NAMIC Wiki - User contributions [en]

2011 Winter Project Week:MIDAS for data hosting

2011-01-10T15:08:18Z

Zach.mullen: /* Delivery Mechanism */

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Kitware: Zach Mullen
* UIowa: Hans Johnson

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

<h3>Objective</h3>
Make use of the [http://www.kitware.com/midaswiki/index.php/Main_Page MIDAS] data archiving system to host data related to tests such as baseline and comparison images.

Motivation:
* Not all users will want to build and test every module of Slicer, so they shouldn't have to download the testing data for every part of Slicer
* Encourage the optional use of testing with "large" datasets that aren't downloaded unless the "large-data" tests are configured to run
* Don't download any duplicated test data more than once

</div>

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

<h3>Approach, Plan</h3>
* MIDAS+CTest: create a thin wrapper for "add_test" calls that will allow for adding a test that references remote data on a MIDAS server in a human-readable way
* The underlying mechanism will address data by its checksum to ensure integrity and no duplication of downloads, but test creators and users shouldn't have to deal with checksums
* Create an "Easy Upload" page for the Slicer community to allow test data to be uploaded and ready to test against with as few clicks as possible
* MIDASDesktop: A GUI application for moving data between a client machine and a MIDAS server

</div>

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

<h3>Progress</h3>
* MIDAS+CTest macro has been created and is currently in use successfully with the BRAINSTools test data.
* Easy Upload page has a working prototype and requires further improvements and customization for Slicer
* MIDASDesktop: svn repo is here [https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp]

</div>
</div>

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

==Delivery Mechanism==

* Test data will be hosted publicly (with any necessary access control) on [http://midas.kitware.com midas.kitware.com]
* Test data in the Slicer4 repository will be replaced by a reference
* That site will also host the Slicer Easy Upload page.

</div>

2011 Winter Project Week:MIDAS for data hosting

2011-01-10T15:04:25Z

Zach.mullen: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Kitware: Zach Mullen
* UIowa: Hans Johnson

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

<h3>Objective</h3>
Make use of the [http://www.kitware.com/midaswiki/index.php/Main_Page MIDAS] data archiving system to host data related to tests such as baseline and comparison images.

Motivation:
* Not all users will want to build and test every module of Slicer, so they shouldn't have to download the testing data for every part of Slicer
* Encourage the optional use of testing with "large" datasets that aren't downloaded unless the "large-data" tests are configured to run
* Don't download any duplicated test data more than once

</div>

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

<h3>Approach, Plan</h3>
* MIDAS+CTest: create a thin wrapper for "add_test" calls that will allow for adding a test that references remote data on a MIDAS server in a human-readable way
* The underlying mechanism will address data by its checksum to ensure integrity and no duplication of downloads, but test creators and users shouldn't have to deal with checksums
* Create an "Easy Upload" page for the Slicer community to allow test data to be uploaded and ready to test against with as few clicks as possible
* MIDASDesktop: A GUI application for moving data between a client machine and a MIDAS server

</div>

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

<h3>Progress</h3>
* MIDAS+CTest macro has been created and is currently in use successfully with the BRAINSTools test data.
* Easy Upload page has a working prototype and requires further improvements and customization for Slicer
* MIDASDesktop: svn repo is here [https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp]

</div>
</div>

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

==Delivery Mechanism==

* Test data will be hosted publicly (with any necessary access control) on [http://midas.kitware.com midas.kitware.com]
* That site will also host the Easy Upload page.
* MIDASDesktop lives in the svn repository here: [https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp]

</div>

2011 Winter Project Week:MIDAS for data hosting

2011-01-10T15:01:59Z

Zach.mullen: /* Delivery Mechanism */

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Kitware: Zach Mullen
* UIowa: Hans Johnson

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

<h3>Objective</h3>
Make use of the [http://www.kitware.com/midaswiki/index.php/Main_Page MIDAS] data archiving system to host data related to tests such as baseline and comparison images.

Motivation:
* Not all users will want to build and test every module of Slicer, so they shouldn't have to download the testing data for every part of Slicer
* Encourage the optional use of testing with "large" datasets that aren't downloaded unless the "large-data" tests are configured to run
* Don't download any duplicated test data more than once

</div>

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

<h3>Approach, Plan</h3>
* MIDAS+CTest: create a thin wrapper for "add_test" calls that will allow for adding a test that references remote data on a MIDAS server in a human-readable way
* The underlying mechanism will address data by its checksum to ensure integrity and no duplication of downloads, but test creators and users shouldn't have to deal with checksums
* Create an "Easy Upload" page for the Slicer community to allow test data to be uploaded and ready to test against with as few clicks as possible
* MIDASDesktop: A GUI application for moving data between a client machine and a MIDAS server

</div>

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

<h3>Progress</h3>
* MIDAS+CTest macro has been created and is currently in use successfully with the BRAINSTools test data.
* Easy Upload page has a working prototype and requires further improvements and customization for Slicer
* MIDASDesktop: svn repo is here [https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp]

</div>
</div>

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

==Delivery Mechanism==

* Test data will be hosted publicly (with any necessary access control) on [http://midas.kitware.com midas.kitware.com]
* That site will also host the Easy Upload page.
* MIDASDesktop lives in the svn repository here: [https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp]

</div>

2011 Winter Project Week:MIDAS for data hosting

2011-01-10T15:01:28Z

Zach.mullen: /* Delivery Mechanism */

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Kitware: Zach Mullen
* UIowa: Hans Johnson

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

<h3>Objective</h3>
Make use of the [http://www.kitware.com/midaswiki/index.php/Main_Page MIDAS] data archiving system to host data related to tests such as baseline and comparison images.

Motivation:
* Not all users will want to build and test every module of Slicer, so they shouldn't have to download the testing data for every part of Slicer
* Encourage the optional use of testing with "large" datasets that aren't downloaded unless the "large-data" tests are configured to run
* Don't download any duplicated test data more than once

</div>

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

<h3>Approach, Plan</h3>
* MIDAS+CTest: create a thin wrapper for "add_test" calls that will allow for adding a test that references remote data on a MIDAS server in a human-readable way
* The underlying mechanism will address data by its checksum to ensure integrity and no duplication of downloads, but test creators and users shouldn't have to deal with checksums
* Create an "Easy Upload" page for the Slicer community to allow test data to be uploaded and ready to test against with as few clicks as possible
* MIDASDesktop: A GUI application for moving data between a client machine and a MIDAS server

</div>

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

<h3>Progress</h3>
* MIDAS+CTest macro has been created and is currently in use successfully with the BRAINSTools test data.
* Easy Upload page has a working prototype and requires further improvements and customization for Slicer
* MIDASDesktop: svn repo is here [https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp]

</div>
</div>

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

==Delivery Mechanism==

* Test data will be hosted publicly (with any necessary access control) on [http://midas.kitware.com]
* That site will also host the Easy Upload page.
* MIDASDesktop lives in the svn repository here: [https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp]

</div>

2011 Winter Project Week:MIDAS for data hosting

2011-01-10T15:01:10Z

Zach.mullen: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Kitware: Zach Mullen
* UIowa: Hans Johnson

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

<h3>Objective</h3>
Make use of the [http://www.kitware.com/midaswiki/index.php/Main_Page MIDAS] data archiving system to host data related to tests such as baseline and comparison images.

Motivation:
* Not all users will want to build and test every module of Slicer, so they shouldn't have to download the testing data for every part of Slicer
* Encourage the optional use of testing with "large" datasets that aren't downloaded unless the "large-data" tests are configured to run
* Don't download any duplicated test data more than once

</div>

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

<h3>Approach, Plan</h3>
* MIDAS+CTest: create a thin wrapper for "add_test" calls that will allow for adding a test that references remote data on a MIDAS server in a human-readable way
* The underlying mechanism will address data by its checksum to ensure integrity and no duplication of downloads, but test creators and users shouldn't have to deal with checksums
* Create an "Easy Upload" page for the Slicer community to allow test data to be uploaded and ready to test against with as few clicks as possible
* MIDASDesktop: A GUI application for moving data between a client machine and a MIDAS server

</div>

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

<h3>Progress</h3>
* MIDAS+CTest macro has been created and is currently in use successfully with the BRAINSTools test data.
* Easy Upload page has a working prototype and requires further improvements and customization for Slicer
* MIDASDesktop: svn repo is here [https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp]

</div>
</div>

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

==Delivery Mechanism==

* Test data will be hosted publicly (with any necessary access control) on [http://midas.kitware.com]
* That site will also host the Easy Upload page.
* MIDASDesktop lives in the svn repository here: [https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp]

</div>

2011 Winter Project Week:MIDAS for data hosting

2011-01-10T14:48:34Z

Zach.mullen: /* Delivery Mechanism */

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Kitware: Zach Mullen
* UIowa: Hans Johnson

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

<h3>Objective</h3>
Make use of the [http://www.kitware.com/midaswiki/index.php/Main_Page MIDAS] data archiving system to host data related to tests such as baseline and comparison images.
[http://public.kitware.com/Wiki/TubeTK TubeTK] is a new open-source toolkit that hosts algorithms for applications involving images of tubes.

Two driving applications:
* Surgical guidance: registering pre-operative vascular models with intra-operative images (e.g., ultrasound)
* Characterizing vascular patters: using graph theory to distinguish clinical populations based on vascular patterns (e.g., benign -vs- malignant tumors via tortuosity)

History
* June 2001, UNC released the patent on vessel extraction method from [Aylward, Bullitt 1996...]
* TubeTK released under Apache 2.0 license: includes rights to patents

</div>

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

<h3>Approach, Plan</h3>
* Python module in Slicer 4 for centerline and radius estimation of vasculature in brain MRA
** Workflow: brain envelop segmentation, seeding, extraction
* Integration with VMTK

</div>

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

<h3>Progress</h3>

</div>
</div>

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

==Delivery Mechanism==

* Test data will be hosted publicly (with any necessary access control) on [http://midas.kitware.com]
* That site will also host the Easy Upload page.
* MIDASDesktop lives in the svn repository here: [https://www.kitware.com/svn/KWPublic/trunk/MIDAS/MIDAScpp]

</div>

2011 Winter Project Week:MIDAS for data hosting

2011-01-10T14:39:36Z

Zach.mullen:

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Kitware: Zach Mullen
* UIowa: Hans Johnson

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

<h3>Objective</h3>
Make use of the [http://www.kitware.com/midaswiki/index.php/Main_Page MIDAS] data archiving system to host data related to tests such as baseline and comparison images.
[http://public.kitware.com/Wiki/TubeTK TubeTK] is a new open-source toolkit that hosts algorithms for applications involving images of tubes.

Two driving applications:
* Surgical guidance: registering pre-operative vascular models with intra-operative images (e.g., ultrasound)
* Characterizing vascular patters: using graph theory to distinguish clinical populations based on vascular patterns (e.g., benign -vs- malignant tumors via tortuosity)

History
* June 2001, UNC released the patent on vessel extraction method from [Aylward, Bullitt 1996...]
* TubeTK released under Apache 2.0 license: includes rights to patents

</div>

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

<h3>Approach, Plan</h3>
* Python module in Slicer 4 for centerline and radius estimation of vasculature in brain MRA
** Workflow: brain envelop segmentation, seeding, extraction
* Integration with VMTK

</div>

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

<h3>Progress</h3>

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as follows:

* All software written during the project week will be contributed to TubeTK, and algorithms will be incorporated into 3D Slicer as CLI applications.

</div>

2011 Winter Project Week:MIDAS for data hosting

2011-01-06T22:07:36Z

Zach.mullen:

2011 Winter Project Week:MIDAS for data hosting

2011-01-06T22:06:29Z

Zach.mullen: Created page with '__NOTOC__ <gallery> Image:PW-SLC2011.png|Projects List </gallery> ==Key Investigators== * Kitware: Zach Mullen * Iowa: Hans Johnson <div s…'

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Kitware: Zach Mullen
* Iowa: Hans Johnson

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

<h3>Objective</h3>
[http://public.kitware.com/Wiki/TubeTK TubeTK] is a new open-source toolkit that hosts algorithms for applications involving images of tubes.

Two driving applications:
* Surgical guidance: registering pre-operative vascular models with intra-operative images (e.g., ultrasound)
* Characterizing vascular patters: using graph theory to distinguish clinical populations based on vascular patterns (e.g., benign -vs- malignant tumors via tortuosity)

History
* June 2001, UNC released the patent on vessel extraction method from [Aylward, Bullitt 1996...]
* TubeTK released under Apache 2.0 license: includes rights to patents

</div>

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

<h3>Approach, Plan</h3>
* Python module in Slicer 4 for centerline and radius estimation of vasculature in brain MRA
** Workflow: brain envelop segmentation, seeding, extraction
* Integration with VMTK

</div>

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

<h3>Progress</h3>

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as follows:

* All software written during the project week will be contributed to TubeTK, and algorithms will be incorporated into 3D Slicer as CLI applications.

</div>

2011 Winter Project Week

2011-01-06T21:35:22Z

Zach.mullen: /* NA-MIC Kit Internals */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2011]], [[Events]]

__NOTOC__
[[image:PW-SLC2011.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2011#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2011#Agenda|click here for the agenda for AHM 2011 and Project Week]].

==Background==

From January 10-14, 2011, the twelfth project week for hands-on research and development activity in Image-Guided Therapy and Neuroscience 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==

=== Segmentation ===
* [[2011_Winter_Project_Week:Extension of ABC to detect pathology categories|Extension of ABC (Atlas-Based Classification) to detect pathology categories, with tests on TBI images]] (Bo Wang, Jack Van Horn, Marcel Prastawa, Guido Gerig).
* [[2011_Winter_Project_Week:Atrial_Fibrillation|Segmentation of the left atrial wall for atrial fibrillation ablation therapy]] (Behnood Gholami, Yi Gao, and Allen Tannenbaum)
* [[2011_Winter_Project_Week:The_Vascular_Modeling_Toolkit_in_3D_Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)
* [[2011_Winter_Project_Week:TubeTK_VascularImageSegmentationAndAnalysis|TubeTK for vascular image segmentation and analysis]] (Stephen Aylward, Danielle Pace, Steve Pieper)
* [[2011_Winter_Project_Week:StenosisDetector|A stenosis detector in Slicer4 using VMTK ]](Suares Tamekue, Daniel Haehn, Luca Antiga, Ron Kikinis)
* [[2011_Winter_Project_Week:MeshCurvolver|Surface Region Segmentation for Surgical Planning and Mapping ]] (Peter Karasev, Karol Chudy, Allen Tannenbaum)
* [[2011_Winter_Project_Week:SPECTRE_Integration|Integration of SPECTRE into Slicer]] (Nicole Aucoin, Min Chen)
* [[2011_Winter_Project_Week:NerveSeg|Segmentation of Nerve and Nerve Ganglia in the Spine]] (Adrian Dalca, Giovanna Danagoulian, Ehud Schmidt, Polina Golland)

=== Registration ===
*[[2011_Winter_Project_Week:RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier,Ron Kikinis)
*[[2011_Winter_Project_Week:RegistrationAnisotropy|Voxel Anisotropy and Bias Field Effects on Slicer Image Registration]] (Dominik Meier, Andriy Fedorov, William Wells) (tentative)
* [[2011_Winter_Project_Week:DTIRegistrationWizard|DTI registration & resampling wizard]] (Dominik Meier, Hans Johnson, Francois Budin, Mark Scully)
* [[2011_Winter_Project_Week:Efficient co-registration of multiple MR modalities using the ABC|Efficient co-registration of multiple MR modalities using the ABC (atlas-based classification) framework, joint visualization of multiple co-registered modalities]] (Bo Wang, Jack Van Horn, Marcel Prastawa, Guido Gerig).
* [[2011_Winter_Project_Week:DTI_MRI_Registration|DTI MRI Registration- Evaluation of registration schemes]] (Anuja Sharma, Guido Gerig)
* [[2011_Winter_Project_Week:Atlas_Registration_in_Slicer3|Atlas Registration in Slicer3]] (Daniel Haehn, Dominik Meier, Kilian Pohl, Ryan Eckbo)
* [[2011_Winter_Project_Week:RegistrationInPresenceOfAnatomicVariation|Registration in the presence of anatomic variation (sliding organ registration)]] (Danielle Pace, Marc Niethammer, Petter Risholm, Tina Kapur, Sandy Wells, Stephen Aylward)
* [[2011_Winter_Project_Week:UncertaintyVisualization|Visualizing registration uncertainty in Slicer3]] (Peter Risholm, William Wells)
* [[2011_Winter_Project_Week:LandmarkRegularization|Landmark-based registration with analytic regularization]] (Nadya Shusharina, Gregory Sharp)
* [[2011_Winter_Project_Week:DTIPipeline|DTI registration/processing pipeline in Slicer3]] (Francois Budin, Clement Vachet)

=== IGT ===
*[[2011_Winter_Project_Week:OpenIGTLink| OpenIGTLink 2.0]] (Junichi Tokuda, Nobuhiko Hata)
*[[2011_Winter_Project_Week:Osteomark|Osteormark, navigation tool for Osteotomy]] (Laurent Chauvin, Nobuhiko Hata)
*[[2011_Winter_Project_Week:Intra-ProceduralProstateMotion|Detection and compensation for prostate motion during MR-guided prostate biopsy]] (A.Fedorov, Andras Lasso)
*[[2011_Winter_Project_Week:ThinClientQtInterfaceForIGT|Thin Client QT Interface for IGT]] (Nicholas Herlambang, Steve Pieper, Julien Finet, JC)
*[[2011_Winter_Project_Week:TransformRecorderAndProcedureAnnotation|Transform recorder and (surgical) procedure annotation module]] (Tamas Ungi, Junichi Tokuda)
*[[2011_Winter_Project_Week:SurgicalToolsTracking|Surgical Tools Tracking]] (Martin Rajchl, Feng Li)
*[[2011_Winter_Project_Week:Slicer IGT Looking Forward| Slicer IGT Looking forward]] (Nobuhiko Hata, Junichi Tokuda, Andriy Fedorov, Sandy Wells, Danielle Pace)

=== Radiotherapy ===
* [[2011_Winter_Project_Week:SegEye|Segmentation of the eye structures for Adaptive Radiotherapy]] (Ivan Kolesov, Gregory Sharp, and Allen Tannenbaum)
* [[2011_Winter_Project_Week:DicomRtExport|DICOM-RT export]] (Greg Sharp, Steve Pieper)

=== Analysis ===
* [[2011_Winter_Project_Week:GAMBITCorticalThicknessAnalysis |GAMBIT - Cortical thickness analysis]] - Clement Vachet, Martin Styner
* [[2011_Winter_Project_Week:ParticleShapeAnalysis|Particle shape analysis incorporating surface normals ]] - Beatriz Paniagua, Martin Styner
* [[2011_Winter_Project_Week:NAMICShapeAnalysis |NAMIC shape analysis pipeline in Slicer 3]] - Lucile Bompard, Martin Styner, Clement Vachet, Chris Gloschat
* [[2011_Winter_Project_Week:ParticleShapeEngineering|Particle Systems for Shape Analysis]] - Josh Cates, Manasi Datar, Ross Whitaker
* [[2011_Winter_Project_Week:MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] - Bjoern Menze, Jason Crane, Beck Olson, Polina Golland

=== Informatics ===
* [[2011_Winter_Project_Week:UIowaTHPDTIData|Share all UIowa Traveling Human Phantom DTI data with NAMIC]] - Mark Scully, Hans Johnson, Zack M.
* [[2011_Winter_Project_Week:FetchMIAPI|Recode FetchMI API to work with XNAT 1.5 API]] - Dan Marcus, Misha Milchenko
* [[2011_Winter_Project_Week:XNATSceneSupport|Engineer XNAT infrastructure for handling slicer scene files]] - Dan Marcus, Misha Milchenko

=== Diffusion ===
* [[2011_Winter_Project_Week:DicomToNrrdTestSuite |Test suite for DicomToNrrdConverter]] - Mark Scully, Zach Mullen, Xiaodong Tao, Hans Johnson
* [[2011_Winter_Project_Week:DicomToNrrdRefactoring |Requirements gathering for refactoring DicomToNrrdConverter]] - Mark Scully, Xiaodong Tao, Hans Johnson
* [[2011_Winter_Project_Week:DTIPrepDocumentation |Documentation and 1st Draft Tutorial for DTIPrep]] - Clement Vachet, Mark Scully, Hans Johnson
* [[2011_Winter_Project_Week:VoxelwizeFiberDistributionFromTractography |Voxelwise fiber distribution from tractography]] - Yinpeng Li, Martin Styner
* [[2011_Winter_Project_Week:TwoTensorTracts |Two-tensor full brain tractography pipeline]] - Lauren O'Donnell, Yogesh Rathi, C-F Westin
* [[2011_Winter_Project_Week:FreeWaterElimination |Free-water elimination]] - Ofer Pasternak, Demian Wassermann, C-F Westin
* Finsler tractography in ITK - Antonio Tristan-Vega, C-F Westin
* [[Statistical analysis of WM tracts generated by Tractography and Volumetric framework]] - Gopal Veni, Ross Whitaker

=== NA-MIC Kit Internals ===

* [[2011_Winter_Project_Week:Command_line_module_logic_redesign|Command line module logic redesign]] (passing paramenters, tie into workflows) - Jim, Steve
* 64bit Windows Builds - Dave P
* Dashboards: Factory machine, subprojects, and CDash@Home - Dave P, Zack M, Steve, and Stephen
* [[2011_Winter_Project_Week:MIDAS_for_data_hosting|MIDAS for data hosting]] - Zach M and Hans
* [[2011_Winter_Project_Week:VTK_Widgets|vtkWidgets]] JC and Will, Nicole Aucoin
* [[2011_Winter_Project_Week:Annotation_module_in_Slicer4_Display_widget_intersections|Annotation module in Slicer4: Display widget intersections]] (Daniel Haehn, Nicole Aucoin, Steve Pieper)
* [[2011_Winter_Project_Week: Python and Slicer4| Python and Slicer4]]: Workflows, Scripting, and Porting - JC, Jim, Steve, and Danielle
* [[2011_Winter_Project_Week: Slice View Performance| Improve Performance of Slice Rendering in slicer3 and slicer4]] (Steve, Will, Jc, J2, Jim, Luca)
* [[2011_NAMIC_Project_week:_Real-Time_Volume_Rendering_for_Virtual_Colonoscopy| Real-Time Volume Rendering for Virtual Colonoscopy]] (Steve, Alex)
* [[2011_Winter_Project_Week:_Slicer4-ITK4_Continuous_Integration| Slicer4 - ITK4 Integration]] (Bill, Luis)

=== Execution Model ===
* [[2011_Winter_Project_Week::ExtractSEM|Extract SlicerExecutionModel (SEM) into separate entity]]. SEM is the only component needed to build modules compatible with Slicer3D, so it should be easy incorporate into external applications without all of Slicer3D. Jim, Hans
* [[2011_Winter_Project_Week:ExtendSEMXml|Extend SEM xml]] to include sections for explicit grant acknowledgements, pointers to documentation, and pointers to examples. - Hans, Andriy
* [[2011_Winter_Project_Week:SEMXMLSchema|Create a formal schema for the SEM xml so that eternal tools (i.e. nipype) can validate the xml.]] - Hans Johnson, Jim Miller, Tim Olsen
* [[2011_Winter_Project_Week:XMLToMediaWiki|Improve documentation extractor script that converts XML to MediaWiki format so that it can directly push this information into the Slicer3D MediaWiki.]] - (Wiki Systems Admin), Hans Johnson, Steve Pieper, Stephen Aylward
* [[2011_Winter_Project_Week:ExternalToolsMergingStrategies | Improve merging strategies between software that is part of externals tools and part of Slicer.]] - Mark Scully, Hans Johnson

=== Workflows and Integration ===
# [[Winter_project_week_2011_Workflows_SOA|Workflows and Service Oriented Architecture Solutions for Slicer3 Modules]] (Alexander Zaitsev, Wendy Plesniak, Charles Guttmann, Ron Kikinis)

=== 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 28th, 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 28: Engineering Infrastructure Projects
#*November 4: Engineering Infrastructure Projects
#*November 11: DPB Projects: Iowa, Outcomes from Alg Core Retreat
#*November 18: DPB Projects: MGH
#*November 25: DBP Projects, Funded External Collaborations
#*December 2: Funded External Collaborations
#*December 9: Other External Collaborations
#*December 16:Finalize Engineering Projects
#*January 6: Loose Ends
#By December 16, 2010: [[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 16, 2010: 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. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
##Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
#Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...