
# General Usability issues (e.g. LM,FG,BG blending)
# Callback/Events/Observation best practice + Performance bottleneck discussion (Julien, Steve,...)
# XNAT/Slicer implementation (Sunil, Dan, Steve,...)
# Pilot QIN use cases for Slicer/XNAT integration (Sunil, Steve, Dan, Andriy, Jayashree,...)

==Background==

We are pleased to announce the 15th 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|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 [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 26th 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 [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.

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

== Logistics ==
*'''Dates:''' June 18-22, 2012.
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [https://www.regonline.com/namic2012summerprojweek HERE] to do an on-line registration for the meeting that will allow you to pay by credit card. No checks will be accepted.
*'''Registration Fee:''' $300 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' TBD.

== Preparation ==
# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 26, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 10, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 7, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 14: Create a directory for each project on the [[Engineering:SandBox|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 [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

2012 Summer Project Week

2012-05-05T20:17:21Z

Gveni: /* Atrial Fibrillation */

Back to [[Events]]

[[image:PW-MIT2012.png|200px]]

*'''Dates:''' June 18-22, 2012
*'''Location:''' MIT

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 18
!style="width:18%" |Tuesday, June 19
!style="width:18%" |Wednesday, June 20
!style="width:18%" |Thursday, June 21
!style="width:18%" |Friday, June 22
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-10am:''' Slicer4 (Jean-Christophe Fillion-Robin)
'''10-11am''' Slicer4 Breakout (Continued) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> )<br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>'''10:30am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> <br>
<br>[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:15pm''' Slicer4 Developers Session (Pieper) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
<br>---<br>
'''4:15-5:00pm''' Slicer4 Developer Session Continued <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>---<br>
'''4:15-5:00pm''' Breakout Session: TBD <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Right)]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> TBD
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[2012_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' Breakout Session:TBD
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2012|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''2-4pm: <font color="#4020ff">Core and Site PIs meeting with Ron:'''</font><br>
<br>Star Room
|'''1-4pm: <font color="#4020ff">Breakout Session:'''</font><br>
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

This is where the list of projects goes...

Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template THIS TEMPLATE] to create project pages for this event.

==='''Neurosurgery, Brain and Spine, Traumatic Brain Injury'''===

# [[2012_Summer_Project_Week:Early_Dementia_Diagnostic |Early Dementia Diagnostic Tools]] (Marcel Koek, Sonia Pujol)
# Intraoperative White Matter Tract Detection Module (Lauren O'Donnell, Isaiah Norton)

==='''Radiation Therapy'''===

#Dose Calculation for Interstitial Brachytherapy (Tina Kapur, Greg Sharp)
#[[2012_Summer_Project_Week:Overlapping_structures|Overlapping structures]] (Greg Sharp, Steve Pieper)
#[[2012_Summer_Project_Week:Atlas_based_segmentation_for_head_and_neck|Atlas-based segmentation for head and neck]] (Greg Sharp, Nadya Shusharina, James Shackleford, Polina Golland)

==='''Huntington's Disease'''===
#
#

==='''Atrial Fibrillation'''===
# Model-based segmentation of left atrium using Graph-cuts (Gopal Veni, Ross Whitaker)
#

==='''Device Integration with Slicer and General Image Guided Therapy'''===
# [[2012_Summer_Project_Week:iGyne|iGyne for Gyne Brachytherapy]] (Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper)

==='''General Segmentation'''===
#
#
==='''General Registration'''===
# Interactive registration (Kunlin)
# [[2012_Summer_Project_Week:NiftyReg|NiftyReg integration]] (Marc Modat, Sonia Pujol)

==='''General Diffusion Tractography'''===
#
#

==='''Vessels'''===
#
#
==='''Infrastructure'''===

# [[2012_Summer_Project_Week:SelfTesting|Built-In Self-Testing (BIST) for Slicer]] (Steve, Julien, Jc, Sonia)
# Annotation module redesign (Nicole)
# Multivolume, nrrd, .... (Andriy, Jim)
# Python CLI modules (Demian, JC, Julien)
# Charting (Jim)
# ITKv4
# SimpleITK
# GPU Editor Effects
# XTK/WebGL Exporter (Daniel, Nicolas - Children's Hospital Boston)
# General Usability issues (e.g. LM,FG,BG blending)
# Callback/Events/Observation best practice + Performance bottleneck discussion (Julien, Steve,...)
# XNAT/Slicer implementation (Sunil, Dan, Steve,...)
# Pilot QIN use cases for Slicer/XNAT integration (Sunil, Steve, Dan, Andriy, Jayashree,...)

==Background==

We are pleased to announce the 15th 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|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 [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 26th 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 [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.

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

== Logistics ==
*'''Dates:''' June 18-22, 2012.
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [https://www.regonline.com/namic2012summerprojweek HERE] to do an on-line registration for the meeting that will allow you to pay by credit card. No checks will be accepted.
*'''Registration Fee:''' $300 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' TBD.

== Preparation ==
# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 26, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 10, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 7, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 14: Create a directory for each project on the [[Engineering:SandBox|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 [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

2012 Winter Project Week:DTI pipeline

2012-01-13T06:47:19Z

Gveni: /* Key Partners */

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Partners==
* Utah: Gopal Veni, Ross Whitaker
* Iowa: Hans Johnson (HD Project)

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

<h3>Objective</h3>
* Build a complete DTI processing pipeline for the HD data.
</div>

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

<h3>Approach, Plan</h3>
* Editing our current DTI pipeline by including Brainsfit as our affine registration step.
* Discuss with Hans group about the resulting DTI pipeline.
</div>

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

<h3>Progress</h3>
* Applied rigid and affine registration to our (preliminary) data using BRAINSFit.
* Currently working on embedding this affine transformation file to AtlasWerks.
</div>
</div>

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

2012 Winter Project Week:GraphbasedSeg

2012-01-13T06:35:44Z

Gveni:

<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:multilineblurnoise_scimg.png|[[MLBN_S|Computer generated image]]
Image:multilineblur_scimgop.png|[[MLBN_S|Output]]
Image:Slice20_seg.png|[[left_atrium_slice| segmentation of a Left atrium slice]]
Image:Slice20_segzoom.png|[[left_atrium_slice_zoom| zoomed version]]
</gallery>

==Key Partners==
* Utah: Gopal Veni, Ross Whitaker

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

<h3>Objective</h3>

* Optimal segmentation of the left atrium and its surrounding tissue simultaneously on 3D LGE-MRI images.

</div>

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

<h3>Approach, Plan</h3>

* A graph based technique is used that is capable of segmenting multiple surfaces simultaneously and in an optimal manner.

* Our plan for the project week is to design a cost function that could effectively work on real data including left atrium and its surrounding wall.

</div>

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

<h3>Progress</h3>
* So far, the algorithm has been tested successfully on the 2D synthetic data.
* A model using image profile has been designed and cost functions based on that have been induced to optimally segment the left atrium and its surrounding wall.
</div>
</div>

2012 Winter Project Week:GraphbasedSeg

2012-01-13T04:06:45Z

Gveni:

<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:multilineblurnoise_scimg.png|[[MLBN_S|Computer generated image]]
Image:multilineblur_scimgop.png|[[MLBN_S|Output]]
Image:Slice20_seg.png|[[left_atrium_slice| segmentation of a Left atrium slice]]
Image:Slice20_segzoom.png|[[left_atrium_slice_zoom| zoomed version]]
</gallery>

==Key Partners==
* Utah: Gopal Veni, Ross Whitaker

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

<h3>Objective</h3>

* Optimal segmentation of the left atrium and its surrounding tissue simultaneously on 3D LGE-MRI images.

</div>

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

<h3>Approach, Plan</h3>

* A graph based technique is used that is capable of segmenting multiple surfaces simultaneously and in an optimal manner.

* Our plan for the project week is extend this algorithm on 3D real surfaces.

</div>

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

<h3>Progress</h3>
* So far, the algorithm has been tested successfully on the 2D synthetic data.
</div>
</div>

2012 Winter Project Week:GraphbasedSeg

2012-01-13T04:05:37Z

Gveni:

<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:multilineblurnoise_scimg.png|[[MLBN_S|Computer generated image]]
Image:multilineblur_scimgop.png|[[MLBN_S|Output]] \\
Image:Slice20_seg.png|[[left_atrium_slice| segmentation of a Left atrium slice]]
Image:Slice20_segzoom.png|[[left_atrium_slice_zoom]]
</gallery>

==Key Partners==
* Utah: Gopal Veni, Ross Whitaker

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

<h3>Objective</h3>

* Optimal segmentation of the left atrium and its surrounding tissue simultaneously on 3D LGE-MRI images.

</div>

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

<h3>Approach, Plan</h3>

* A graph based technique is used that is capable of segmenting multiple surfaces simultaneously and in an optimal manner.

* Our plan for the project week is extend this algorithm on 3D real surfaces.

</div>

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

<h3>Progress</h3>
* So far, the algorithm has been tested successfully on the 2D synthetic data.
</div>
</div>

2012 Winter Project Week:GraphbasedSeg

2012-01-13T03:57:53Z

Gveni:

<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:multilineblurnoise_scimg.png|[[MLBN_S|Computer generated image]]
Image:multilineblur_scimgop.png|[[MLBN_S|Output]]
Image::slice20_seg.png|[[left_atrium_slice| segmentation of a Left atrium slice]]
Image::slice20_zoomseg.png|[[left_atrium_slice_zoom]]
</gallery>

==Key Partners==
* Utah: Gopal Veni, Ross Whitaker

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

<h3>Objective</h3>

* Optimal segmentation of the left atrium and its surrounding tissue simultaneously on 3D LGE-MRI images.

</div>

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

<h3>Approach, Plan</h3>

* A graph based technique is used that is capable of segmenting multiple surfaces simultaneously and in an optimal manner.

* Our plan for the project week is extend this algorithm on 3D real surfaces.

</div>

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

<h3>Progress</h3>
* So far, the algorithm has been tested successfully on the 2D synthetic data.
</div>
</div>

File:Slice20 segzoom.png

2012-01-13T03:52:04Z

Gveni:

File:Slice20 seg.png

2012-01-13T03:51:51Z

Gveni:

2012 Winter Project Week:GraphbasedSeg

2012-01-13T03:49:50Z

Gveni:

<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:multilineblurnoise_scimg.png|[[MLBN_S|Computer generated image]]
Image:multilineblur_scimgop.png|[[MLBN_S|Output]]
</gallery>

==Key Partners==
* Utah: Gopal Veni, Ross Whitaker

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

<h3>Objective</h3>

* Optimal segmentation of the left atrium and its surrounding tissue simultaneously on 3D LGE-MRI images.

</div>

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

<h3>Approach, Plan</h3>

* A graph based technique is used that is capable of segmenting multiple surfaces simultaneously and in an optimal manner.

* Our plan for the project week is extend this algorithm on 3D real surfaces.

</div>

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

<h3>Progress</h3>
* So far, the algorithm has been tested successfully on the 2D synthetic data.
</div>
</div>

2012 Winter Project Week:GraphbasedSeg

2012-01-13T03:48:55Z

Gveni:

<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:multilineblurnoise_scimg.png|[[MLBN_S|Computer generated image and its output]]
Image:multilineblur_scimgop.png|[[MLBN_S|Computer generated image and its output]]
</gallery>

==Key Partners==
* Utah: Gopal Veni, Ross Whitaker

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

<h3>Objective</h3>

* Optimal segmentation of the left atrium and its surrounding tissue simultaneously on 3D LGE-MRI images.

</div>

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

<h3>Approach, Plan</h3>

* A graph based technique is used that is capable of segmenting multiple surfaces simultaneously and in an optimal manner.

* Our plan for the project week is extend this algorithm on 3D real surfaces.

</div>

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

<h3>Progress</h3>
* So far, the algorithm has been tested successfully on the 2D synthetic data.
</div>
</div>

2012 Winter Project Week:GraphbasedSeg

2012-01-13T03:43:46Z

Gveni:

<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:multilineblurnoise_scimg.png|[[MLBN_S|Computer generated image and its output]]
</gallery>

==Key Partners==
* Utah: Gopal Veni, Ross Whitaker

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

<h3>Objective</h3>

* Optimal segmentation of the left atrium and its surrounding tissue simultaneously on 3D LGE-MRI images.

</div>

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

<h3>Approach, Plan</h3>

* A graph based technique is used that is capable of segmenting multiple surfaces simultaneously and in an optimal manner.

* Our plan for the project week is extend this algorithm on 3D real surfaces.

</div>

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

<h3>Progress</h3>
* So far, the algorithm has been tested successfully on the 2D synthetic data.
</div>
</div>

2012 Winter Project Week:GraphbasedSeg

2012-01-13T03:41:54Z

Gveni:

<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:multilineblurnoise_scimg.png|[[left_atrium_graph_cut_results|Projects List]]
</gallery>

==Key Partners==
* Utah: Gopal Veni, Ross Whitaker

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

<h3>Objective</h3>

* Optimal segmentation of the left atrium and its surrounding tissue simultaneously on 3D LGE-MRI images.

</div>

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

<h3>Approach, Plan</h3>

* A graph based technique is used that is capable of segmenting multiple surfaces simultaneously and in an optimal manner.

* Our plan for the project week is extend this algorithm on 3D real surfaces.

</div>

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

<h3>Progress</h3>
* So far, the algorithm has been tested successfully on the 2D synthetic data.
</div>
</div>

2012 Winter Project Week:GraphbasedSeg

2012-01-13T03:40:05Z

Gveni:

File:Multilineblur scimgop.png

2012-01-13T03:30:17Z

Gveni:

File:Multilineblurnoise scimg.png

2012-01-13T03:29:17Z

Gveni:

2012 Winter Project Week:GraphbasedSeg

2012-01-13T02:15:33Z

Gveni:

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:atrium_20sliceopimg.png|[[left_atrium_graph_cut_results|Projects List]]
</gallery>

==Key Partners==
* Utah: Gopal Veni, Ross Whitaker

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

<h3>Objective</h3>

* Optimal segmentation of the left atrium and its surrounding tissue simultaneously on 3D LGE-MRI images.

</div>

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

<h3>Approach, Plan</h3>

* A graph based technique is used that is capable of segmenting multiple surfaces simultaneously and in an optimal manner.

* Our plan for the project week is extend this algorithm on 3D real surfaces.

</div>

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

<h3>Progress</h3>
* So far, the algorithm has been tested successfully on the 2D synthetic data.
</div>
</div>

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

File:Atrium 20sliceopimg.png

2012-01-13T02:12:12Z

Gveni:

2012 Winter Project Week:DTI pipeline

2012-01-01T23:24:25Z

Gveni: Created page with '__NOTOC__ <gallery> Image:PW-SLC2012.png|Projects List </gallery> ==Key Partners== * Utah: Gopal Veni, Ross Whitaker * Iowa: Hans Johnson (…'

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Partners==
* Utah: Gopal Veni, Ross Whitaker
* Iowa: Hans Johnson (HD Project)
* UNC: Martin Styner

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

<h3>Objective</h3>
* Build a complete DTI processing pipeline for the HD data.
</div>

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

<h3>Approach, Plan</h3>
* Editing our current DTI pipeline by including Brainsfit as our affine registration step.
* Discuss with Hans and Martin group about the resulting DTI pipeline.
</div>

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

<h3>Progress</h3>
To be added
</div>
</div>

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

2012 Winter Project Week:GraphbasedSeg

2012-01-01T23:07:24Z

Gveni: Created page with '__NOTOC__ <gallery> Image:PW-SLC2012.png|Projects List </gallery> ==Key Partners== * Utah: Gopal Veni, Ross Whitaker <div style="margin: 2…'

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Partners==
* Utah: Gopal Veni, Ross Whitaker

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

<h3>Objective</h3>

* Optimal segmentation of the left atrium and its surrounding tissue simultaneously on 3D LGE-MRI images.

</div>

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

<h3>Approach, Plan</h3>

* A graph based technique is used that is capable of segmenting multiple surfaces simultaneously and in an optimal manner.

* Our plan for the project week is extend this algorithm on 3D real surfaces.

</div>

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

<h3>Progress</h3>
* So far, the algorithm has been tested successfully on the 2D synthetic data.
</div>
</div>

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

2012 Winter Project Week

2012-01-01T00:52:25Z

Gveni: /* Atrial fibrillation */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2012]], [[Events]]

__NOTOC__
[[image:PW-SLC2012.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== Agenda and Project List==

Please:
* [[AHM_2012#Agenda|'''Click here for the agenda for AHM 2012 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

==Background==

From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

==Projects==

===Traumatic Brain Injury ===

* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Segmentation of Serial MRI of TBI patients
using Personalized Atlas Construction]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIDTIAnalysis|Registration and analysis of white matter tract changes in TBI]] (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig, Martin Styner, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIValidation|Validation, visualization and analysis of segmentation for TBI]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
*Geometric Metamorphosis for TBI (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Integration of unscented Kalman filter (UKF) based multi-tensor tractography in Slicer]] (Christian Baumgartner, Yogesh Rathi, Carl-Fredrik Westin)

===Predict Huntington's Disease===
* [[2012_Winter_Project_Week:SPIEWorkshop|SPIE DTI Workshop Preparation: Perform DTI Quality Control]] (Jean-Baptiste Berger, Sonia Pujol, Guido Gerig, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DWIPhantom|DTI tractography phantom: a software for evaluating tractography algorithms]] (Gwendoline Roger,Yundi Shi, Clement Vachet, Martin Styner, Sylvain Gouttard)
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:ShapeAnalysisSubcorticalStructuresHD|Morphometric analysis in subcortical structures in HD]] (Beatriz Paniagua, Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:DTI pipeline|Applying our DTI pipeline to analyse HD data]] (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)
* [[2012_Winter_Project_Week: DTI Change Modeling | Longitudinal change modeling of fiber tracts in serial HD DTI data]] (Anuja Sharma, Hans Johnson, Guido Gerig)
* [[2012_Winter_Project_Week: Continuous 4D shapes | Continuous 4d shape models from time-discrete data: Subcortical structures in HD]] (James Fishbaugh, Hans Johnson, Guido Gerig)

===Atrial fibrillation ===
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:LAWallRegistration|Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:PVRegistration|Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:RealTime|OpenIGT for realtime MRI-guided RF ablation]] (Gene Payne, Rob MacLeod, and Junichi Tokuda)
* [[2012_Winter_Project_Week:GraphbasedSeg|Graph based segmentation on LGE-MRI data]] (Gopal Veni, Ross Whitaker)

===Head and Neck Cancer ===
* [[2012_Winter_Project_Week:PatchBased|A patch-based approach to the segmentation of organs of risk]] (Christian Wachinger, Polina Golland)
* [[2012_Winter_Project_Week:PairwiseLF|Label fusion with pairwise interactions]] (Ramesh Sridharan, Christian Wachinger, Polina Golland)
* [[RT dose comparison tool for Slicer]] (Nadya Shusharina, Greg Sharp)
* [[2012_Winter_Project_Week:InteractiveSegmentation|Interactive editing tools for segmentation]] (Greg Sharp, Steve Pieper)
* [[2012_Winter_Project_Week:UserInTheLoop_InteractiveSegmn|Interactive 3D Level-Set Segmentation]] (Peter Karasev, Karl Fritscher, Ivan Kolesov, Allen Tannenbaum)

===IGT for Surgery and Radiation Treatments===
*[[2012_Winter_Project_Week:PelvicRegistration|Deformable prostate registration: 3D ultrasound to MRI]] (Mehdi Moradi, Jan Egger, Andrey Fedorov)
*[[2012_Winter_Project_Week:iGyne | iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO]] (Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Antonio Damato, Kanokpis Townamchai, Tina Kapur, Akila Viswanathan)
*[[2012_Winter_Project_Week:OpenIGTLink_Interface_for_Slicer4| OpenIGTLink interface for Slicer4]] (Junichi Tokuda, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)
*[[2012_Winter_Project_Week:Needle Detection in MR Images for Brachytherapy in AMIGO|Needle Detection in MR Images for Brahytherapy in AMIGO]] (Radhika Tibrewal, Jan Egger, Xiaojun Chen, Stephen Aylward)
*[[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen)
*[[2012_Winter_Project_Week:4DUltrasound|4D Ultrasound Storage and Volume Rendering on Slicer 3.6]] (Laurent, Noby)
*[[2012_Winter_Project_Week:BKPLUSSlicer|Integration of BK Ultrasound into PLUS and Slicer]] (Mehdi Moradi, Isaiah Norton, PLUS developers?)
*[[2012_Winter_Project_Week:hybridMRS | Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer]] (Jan Egger, Isaiah Norton, Bjoern Menze, Daniel Hořínek, Antonín Škoch, Christopher Nimsky, Tina Kapur)
*[[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)
*[[2012_Winter_Project_Week:RTSS|RT structure set data representation]] (Greg Sharp, Andras Lasso, Steve Pieper, etc.)

===Musculoskeletal System===
* [[2012_Winter_Project_Week:Radnostics|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)

===Registration===
* [[2012_Winter_Project_Week:CMFreg|Framework for Cranio-Maxillo Facial registration in Slicer3]] (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)
* [[2012_Winter_Project_Week:SlidingOrgans|Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)]]
* [[2012_Winter_Project_Week:GeometricMetamorphosis|Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)]]
* [[2012_Winter_Project_Week:FastInterpolation|Fast Image Interpolation Given Parameterized Deformations For Image Registration (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)]]

===Shape Analysis===
* [[2012_Winter_Project_Week:PNSnormals|Principal Nested Spheres Normal Consistency in ShapeWorks]] (Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:GeomIndicesSlicer4|Porting of White Matter Geometric Indices Module to Slicer4]] (Peter Savadjiev)
* [[2012_Winter_Project_Week:ParticleWrapper|Slicer end-to-end particle correspondence wrapper module]] (Ipek Oguz, Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)

===NA-MIC Kit Internals===
*Slicer4 release (Jean-Christophe Fillion-Robin (JC), and Julien Finet (J2))
*Slicer4 extensions (JC)
*Slicer4 documentation (JC)
*Slicer4 GUI Testing (Benjamin Long, JC, J2)
*Slicer4 data on MIDAS (Josh Cates, Patrick Reynolds)
*[[2012_Project_Week:SceneViews|Slicer4 Scene Views Module]] (Nicole Aucoin, Ron Kikinis, Julien Finet)
*[[2012_Project_Week:AnnotationsFileFormatRefactor|Annotations Module File Format Refactor]] (Nicole Aucoin)
*[[2012_Project_Week:QT3DTextRendering|QT 3D Text rendering proof of concept]] (Julien Finet, Steve Pieper, Nicole Aucoin)
*[[2012_Project_Week:DICOM|DICOM Networking, Database, and Slicer Integration]] (Steve, Andrey, Andras)
*[[2012_Project_Week:EditorExtensions|Editor Extension Examples and Debugging]] (Steve, Andrey, Jc, Hans, Satra)
*[[2012_Project_Week:GeneralGUI|General minor GUI redesign]] (Wendy Plezniak, Julien Finet, Ron Kikinis)
*[[2012_Project_Week:ViewerControls|Redesign of the slice viewer control panels]] (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)
*[[2012_Project_Week:AutomatedTesting |Automated Testing (Sonia Pujol, Steve Pieper, Jc, Benjamin)]]
* Remove legacy code from slicer4 (itk, modules, build scripts) (Hans, Jim, Steve, J2, JC)
*[[2012_Project_Week:BatchProcessing|Batch Processing with Slicer Modules]] (Steve, Andrey, JC, Hans, Satra)
*[[2012_Project_Week:4DImageSlicer4|Support for 4D Images in Slicer4]] (Andrey, Steve, Junichi, Alex)
*[[2012_Project_Week:QIN-SAM|QIN Slicer Annotation Module: AIM, DICOM SR and Slicer annotations]] (Andrey, Steve, Nicole, Jayashree)

=== Preparation ===

#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]
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 27: MGH DBP
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics
#*November 10: Utah Atrial Fibrillation DBP
#*November 17: UCLA TBI DBP
#*November 24: No call. thanksgiving.
#*December 1:
#*December 8:
#*December 15:Finalize Projects
#*January 5: Loose Ends
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
##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. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
##Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
#Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

2012 Winter Project Week

2011-11-23T10:24:21Z

Gveni: /* Predict Huntington's Disease DBP */

2012 Winter Project Week

2011-11-22T00:09:33Z

Gveni: /* Predict Huntington's Disease DBP */

2011 Summer Project Week DTI Volumetric Segmentation for Group studies

2011-06-24T14:42:23Z

Gveni: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
</gallery>

'''DTI Volumetric Segmentation for Group studies'''

==Key Investigators==
* University of Utah: Gopal Veni, Ross Whitaker

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

<h3>Objective</h3>
Embedding a software module into the Slicer that does Groupwise statistical analysis on DTI volumetric segmentation.

</div>

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

<h3>Approach, Plan</h3>
* So far, the preliminary code of statistical analysis on DTI measures, obtained from volumetric segmentation, is running in MATLAB.
* The goal for this week is to learn how to extend this module and integrate it into the Slicer.

</div>

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

<h3>Progress</h3>
Discussed our approach on group analysis of DTI volumetric segmentation framework with Jim Miller and took some guidelines on how to interface a third party software (MATLAB) as an external plug-in into the slicer.

2011 Summer Project Week DTI analysis for Huntington's disease

2011-06-24T14:39:01Z

Gveni: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* University of Utah - Gopal Veni, Ross Whitaker
* University of Iowa - Hans Johnson

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

<h3>Objective</h3>

Apply our DTI pipeline to perform longitudinal analysis of HD.

</div>

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

<h3>Approach, Plan</h3>
* The pipeline mainly comprises Tensor estimation, Registration, Tractography and Statistical analysis.
* Tensor estimation and Registration (using AtlasWerks) is done on four HD data-sets.

</div>

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

<h3>Progress</h3>
* Discussed our DTI pipeline with Hans group and UNC group.
* Modified some initial parameters and re-running the complete pipeline.

</div>
</div>

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

2011 Summer Project Week DTI analysis for Huntington's disease

2011-06-24T14:27:44Z

Gveni:

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* University of Utah - Gopal Veni, Ross Whitaker
* University of Iowa - Hans Johnson

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

<h3>Objective</h3>

Apply our DTI pipeline to perform longitudinal analysis of HD.

</div>

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

<h3>Approach, Plan</h3>
* The pipeline mainly comprises Tensor estimation, Registration, Tractography and Statistical analysis.
* Tensor estimation and Registration (using AtlasWerks) is done on four HD data-sets.

</div>

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

<h3>Progress</h3>
* Discussed with Hans group and UNC group about our DTI pipeline.
* Modified some initial parameters and re-running the complete pipeline.

</div>
</div>

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

2011 Summer Project Week DTI Volumetric Segmentation for Group studies

2011-06-24T14:26:00Z

Gveni: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
</gallery>

'''DTI Volumetric Segmentation for Group studies'''

==Key Investigators==
* University of Utah: Gopal Veni, Ross Whitaker

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

<h3>Objective</h3>
Embedding a software module into the Slicer that does Groupwise statistical analysis on DTI volumetric segmentation.

</div>

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

<h3>Approach, Plan</h3>
* So far, the preliminary code of statistical analysis on DTI measures, obtained from volumetric segmentation, is running in MATLAB.
* The goal for this week is to learn how to extend this module and integrate it into the Slicer.

</div>

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

<h3>Progress</h3>
Discussed our approach on group analysis of DTI volumetric segmentation framework with Jim and took some guidelines on how to interface a third party software (MATLAB) as an external plug-in into the slicer.

2011 Summer Project Week DTI analysis for Huntington's disease

2011-06-24T14:18:14Z

Gveni: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:maxcurveFA_AtlasWerksregistered.png | maxcurveFA_registered images
</gallery>

==Key Investigators==
* University of Utah - Gopal Veni, Ross Whitaker
* University of Iowa - Hans Johnson

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

<h3>Objective</h3>

Apply our DTI pipeline to perform longitudinal analysis of HD.

</div>

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

<h3>Approach, Plan</h3>
* The pipeline mainly comprises Tensor estimation, Registration, Tractography and Statistical analysis.
* Tensor estimation and Registration (using AtlasWerks) is done on four HD data-sets.

</div>

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

<h3>Progress</h3>
* Discussed with Hans group and UNC group about our DTI pipeline.
* Modified some initial parameters and re-running the complete pipeline.

</div>
</div>

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

2011 Summer Project Week DTI analysis for Huntington's disease

2011-06-20T18:04:07Z

Gveni:

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:maxcurveFA_AtlasWerksregistered.png | maxcurveFA_registered images
</gallery>

==Key Investigators==
* University of Utah - Gopal Veni, Ross Whitaker
* University of Iowa - Hans Johnson

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

<h3>Objective</h3>

Apply our DTI pipeline to perform longitudinal analysis of HD.

</div>

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

<h3>Approach, Plan</h3>
* The pipeline mainly comprises Tensor estimation, Registration, Tractography and Statistical analysis.
* Tensor estimation and Registration (using AtlasWerks) is done on four HD data-sets.
* The next task is to perform tractography on the interested fiber tracts and do longitudinal analysis.

</div>

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

<h3>Progress</h3>

</div>
</div>

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

2011 Summer Project Week DTI analysis for Huntington's disease

2011-06-20T18:03:41Z

Gveni:

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:maxcurveFA_AtlasWerksregistered.png | maxcurveFA_registered images
</gallery>

==Key Investigators==
* University of Utah Gopal Veni, Ross Whitaker
* University of Iowa Hans Johnson

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

<h3>Objective</h3>

Apply our DTI pipeline to perform longitudinal analysis of HD.

</div>

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

<h3>Approach, Plan</h3>
* The pipeline mainly comprises Tensor estimation, Registration, Tractography and Statistical analysis.
* Tensor estimation and Registration (using AtlasWerks) is done on four HD data-sets.
* The next task is to perform tractography on the interested fiber tracts and do longitudinal analysis.

</div>

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

<h3>Progress</h3>

</div>
</div>

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

2011 Summer Project Week DTI analysis for Huntington's disease

2011-06-20T18:02:36Z

Gveni:

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:maxcurveFA_AtlasWerksregistered.png | maxcurveFA_registered images
</gallery>

==Key Investigators==
* Gopal Veni, Ross Whitaker, Hans Johnson

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

<h3>Objective</h3>

Apply our DTI pipeline to perform longitudinal analysis of HD.

</div>

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

<h3>Approach, Plan</h3>
* The pipeline mainly comprises Tensor estimation, Registration, Tractography and Statistical analysis.
* Tensor estimation and Registration (using AtlasWerks) is done on four HD data-sets.
* The next task is to perform tractography on the interested fiber tracts and do longitudinal analysis.

</div>

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

<h3>Progress</h3>

</div>
</div>

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

2011 Summer Project Week DTI analysis for Huntington's disease

2011-06-20T17:53:19Z

Gveni:

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:maxcurveFA_AtlasWerksregistered.png | maxcurveFA_registered images
</gallery>

==Key Investigators==
* University of Utah: Gopal Veni, Ross Whitaker,
* University of Iowa: Hans Johnson

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

<h3>Objective</h3>

Apply our DTI pipeline to perform longitudinal analysis of HD.

</div>

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

<h3>Approach, Plan</h3>
* The pipeline mainly comprises Tensor estimation, Registration, Tractography and Statistical analysis.
* Tensor estimation and Registration (using AtlasWerks) is done on four HD data-sets.
* The next task is to perform tractography on the interested fiber tracts and do longitudinal analysis.

</div>

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

<h3>Progress</h3>

</div>
</div>

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

2011 Summer Project Week DTI analysis for Huntington's disease

2011-06-20T17:52:54Z

Gveni:

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:maxcurveFA_AtlasWerksregistered.png | maxcurveFA_AtlasWerksregistered images
</gallery>

==Key Investigators==
* University of Utah: Gopal Veni, Ross Whitaker,
* University of Iowa: Hans Johnson

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

<h3>Objective</h3>

Apply our DTI pipeline to perform longitudinal analysis of HD.

</div>

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

<h3>Approach, Plan</h3>
* The pipeline mainly comprises Tensor estimation, Registration, Tractography and Statistical analysis.
* Tensor estimation and Registration (using AtlasWerks) is done on four HD data-sets.
* The next task is to perform tractography on the interested fiber tracts and do longitudinal analysis.

</div>

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

<h3>Progress</h3>

</div>
</div>

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

2011 Summer Project Week DTI analysis for Huntington's disease

2011-06-20T17:52:30Z

Gveni:

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:File:maxcurveFA_AtlasWerksregistered.png | maxcurveFA_AtlasWerksregistered images
</gallery>

[[]]

==Key Investigators==
* University of Utah: Gopal Veni, Ross Whitaker,
* University of Iowa: Hans Johnson

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

<h3>Objective</h3>

Apply our DTI pipeline to perform longitudinal analysis of HD.

</div>

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

<h3>Approach, Plan</h3>
* The pipeline mainly comprises Tensor estimation, Registration, Tractography and Statistical analysis.
* Tensor estimation and Registration (using AtlasWerks) is done on four HD data-sets.
* The next task is to perform tractography on the interested fiber tracts and do longitudinal analysis.

</div>

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

<h3>Progress</h3>

</div>
</div>

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

File:MaxcurveFA AtlasWerksregistered.png

2011-06-20T17:51:25Z

Gveni:

2011 Summer Project Week DTI analysis for Huntington's disease

2011-06-20T17:49:34Z

Gveni:

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
</gallery>

[[File:maxcurveFA_AtlasWerksregistered.png]]

==Key Investigators==
* University of Utah: Gopal Veni, Ross Whitaker,
* University of Iowa: Hans Johnson

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

<h3>Objective</h3>

Apply our DTI pipeline to perform longitudinal analysis of HD.

</div>

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

<h3>Approach, Plan</h3>
* The pipeline mainly comprises Tensor estimation, Registration, Tractography and Statistical analysis.
* Tensor estimation and Registration (using AtlasWerks) is done on four HD data-sets.
* The next task is to perform tractography on the interested fiber tracts and do longitudinal analysis.

</div>

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

<h3>Progress</h3>

</div>
</div>

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

File:MaxcurveFA registered.png

2011-06-20T17:45:39Z

Gveni: