NAMIC Wiki - User contributions [en]

2010 Winter Project Week xnatfs

2010-01-08T15:58:14Z

Johnpaulett: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]]
Image:genuFAp.jpg|...
Image:genuFA.jpg|...
</gallery>

==Key Investigators==
* Dan Blezek
* John Paulett
* Tim Olsen
* Dan Marcus

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

<h3>Objective</h3>
Integrate Dan's work on [http://code.google.com/p/xnatfs/ xnatfs], a Webdav server for XNAT's [http://nrg.wikispaces.com/XNAT+REST+API REST API], into the the core XNAT distribution.

</div>

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

<h3>Approach, Plan</h3>
Consolidation of current capabilities into a polished version that can be distributed as a core (though experimental) component of the impending XNAT 1.4 release.
</div>

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

<h3>Progress</h3>
xnatfs currently models the REST API as a Webdav filesystem and provides access to search results within this filesystem.

We have successfully embedded xnatfs inside a standard XNAT installation.

We [http://code.google.com/p/xnatfs/wiki/ToDosAndNiceToHave identified] and started working on usability and performance aspects.
</div>
</div>

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

Project Page: http://code.google.com/p/xnatfs/

Source code:
<pre>hg clone https://xnatfs.googlecode.com/hg/ xnatfs</pre>

</div>

2010 Winter Project Week xnatfs

2010-01-08T15:57:30Z

Johnpaulett: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]]
Image:genuFAp.jpg|...
Image:genuFA.jpg|...
</gallery>

==Key Investigators==
* Dan Blezek
* John Paulett
* Tim Olsen
* Dan Marcus

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

<h3>Objective</h3>
Integrate Dan's work on [http://code.google.com/p/xnatfs/ xnatfs], a Webdav server for XNAT's [http://nrg.wikispaces.com/XNAT+REST+API REST API], into the the core XNAT distribution.

</div>

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

<h3>Approach, Plan</h3>
Consolidation of current capabilities into a polished version that can be distributed as a core (though experimental) component of the impending XNAT 1.4 release.
</div>

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

<h3>Progress</h3>
xnatfs currently models the REST API as a Webdav filesystem and provides access to search results within this filesystem.

We have successfully embedded xnatfs inside a standard XNAT installation.

We identified and started working on usability and performance aspects: http://code.google.com/p/xnatfs/wiki/ToDosAndNiceToHave
</div>
</div>

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

Project Page: http://code.google.com/p/xnatfs/

Source code:
<pre>hg clone https://xnatfs.googlecode.com/hg/ xnatfs</pre>

</div>

2010 Winter Project Week xnatfs

2010-01-08T15:54:04Z

Johnpaulett: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]]
Image:genuFAp.jpg|...
Image:genuFA.jpg|...
</gallery>

==Key Investigators==
* Dan Blezek
* John Paulett
* Tim Olsen
* Dan Marcus

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

<h3>Objective</h3>
Integrate Dan's work on [http://code.google.com/p/xnatfs/ xnatfs], a Webdav server for XNAT's [http://nrg.wikispaces.com/XNAT+REST+API REST API], into the the core XNAT distribution.

</div>

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

<h3>Approach, Plan</h3>
Consolidation of current capabilities into a polished version that can be distributed as a core (though experimental) component of the impending XNAT 1.4 release.
</div>

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

<h3>Progress</h3>
xnatfs currently models the REST API as a Webdav filesystem and provides access to search results within this filesystem.

We have successfully embedded xnatfs inside a standard XNAT installation.

We identified and started working on usability and performance aspects.
</div>
</div>

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

Project Page: http://code.google.com/p/xnatfs/

Source code:
<pre>hg clone https://xnatfs.googlecode.com/hg/ xnatfs</pre>

</div>

2010 Winter Project Week catalyst

2010-01-05T00:16:07Z

Johnpaulett:

==Key Investigators==
* Yong Gao
* Randy Gollub
* John Paulett
* Tim Olsen
* Dan Marcus

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

<h3>Objective</h3>
Provide support to the Harvard Catalyst as they work to stand up XNAT throughout their user community. Investigate the possibility that the Harvard Catalyst use case could be a model for additional CTSC sites that are also using the i2b2 framework, such as Emory University.

</div>

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

<h3>Approach, Plan</h3>
Specific open issues:
#Contributing SubjectHandler Yong wrote into DicomServer release.
#Scan Level search capabilities for queries like "find all mr sessions with a usable MPRAGE scan". According to Tim, this is not an out-of-the-box thing offered by the REST API.
#Processing and loading images in NRRD format.

</div>

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

<h3>Progress</h3>
</div>
</div>

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

</div>
==References==
<div>
[http://nrg.wikispaces.com/XNAT+Imaging+Data+Strategies http://nrg.wikispaces.com/XNAT+Imaging+Data+Strategies]

</div>

AHM2010:NA-MIC Kit Update

2010-01-04T20:31:19Z

Johnpaulett: /* XNAT */

Back to [[AHM_2010#Agenda|AHM 2010]]
==Goals==
Information about NA-MIC Kit component developments over the past year so that developers will have an idea of what new features are available for their use.

=== ITK ===

* [http://www.itk.org/Wiki/ITK_10th_Anniversary_Activities ITK turned 10 years old!]
* Slicer currently uses [http://www.kitware.com/news/home/browse/ITK?2009_09_16&ITK+3.16+Released ITK 3.16]
* [http://www.insight-journal.org/browse/publication/149 Label image classes], [http://hdl.handle.net/1926/584 Label map classes], Label map morphology
* [http://hdl.handle.net/10380/3055 Region based Level Sets]
* Improvements in Streaming large images
* QuadEdgeMesh spherical registration
** Rigid (in NAMIC Sandbox)
** Deformable (Diffeomorphic Demons) (in NAMIC Sandbox)
** Improvements in the QuadEdgeMesh filter class (in ITK to support the two above).
* Pixel coordinates consistency
* Multi-threaded registration framework (fixes)
** multi-threaded metrics
** thread-safe transforms
* Hessian-based shape descriptors
* Fractal dimensions
* [http://hdl.handle.net/1926/585 FFT based image reconstruction]

=== VTK ===
* VTK 5.4 released
* vtkWidgets
* [http://www.vtk.org/Wiki/VTK/ARB VTK ARB] formed
* [http://vtk.uservoice.com/pages/31508-general User Voice] added to gather community feedback
* [http://www.midasjournal.org/?journal=35 VTK Journal]
* [http://www.vtkedge.org/ VTK Edge] will be consolidated into VTK
* In progress:
** [http://blog.cryos.net/archives/236-VTK-New-2D-API,-Canvas-and-Charting-Features.html VTK 2D Charting]
** Informatics
** Examples makeover
** git mirror of VTK

=== Teem ===
* [http://teem.sf.net Teem] 1.11 Soon to be Released
** release branch being used in slicer3 nightly builds
** Many improvements and new features described in the [http://sourceforge.net/mailarchive/forum.php?thread_name=9FE12D1D-D52B-40F6-B793-D8AA9D2124CB%40uchicago.edu&forum_name=teem-users Teem 1.11 Change Log Message]
* Python wrappers (auto-generated by ctypeslib) now included in teem/python/ctypes; used previously for [[Two-tensor tractography in Slicer using Python and Teem]]
* The tenGage kind (for doing convolution-based measurements in tensor fields) now includes direct computation of the fiber curving (tenGageFiberCurving) and fiber dispersion (tenGageFiberDispersion) indices used in [[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev BWH)
* New [http://people.cs.uchicago.edu/~glk/ssp/ scale space partices] functionality, with applications to lung airway segmentation and white matter skeletonization from DTI
* New applications of scale-space particles for COPD with Raul San Jose (see http://www.airwayinspector.org/)
* New functionality from Thomas Schultz to implement fast crease surface extraction (see his recent TVCG paper [[http://www.ci.uchicago.edu/~schultz/papers/schultz-crease-2008.pdf]])

=== XNAT ===

* [http://groups.google.com/group/xnat_discussion/browse_thread/thread/f46581afed629a5c XNAT 1.4 RC3] available
** More robust QC modeling via xnat:qcManualAssessorData.
** New 'columns' variable for REST based listings.
** LDAP support.
** Improved memory footprint and efficiency.
** Refactored Search UI in the listing engine.
** Prebuilt XNAT images using VMWare and Virtualbox
* [http://code.google.com/p/xnatfs/ xnatfs] provides WebDav access to XNAT instances

=== GWE ===

* Interactive experiments' results browser.
* CSV and generated commands dumps and preview.
* Support for LSF and Lava cluster DRMs.
* Ability to override auto-discovered DRMs with configured ones.
* Ability to override default database installation location.
* Function to extract experiments' parameters from text files.
* Operations to delete, pause and resume experiments.
* Recommended to watch: [http://www.youtube.com/watch?v=yXdRks5Wu5Q 5 minutes demo video].

=== BatchMake ===
* Improvement in the integration of grid computing using condor.
* Semi-Automatic conversion of Slicer modules for batch processing
* Parameter exploration is now possible
* Execution of algorithms are faster

=== CMake/CPack/CTest/CDash ===
* parallel ctest (ctest -j)
* cpack
* conversion to cmake in-progress
* linkage between CTest and MIDAS in progress
** Host large datasets for algorithm validation and performance testing
*** Demonstrated using RegisterImages

=== 3D Slicer ===
* List of new modules and features (TBD)
** See here for a list of [http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.5#List_of_Modules_new_to_3.5 modules new to 3.5].
* 3.4/3.4.1 release information
* Extension Architecture and Extension Modules
* ARRA Supplement Projects
* Qt Port (lead in to Julien's 8:30 session)
** Co-existence of KWWidgets and Qt
** Creation of a subset of the needed Qt widgets
** Full port in Qt of first modules
** Design of the core architecture in Qt (plugin mechanism, Command line modules, widget libraries...)
** Tutorials for the slicer developer community to port modules
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Developers:Projects:QtSlicer/Gallery Gallery] and [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Developers:Projects:QtSlicer/Tutorials Tutorials]
* More info on the [http://www.slicer.org/slicerWiki/index.php/Main_Page#News Slicer wiki News Page]
* multi-camera view in Slicer (endoscopy application)

=== Other Topics ===

* [http://Commontk.org Common Toolkit]

AHM2010:NA-MIC Kit Update

2009-12-31T21:14:45Z

Johnpaulett: /* Goals */

Back to [[AHM_2010#Agenda|AHM 2010]]
==Goals==
Information about NA-MIC Kit component developments over the past year so that developers will have an idea of what new features are available for their use.

=== ITK ===

* Label image classes
* QuadEdgeMesh spherical registration
** Rigid
** Deformable (Diffeomorphic Demons)
* Region based Level Sets
* Pixel coordinates consistency
* Multi-threaded registration framework
** multi-threaded metrics
** thread-safe transforms

=== VTK ===
* vtkWidgets

=== Teem ===
* [http://teem.sf.net Teem] 1.11 Soon to be Released
** release branch being used in slicer3 nightly builds
** Many improvements and new features described in the [http://sourceforge.net/mailarchive/forum.php?thread_name=9FE12D1D-D52B-40F6-B793-D8AA9D2124CB%40uchicago.edu&forum_name=teem-users Teem 1.11 Change Log Message]
* New [http://people.cs.uchicago.edu/~glk/ssp/ scale space crease] functionality
* New applications for COPD with Raul San Jose (see http://www.airwayinspector.org/)

=== XNAT ===

* [http://groups.google.com/group/xnat_discussion/browse_thread/thread/f46581afed629a5c XNAT 1.4 RC3] available
** More robust QC modeling via xnat:qcManualAssessorData.
** New 'columns' variable for REST based listings.
** LDAP support.
** Improved memory footprint and efficiency.
** Refactored Search UI in the listing engine.
* [http://code.google.com/p/xnatfs/ xnatfs] provides WebDav access to XNAT instances

=== GWE ===

* Interactive experiments' results browser.
* CSV and generated commands dumps and preview.
* Support for LSF and Lava cluster DRMs.
* Ability to override auto-discovered DRMs with configured ones.
* Ability to override default database installation location.
* Function to extract experiments' parameters from text files.
* Operations to delete, pause and resume experiments.
* Recommended to watch: [http://www.youtube.com/watch?v=yXdRks5Wu5Q 5 minutes demo video].

=== BatchMake ===
* Improvement in the integration of grid computing using condor.
* Semi-Automatic conversion of Slicer modules for batch processing
* Parameter exploration is now possible
* Execution of algorithms are faster

=== CMake/CPack/CTest/CDash ===
* parallel ctest (ctest -j)
* cpack
* conversion to cmake in-progress
* linkage between CTest and MIDAS in progress
** Host large datasets for algorithm validation and performance testing
*** Demonstrated using RegisterImages

=== 3D Slicer ===
* List of new modules and features (TBD)
** See here for a list of [http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.5#List_of_Modules_new_to_3.5 modules new to 3.5].
* 3.4/3.4.1 release information
* Extension Architecture and Extension Modules
* ARRA Supplement Projects
* Qt Port (lead in to Julien's 8:30 session)
** Co-existence of KWWidgets and Qt
** Creation of a subset of the needed Qt widgets
** Full port in Qt of first modules
** Design of the core architecture in Qt (plugin mechanism, Command line modules, widget libraries...)
** Tutorials for the slicer developer community to port modules
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Developers:Projects:QtSlicer/Gallery Gallery] and [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Developers:Projects:QtSlicer/Tutorials Tutorials]
* More info on the [http://www.slicer.org/slicerWiki/index.php/Main_Page#News Slicer wiki News Page]
* multi-camera view in Slicer (endoscopy application)

=== Other Topics ===

* [http://Commontk.org Common Toolkit]

2010 Winter Project Week xnatfs

2009-12-10T22:37:39Z

Johnpaulett:

__NOTOC__
<gallery>
Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]]
Image:genuFAp.jpg|...
Image:genuFA.jpg|...
</gallery>

==Key Investigators==
* Dan Blezek
* John Paulett
* Tim Olsen
* Dan Marcus

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

<h3>Objective</h3>
Integrate Dan's work on [http://code.google.com/p/xnatfs/ xnatfs], a Webdav server for XNAT's [http://nrg.wikispaces.com/XNAT+REST+API REST API], into the the core XNAT distribution.

</div>

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

<h3>Approach, Plan</h3>
...

</div>

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

<h3>Progress</h3>
xnatfs currently models the REST API as a Webdav filesystem and provides access to search results within this filesystem.
</div>
</div>

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

Project Page: http://code.google.com/p/xnatfs/

Source code:
<pre>hg clone https://xnatfs.googlecode.com/hg/ xnatfs</pre>

</div>

2010 Winter Project Week

2009-12-10T21:29:45Z

Johnpaulett: link to xnatfs

Back to [[Project Events]], [[AHM_2010]], [[Events]]

__NOTOC__

==Background==

From January 4-8, 2010, the tenth 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 engange 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]].

== Dates.Venue.Registration ==

Please [[AHM_2010#Dates._Venue._Registration| click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2010#Agenda|click here for the agenda for AHM 2010 and Project Week]].

== Modules and extensions==

* [[Media:3DSlicer-Modules%2BExtensions-2009-11-27.ppt|Overview]]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.5#Requirements_for_Modules Requirements for modules]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.5#Introduction User-side explanations]
* [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Extensions Developer-side explanations]

==Projects==

=== Segmentation ===
#[[2010_Winter_Project_Week_Spine_Segmentation_Module_in_Slicer3|Spine Segmentation Module in Slicer3]] (Martin Loepprich, Sylvain Jaume, Polina Golland, Ron Kikinis, Steve Pieper)
#[[2010_Winter_Project_Week_The_Vascular_Modeling_Toolkit_in_3D_Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Steve Pieper)
#[[2010_Winter_Project_Week_RobustStatisticsDrivenActiveContourSegmentation|Active contour segmentation using robust statistics]] (Yi Gao, Allen Tannenbaum, GT; Andriy Fedorov, Katie Hayes Ron Kikinis, BWH)
#[[2010_Winter_Project_Week_SegmentationWizard|High Level Wizard for Segmentation of Images]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_LongitudinalLupusAnalyses|Longitudinal Analyses of Lesions in Lupus]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_MultiscaleLupusAnalyses|Multiscale Analyses of Lupus Patients]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_ProstateSeg|Prostate segmentation using shape-based method]] (Andras Lasso, Gabor Fichtinger, Yi Gao, Allen Tannenbaum, Andriy Fedorov)
#[[2010_Winter_Project_Week_TubularTreeSeg|Tubular Tree Segmentation for brain and cardiac imagery]] (Vandana Mohan, Allen Tannenbaum, GT; Marek Kubicki, BWH)
#[[2010_Winter_Project_Week_SegmentationEpicardialWall|Epicardial Wall Segmentation]] (Behnood Gholami, Yi Gao, Allen Tannenbaum, GT; Rob MacLeod, Josh Blauer, University of Utah)
#[[2010_Winter_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Matias Perez, Allen Tannenbaum, GT; Ron Kikinis, BWH)
#[[2010_Winter_Project_Week_TBISegmentation|Segmentation of TBI (Traumatic Brain Injury) Subjects from Multimodal MRI]] (Marcel Prastawa, Guido Gerig, Ron Kikinis)

=== Registration ===
#[[2010_Winter_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library Project]] (Dominik Meier, Casey Goodlett, Ron Kikinis)
#[[Tissue_Dependent_Registration|Registration with Varying Elastic Parameters]] (Petter Risholm, Sandy Wells)

=== IGT ===
# [[2010_Winter_Project_Week_Fast_Imaging_Library_%2B_Siemens_EPI]] (Scott Hoge, Nick Todd, Dennis Parker, Katie Hayes)
# [[2010_Winter_Project_Week_MRI_Guided_Robotic_Prostate_Intervention| MRI-guided Robotic Prostate Intervention]] (Andras Lasso and Junichi Tokuda)

=== Radiotherapy ===
# [[2010_Winter_Project_Week_DicomRT_Plugin]] (Greg Sharp, others)
# [[Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Vandana Mohan, Greg Sharp, Allen Tannenbaum )

=== Analysis ===
#[[2010_Winter_Project_Week_VervetMRILongitudinalAnalysis|Vervet MRI Longitudinal Analysis]] (Andriy Fedorov, Ron Rikinis, Ginger Li, Chris Wyatt)
#[[2010_WinterProject_Week_MRSIModule|MRSI Module]] (Bjoern Menze, Polina Golland)

=== Informatics ===
#XNAT Desktop User Interface (Dan M, Wendy P, Ron K)
#Slicer 3 XNAT Performance Tuning (Wendy P, Dan M, Tim Olson, Nicole Aucoin)
#Harvard CTSC XNAT (Yong Gao, Dan M, Tim Olson, John Paulett)
##Contributing SubjectHandler Yong wrote into DicomServer release.
##Scan Level search capabilities for queries like "find all mr sessions with a usable MPRAGE scan". According to Tim, this is not an out-of-the-box thing offered by the REST API.
##Processing and loading images in NRRD format.
#[[2010_Winter_Project_Week_xnatfs|xnatfs Integration into XNAT core]] (Dan Blezek, John Paulett, Tim Olsen)

=== Diffusion ===
#[[ 2010_Winter_Project_Week_HARDI_RSH|Integration of Real Spherical Harmonic basis for HARDI models]] (Luke Bloy, C-F Westin)
#[[ 2010_Winter_Project_Week_Tractography|Filtered tractography]] (James Malcolm, Peter Savadjiev, Yogesh Rathi, C-F Westin, Casey Goodlett)
#[[ 2010_Winter_Project_Week_HARDI_CONNECTIVITY|Connectivity Study of Neonatal Brain Data using HARDI Techniques]] ( Yundi(Wendy) Shi, Deepika Mahalingam, Martin Styner )
#[[ 2010_Winter_Project_Week_WM_ATLAS|Atlas-Based White Matter Segmentation]] (Lauren O'Donnell, C-F Westin, Alexandra J. Golby)
#[[2010_Winter_Project_Week_TractographyPickingEditing|Tractography Picking and Bundle Editing]] (Jim Miller)

=== Python ===

=== NA-MIC Kit Internals ===
#Testing for Extensions (Steve, Andre, Jim, Julien Jomier, Katie Hayes, Stuart Wallace)
#[[2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration|Integration of SPECTRE Java module into 3D Slicer]] (Nicole Aucoin, Aaron Carass, Min Chen)
#VTK 3D Widgets in Slicer3 (Nicole Aucoin, Karthik, Will)
#Updates to Slicer3 Colors Module (Nicole Aucoin)
#Whole Body CT/MR open source data set publishing (Dan Marcus)
#CMAKE Build process (Dave Partyka, Katie Hayes)
#Integration of XNAT Packaging for Slicer Internals (Dan, Tim Olsen, Dave Partyka, Wendy, Randy)

(Other possibilities: Plotting, Layouts)

=== NA-MIC Outreach ===
#[[AHM 2010 Tutorial Polishing | Tutorial Polishing]] (Stuart Wallace, Randy Gollub, Sonia Pujol, all contributing tutorial contest developers)

=== Execution Model ===
# [[2010_Winter_Project_Week_Qt-ing the Command Line Module | Qt-ing the Command Line Module]] (Jim Miller)
# [[2010_Winter_Project_Week_Command Line Module Simple Return Types | Simple Return Types]] (Jim Miller)

=== 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 15th, 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 15: Engineering Infrastructure Projects
#*October 22: Funded External Collaboration Projects
#*October 29: Funded External Collaboration Projects
#*November 5: DPB Projects
#*November 19: DPB Projects
#*December 3: Other/new collaborations
#*December 10: Finalize Engineering Projects
#*December 17: Loose Ends
#By December 17, 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 17, 2009: 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...

2010 Winter Project Week xnatfs

2009-12-10T21:28:14Z

Johnpaulett: Created page with '__NOTOC__ <gallery> Image:PW-SLC2010.png|Projects List Image:genuFAp.jpg|... Image:genuFA.jpg|... </gallery> ==Key Investigators== * Dan Bl…'

2010 Winter Project Week

2009-12-10T21:11:04Z

Johnpaulett: added xnatfs people

Back to [[Project Events]], [[AHM_2010]], [[Events]]

__NOTOC__

==Background==

From January 4-8, 2010, the tenth 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 engange 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]].

== Dates.Venue.Registration ==

Please [[AHM_2010#Dates._Venue._Registration| click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2010#Agenda|click here for the agenda for AHM 2010 and Project Week]].

== Modules and extensions==

* [[Media:3DSlicer-Modules%2BExtensions-2009-11-27.ppt|Overview]]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.5#Requirements_for_Modules Requirements for modules]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.5#Introduction User-side explanations]
* [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Extensions Developer-side explanations]

==Projects==

=== Segmentation ===
#[[2010_Winter_Project_Week_Spine_Segmentation_Module_in_Slicer3|Spine Segmentation Module in Slicer3]] (Martin Loepprich, Sylvain Jaume, Polina Golland, Ron Kikinis, Steve Pieper)
#[[2010_Winter_Project_Week_The_Vascular_Modeling_Toolkit_in_3D_Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Steve Pieper)
#[[2010_Winter_Project_Week_RobustStatisticsDrivenActiveContourSegmentation|Active contour segmentation using robust statistics]] (Yi Gao, Allen Tannenbaum, GT; Andriy Fedorov, Katie Hayes Ron Kikinis, BWH)
#[[2010_Winter_Project_Week_SegmentationWizard|High Level Wizard for Segmentation of Images]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_LongitudinalLupusAnalyses|Longitudinal Analyses of Lesions in Lupus]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_MultiscaleLupusAnalyses|Multiscale Analyses of Lupus Patients]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_ProstateSeg|Prostate segmentation using shape-based method]] (Andras Lasso, Gabor Fichtinger, Yi Gao, Allen Tannenbaum, Andriy Fedorov)
#[[2010_Winter_Project_Week_TubularTreeSeg|Tubular Tree Segmentation for brain and cardiac imagery]] (Vandana Mohan, Allen Tannenbaum, GT; Marek Kubicki, BWH)
#[[2010_Winter_Project_Week_SegmentationEpicardialWall|Epicardial Wall Segmentation]] (Behnood Gholami, Yi Gao, Allen Tannenbaum, GT; Rob MacLeod, Josh Blauer, University of Utah)
#[[2010_Winter_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Matias Perez, Allen Tannenbaum, GT; Ron Kikinis, BWH)
#[[2010_Winter_Project_Week_TBISegmentation|Segmentation of TBI (Traumatic Brain Injury) Subjects from Multimodal MRI]] (Marcel Prastawa, Guido Gerig, Ron Kikinis)

=== Registration ===
#[[2010_Winter_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library Project]] (Dominik Meier, Casey Goodlett, Ron Kikinis)
#[[Tissue_Dependent_Registration|Registration with Varying Elastic Parameters]] (Petter Risholm, Sandy Wells)

=== IGT ===
# [[2010_Winter_Project_Week_Fast_Imaging_Library_%2B_Siemens_EPI]] (Scott Hoge, Nick Todd, Dennis Parker, Katie Hayes)
# [[2010_Winter_Project_Week_MRI_Guided_Robotic_Prostate_Intervention| MRI-guided Robotic Prostate Intervention]] (Andras Lasso and Junichi Tokuda)

=== Radiotherapy ===
# [[2010_Winter_Project_Week_DicomRT_Plugin]] (Greg Sharp, others)
# [[Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Vandana Mohan, Greg Sharp, Allen Tannenbaum )

=== Analysis ===
#[[2010_Winter_Project_Week_VervetMRILongitudinalAnalysis|Vervet MRI Longitudinal Analysis]] (Andriy Fedorov, Ron Rikinis, Ginger Li, Chris Wyatt)
#[[2010_WinterProject_Week_MRSIModule|MRSI Module]] (Bjoern Menze, Polina Golland)

=== Informatics ===
#XNAT Desktop User Interface (Dan M, Wendy P, Ron K)
#Slicer 3 XNAT Performance Tuning (Wendy P, Dan M, Tim Olson, Nicole Aucoin)
#Harvard CTSC XNAT (Yong Gao, Dan M, Tim Olson, John Paulett)
##Contributing SubjectHandler Yong wrote into DicomServer release.
##Scan Level search capabilities for queries like "find all mr sessions with a usable MPRAGE scan". According to Tim, this is not an out-of-the-box thing offered by the REST API.
##Processing and loading images in NRRD format.
#xnatfs Integration into XNAT core (Dan Blezek, John Paulett, Tim Olsen)

=== Diffusion ===
#[[ 2010_Winter_Project_Week_HARDI_RSH|Integration of Real Spherical Harmonic basis for HARDI models]] (Luke Bloy, C-F Westin)
#[[ 2010_Winter_Project_Week_Tractography|Filtered tractography]] (James Malcolm, Peter Savadjiev, Yogesh Rathi, C-F Westin, Casey Goodlett)
#[[ 2010_Winter_Project_Week_HARDI_CONNECTIVITY|Connectivity Study of Neonatal Brain Data using HARDI Techniques]] ( Yundi(Wendy) Shi, Deepika Mahalingam, Martin Styner )
#[[ 2010_Winter_Project_Week_WM_ATLAS|Atlas-Based White Matter Segmentation]] (Lauren O'Donnell, C-F Westin, Alexandra J. Golby)
#[[2010_Winter_Project_Week_TractographyPickingEditing|Tractography Picking and Bundle Editing]] (Jim Miller)

=== Python ===

=== NA-MIC Kit Internals ===
#Testing for Extensions (Steve, Andre, Jim, Julien Jomier, Katie Hayes, Stuart Wallace)
#[[2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration|Integration of SPECTRE Java module into 3D Slicer]] (Nicole Aucoin, Aaron Carass, Min Chen)
#VTK 3D Widgets in Slicer3 (Nicole Aucoin, Karthik, Will)
#Updates to Slicer3 Colors Module (Nicole Aucoin)
#Whole Body CT/MR open source data set publishing (Dan Marcus)
#CMAKE Build process (Dave Partyka, Katie Hayes)
#Integration of XNAT Packaging for Slicer Internals (Dan, Tim Olsen, Dave Partyka, Wendy, Randy)

(Other possibilities: Plotting, Layouts)

=== NA-MIC Outreach ===
#[[AHM 2010 Tutorial Polishing | Tutorial Polishing]] (Stuart Wallace, Randy Gollub, Sonia Pujol, all contributing tutorial contest developers)

=== Execution Model ===
# [[2010_Winter_Project_Week_Qt-ing the Command Line Module | Qt-ing the Command Line Module]] (Jim Miller)
# [[2010_Winter_Project_Week_Command Line Module Simple Return Types | Simple Return Types]] (Jim Miller)

=== 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 15th, 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 15: Engineering Infrastructure Projects
#*October 22: Funded External Collaboration Projects
#*October 29: Funded External Collaboration Projects
#*November 5: DPB Projects
#*November 19: DPB Projects
#*December 3: Other/new collaborations
#*December 10: Finalize Engineering Projects
#*December 17: Loose Ends
#By December 17, 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 17, 2009: 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...

2010 Winter Project Week

2009-12-10T21:10:15Z

Johnpaulett: xnatfs project

Back to [[Project Events]], [[AHM_2010]], [[Events]]

__NOTOC__

==Background==

From January 4-8, 2010, the tenth 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 engange 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]].

== Dates.Venue.Registration ==

Please [[AHM_2010#Dates._Venue._Registration| click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2010#Agenda|click here for the agenda for AHM 2010 and Project Week]].

== Modules and extensions==

* [[Media:3DSlicer-Modules%2BExtensions-2009-11-27.ppt|Overview]]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.5#Requirements_for_Modules Requirements for modules]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.5#Introduction User-side explanations]
* [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Extensions Developer-side explanations]

==Projects==

=== Segmentation ===
#[[2010_Winter_Project_Week_Spine_Segmentation_Module_in_Slicer3|Spine Segmentation Module in Slicer3]] (Martin Loepprich, Sylvain Jaume, Polina Golland, Ron Kikinis, Steve Pieper)
#[[2010_Winter_Project_Week_The_Vascular_Modeling_Toolkit_in_3D_Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Steve Pieper)
#[[2010_Winter_Project_Week_RobustStatisticsDrivenActiveContourSegmentation|Active contour segmentation using robust statistics]] (Yi Gao, Allen Tannenbaum, GT; Andriy Fedorov, Katie Hayes Ron Kikinis, BWH)
#[[2010_Winter_Project_Week_SegmentationWizard|High Level Wizard for Segmentation of Images]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_LongitudinalLupusAnalyses|Longitudinal Analyses of Lesions in Lupus]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_MultiscaleLupusAnalyses|Multiscale Analyses of Lupus Patients]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_ProstateSeg|Prostate segmentation using shape-based method]] (Andras Lasso, Gabor Fichtinger, Yi Gao, Allen Tannenbaum, Andriy Fedorov)
#[[2010_Winter_Project_Week_TubularTreeSeg|Tubular Tree Segmentation for brain and cardiac imagery]] (Vandana Mohan, Allen Tannenbaum, GT; Marek Kubicki, BWH)
#[[2010_Winter_Project_Week_SegmentationEpicardialWall|Epicardial Wall Segmentation]] (Behnood Gholami, Yi Gao, Allen Tannenbaum, GT; Rob MacLeod, Josh Blauer, University of Utah)
#[[2010_Winter_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Matias Perez, Allen Tannenbaum, GT; Ron Kikinis, BWH)
#[[2010_Winter_Project_Week_TBISegmentation|Segmentation of TBI (Traumatic Brain Injury) Subjects from Multimodal MRI]] (Marcel Prastawa, Guido Gerig, Ron Kikinis)

=== Registration ===
#[[2010_Winter_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library Project]] (Dominik Meier, Casey Goodlett, Ron Kikinis)
#[[Tissue_Dependent_Registration|Registration with Varying Elastic Parameters]] (Petter Risholm, Sandy Wells)

=== IGT ===
# [[2010_Winter_Project_Week_Fast_Imaging_Library_%2B_Siemens_EPI]] (Scott Hoge, Nick Todd, Dennis Parker, Katie Hayes)
# [[2010_Winter_Project_Week_MRI_Guided_Robotic_Prostate_Intervention| MRI-guided Robotic Prostate Intervention]] (Andras Lasso and Junichi Tokuda)

=== Radiotherapy ===
# [[2010_Winter_Project_Week_DicomRT_Plugin]] (Greg Sharp, others)
# [[Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Vandana Mohan, Greg Sharp, Allen Tannenbaum )

=== Analysis ===
#[[2010_Winter_Project_Week_VervetMRILongitudinalAnalysis|Vervet MRI Longitudinal Analysis]] (Andriy Fedorov, Ron Rikinis, Ginger Li, Chris Wyatt)
#[[2010_WinterProject_Week_MRSIModule|MRSI Module]] (Bjoern Menze, Polina Golland)

=== Informatics ===
#XNAT Desktop User Interface (Dan M, Wendy P, Ron K)
#Slicer 3 XNAT Performance Tuning (Wendy P, Dan M, Tim Olson, Nicole Aucoin)
#Harvard CTSC XNAT (Yong Gao, Dan M, Tim Olson, John Paulett)
##Contributing SubjectHandler Yong wrote into DicomServer release.
##Scan Level search capabilities for queries like "find all mr sessions with a usable MPRAGE scan". According to Tim, this is not an out-of-the-box thing offered by the REST API.
##Processing and loading images in NRRD format.
#xnatfs Integration into XNAT core

=== Diffusion ===
#[[ 2010_Winter_Project_Week_HARDI_RSH|Integration of Real Spherical Harmonic basis for HARDI models]] (Luke Bloy, C-F Westin)
#[[ 2010_Winter_Project_Week_Tractography|Filtered tractography]] (James Malcolm, Peter Savadjiev, Yogesh Rathi, C-F Westin, Casey Goodlett)
#[[ 2010_Winter_Project_Week_HARDI_CONNECTIVITY|Connectivity Study of Neonatal Brain Data using HARDI Techniques]] ( Yundi(Wendy) Shi, Deepika Mahalingam, Martin Styner )
#[[ 2010_Winter_Project_Week_WM_ATLAS|Atlas-Based White Matter Segmentation]] (Lauren O'Donnell, C-F Westin, Alexandra J. Golby)
#[[2010_Winter_Project_Week_TractographyPickingEditing|Tractography Picking and Bundle Editing]] (Jim Miller)

=== Python ===

=== NA-MIC Kit Internals ===
#Testing for Extensions (Steve, Andre, Jim, Julien Jomier, Katie Hayes, Stuart Wallace)
#[[2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration|Integration of SPECTRE Java module into 3D Slicer]] (Nicole Aucoin, Aaron Carass, Min Chen)
#VTK 3D Widgets in Slicer3 (Nicole Aucoin, Karthik, Will)
#Updates to Slicer3 Colors Module (Nicole Aucoin)
#Whole Body CT/MR open source data set publishing (Dan Marcus)
#CMAKE Build process (Dave Partyka, Katie Hayes)
#Integration of XNAT Packaging for Slicer Internals (Dan, Tim Olsen, Dave Partyka, Wendy, Randy)

(Other possibilities: Plotting, Layouts)

=== NA-MIC Outreach ===
#[[AHM 2010 Tutorial Polishing | Tutorial Polishing]] (Stuart Wallace, Randy Gollub, Sonia Pujol, all contributing tutorial contest developers)

=== Execution Model ===
# [[2010_Winter_Project_Week_Qt-ing the Command Line Module | Qt-ing the Command Line Module]] (Jim Miller)
# [[2010_Winter_Project_Week_Command Line Module Simple Return Types | Simple Return Types]] (Jim Miller)

=== 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 15th, 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 15: Engineering Infrastructure Projects
#*October 22: Funded External Collaboration Projects
#*October 29: Funded External Collaboration Projects
#*November 5: DPB Projects
#*November 19: DPB Projects
#*December 3: Other/new collaborations
#*December 10: Finalize Engineering Projects
#*December 17: Loose Ends
#By December 17, 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 17, 2009: 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...