2009 Annual Scientific Report - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2017-07-10T17:36:56Z

Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Tkapur at 15:29, 20 May 2009

2009-05-20T15:29:21Z

Tkapur at 15:29, 20 May 2009

2009-05-20T15:29:06Z

Whitaker: /* Core 5 Timelines and Milestones */

2009-05-18T17:33:55Z

Core 5 Timelines and Milestones

Whitaker: /* Core 4 Timelines and Milestones */

2009-05-18T17:32:25Z

Core 4 Timelines and Milestones

Whitaker: /* Core 2 Timelines and Milestones */

2009-05-18T17:31:28Z

Core 2 Timelines and Milestones

Whitaker: /* Core 2 Timelines and Milestones */

2009-05-18T17:30:39Z

Core 2 Timelines and Milestones

Whitaker: /* Timelines and Milestones */

2009-05-18T17:28:59Z

Timelines and Milestones

Will: /* Advanced Algorithms */

2009-05-18T13:28:47Z

Advanced Algorithms

Will: /* Advanced Algorithms */

2009-05-18T13:24:13Z

Advanced Algorithms

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 '''Modularity and Deployment'''
-The current tutorial has been difficult for some users to implement due to the requirement that the lesion detection module be compiled locally on the user's machine.  Non-developers understandably find this to be a difficult requirement, so we are integrating the lesion segmentation code into the [http://www.slicer.org/slicerWiki/index.php/Slicer3:Loadable_Modules:Status Slicer3 loadable module project] so that pre-compiled versions of the module are available for users.  To implement this, we are following the templates provided by the [http://www.nitrc.org/projects/slicer3examples/ slicer example modules] provided on the nitrc.org website.  This infrastructure was created via a supplement to NA-MIC provided by the NITRC project.  The [http://www.nitrc.org/projects/lupuslesion/ project page on nitrc.org] is being updated as new features are added to the modules.
+The current tutorial has been difficult for some users to implement due to the requirement that the lesion detection module be compiled locally on the user's machine.  Non-developers understandably find this to be a difficult requirement, so we are integrating the lesion segmentation code into the [https://www.slicer.org/wiki/Slicer3:Loadable_Modules:Status Slicer3 loadable module project] so that pre-compiled versions of the module are available for users.  To implement this, we are following the templates provided by the [http://www.nitrc.org/projects/slicer3examples/ slicer example modules] provided on the nitrc.org website.  This infrastructure was created via a supplement to NA-MIC provided by the NITRC project.  The [http://www.nitrc.org/projects/lupuslesion/ project page on nitrc.org] is being updated as new features are added to the modules.
 '''Core Implementation Support'''
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 ===Slicer3 and the Software Framework===
-One of the major achievements of the past year has been the release of [http://www.slicer.org/slicerWiki/index.php/Documentation-3.4 version 3.4 of 3D Slicer] in May of 2009.  A number of important improvements have been made by the Engineering Core and significant new functionality has been added through other NA-MIC cores and collaborators since the release of version 3.2 in August of 2008.  A few notable examples include:
+One of the major achievements of the past year has been the release of [https://www.slicer.org/wiki/Documentation-3.4 version 3.4 of 3D Slicer] in May of 2009.  A number of important improvements have been made by the Engineering Core and significant new functionality has been added through other NA-MIC cores and collaborators since the release of version 3.2 in August of 2008.  A few notable examples include:
-* [http://www.slicer.org/slicerWiki/index.php/Modules:Saving-Documentation-3.4 An Integrated Data Save Dialog]
+* [https://www.slicer.org/wiki/Modules:Saving-Documentation-3.4 An Integrated Data Save Dialog]
-* [http://www.slicer.org/slicerWiki/index.php/Modules:Fiducials-Documentation-3.4 Significant Rework of the Fiducials Interface]
+* [https://www.slicer.org/wiki/Modules:Fiducials-Documentation-3.4 Significant Rework of the Fiducials Interface]
-* [http://www.slicer.org/slicerWiki/index.php/Modules:Slices-Documentation-3.4 A Slices Module to Support Advanced Visualization Modes]
+* [https://www.slicer.org/wiki/Modules:Slices-Documentation-3.4 A Slices Module to Support Advanced Visualization Modes]
-* [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation Significant Improvements to the Interactive Label Map Editor]
+* [https://www.slicer.org/wiki/Modules:Editor-Documentation Significant Improvements to the Interactive Label Map Editor]
-* [http://www.slicer.org/slicerWiki/index.php/Modules:ChangeTracker-Documentation-3.4 Integration of a Brain Tumor Change Tracking Module in collaboration with the Brain Science Foundation]
+* [https://www.slicer.org/wiki/Modules:ChangeTracker-Documentation-3.4 Integration of a Brain Tumor Change Tracking Module in collaboration with the Brain Science Foundation]
-* [http://www.slicer.org/slicerWiki/index.php/Modules:IA_FEMesh-Documentation-3.4 Integration of a Finite Element Meshing Module as a deliverable of the NA-MIC Collaboration Grant at the University of Iowa]
+* [https://www.slicer.org/wiki/Modules:IA_FEMesh-Documentation-3.4 Integration of a Finite Element Meshing Module as a deliverable of the NA-MIC Collaboration Grant at the University of Iowa]
-* [http://www.slicer.org/slicerWiki/index.php/Modules:FetchMI-Documentation-3.4 A Medical Informatics Interface to XNAT in collaboration with BIRN]
+* [https://www.slicer.org/wiki/Modules:FetchMI-Documentation-3.4 A Medical Informatics Interface to XNAT in collaboration with BIRN]
-* [http://www.slicer.org/slicerWiki/index.php/Slicer3:Python The Ability to Interactively Script Slicer in Python as well as Tcl]
+* [https://www.slicer.org/wiki/Slicer3:Python The Ability to Interactively Script Slicer in Python as well as Tcl]
 In addition, there have been major extensions to the diffusion imaging tools, registration tools, filters, image guided therapy, and other core changes that enhance the utility and applicability of the software.

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	Back to [[2009_Progress_Report]]		Back to [[2009_Progress_Report]]
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 | 2
 | Programming workshops
-| Yrs 1-5
+| Yrs 1--6
 | On schedule, ongoing
 |-
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 | 2
 | One-on-one mentoring, Cores 1, 2, 3
-| Yrs 1-5
+| Yrs 1--6
 | On schedule, ongoing
 |-
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 | 3
 | Regular telephone conferences
-| Yrs 1-5
+| Yrs 1-6
 | On schedule, ongoing
 |-
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 | 4
 | Slicer training modules
-| Yr 2-5
+| Yr 2-6
 | Slicer 2.x tutorials complete, More than 10 Slicer 3 tutorials and modules.
 |-
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 | 5
 | Various workshops and conferences
-| Yrs 1--5
+| Yrs 1--6
 | On schedule, ongoing
 |}

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 | 1
 | Communications
-| Yrs 1
+| Yrs 1-6
 | Complete, ongoing
 |-
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 | 2
 | Secure developer database
-| Yr 1
+| Yr 1-6
 | Complete, ongoing
 |-
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 | 4
 | Esablish support infrastructure
-| Yrs 1--5
+| Yrs 1--6
 | On schedule, ongoing
 |-
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 | 5
 | Manage NAMIC Software Releases
-| Yrs 1--5
+| Yrs 1--6
 | On schedule, ongoing
 |}

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 | 1
 | Testing infrastructure
-| Year 4
+| Year 4-6
 | Completed (testing ongoing)
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 | 3
 | Persistent testing system
-| Yr 5
+| Yr 5-6
 | Complete (ongoing support)
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 | 3
 | Automatic defect detection
-| Yr 5
+| Yr 5-6
 | Complete (ongoing support, revisions)
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 | 2
 | CableSWIG deployment
-| Yr 3
+| Yr 3-6
 | Complete (integration ongoing)
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 | 3
 | Deploy applications
-| Yr 1
+| Yr 1-6
 | Complete (ongoing)
 |-

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 | 2.3
 | Validation of shape methods on application data
-| Year 5
+| Year 5-6
 | Completed, refinements ongoing
 |-
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 | 3.2
 | Fiber statistics
-| Year 5
+| Year 5-6
 | Completed, new developments ongoing
 |-
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 | 3.3
 | Validation on real data
-| Year 5
+| Year 5-6
 | Completed, refinements ongoing
 |-
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 | 1.5
 | Joint analysis of DTI and functional data
-| Year 5
+| Year 5-6
 | Ongoing
 |-
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 | 2.4
 | Demonstration of NP shape representations on clinical hypotheses from Core 3
-| Year 5
+| Year 5-6
-| Complete
+| Complete, preparing publications.
 |-
 | '''Utah'''
 | 2.6
 | Integration into NAMIC-kit
-| Year 5
+| Year 5-6
 | In progress
 |-
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 | 2.7
 | Shape regression
-| Year 5
+| Year 5-6
 | Complete, validation ongoing.
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 | 1.3
 | Statistical shape analysis incl. patient variable
-| Year 5
+| Year 5-6
 | Complete, extensions ongoing.
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 | 2.0
 | Integration in to Slicer
-| Year 4-5
+| Year 5-6
 | Ongoing
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 | 5
 | XNAT Desktop
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+| Years 4-6
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 | XNAT Central
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 | 6.2
 | Coordinate with NAMIC sites to upload project data
-| Years 4-5
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 | Incomplete (ongoing)
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 | 6.3
 | Continue developing XNAT Central based on feedback from NAMIC sites
-| Years 4-5
+| Years 5-6
 | Complete, refinement ongoing
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 | 7.1
 | Implement web services to exchange data with Slicer, Batchmake, and other client applications
-| Years 4-5
+| Years 5-6
 |  Complete, testing ongoing
 |-

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 ** Another area of productive work was in structural analysis. Some of the advances include developing new models for tubular surface segmentation, which transforms the problem of detecting a surface in 3D to detecting a curve in 4D. Another novel local-global segmentation approach was developed that combines the advantages of local and global approaches to segmentation, by using statistics over regions that are local to each point on an evolving contour.
 ** Development of a new method for characterizing functional connectivity patterns from fMRI based on a clustering approach.
-* NAMIC work continues to be published in well regarded journals and venues. Two typical examples from the journal ''Schizophrenia Research'' include (this is just a small sampling of the approximately xxx publications in the last reporting period):
+* NAMIC work continues to be published in well regarded journals and venues. Two typical examples from the journal ''Schizophrenia Research'' include (this is just a small sampling of the approximately [XXX FILL IN] publications in the last reporting period):
 ** JJ Levitt, M Styner, et al ''Shape Abnormalities of Caudate Nucleus in Schizotypal Personality Disorder''
 ** M Kubicki, M Styner, et al. ''Reduced Interhemispheric Connectivity in Schizophrenia-Tractography Based Segmentation of the Corpus Callosum''

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 * Significant progress on developing new computational processes and algorithms is proceeding. Examples include:
 ** A Slicer3 module for performing individual regional cortical thickness analysis was completed this past year: ARCTIC (Automatic Regional Cortical ThICkness).
 ** The VCFS Stochastic Tractography roadmap project has added several pre- and postprocessing steps to the algorithm pipeline including eddy current and geometric distortion correction methods and DTI filtering. Also new methods for visualizing and quantifying stochastic tractography output, including the creation of connection probability distribution maps, have been developed.
 ** Significant progress was realized towards refining the DWI tools and applying existing implementations clinical studies, documented in seventeen publications since last year's report. Advances were seen in Fiber Tract Modeling, Clustering and Quantitative Analysis; Stochastic Tractography; Geodesic Tractography Segmentation; DTI processing and statistical tools; and Population-based analysis of white matter tracts.