https://www.na-mic.org/w/api.php?action=feedcontributions&user=Jibberger&feedformat=atomNAMIC Wiki - User contributions [en]2024-03-29T10:39:10ZUser contributionsMediaWiki 1.33.0https://www.na-mic.org/w/index.php?title=Projects:ShapeAnalysisFrameworkUsingSPHARMPDM&diff=76682Projects:ShapeAnalysisFrameworkUsingSPHARMPDM2012-06-21T13:44:38Z<p>Jibberger: </p>
<hr />
<div> Back to [[NA-MIC_Internal_Collaborations:StructuralImageAnalysis|NA-MIC Collaborations]], [[Algorithm:UNC|UNC Algorithms]], [[Algorithm:Utah|Utah Algorithms]]<br />
__NOTOC__<br />
= Shape Analysis Framework using SPHARM-PDM =<br />
<br />
[[Image:UNCShape_OverviewAnalysis_MICCAI06.gif|thumb|300px|]]<br />
<br />
The UNC shape analysis is based on an analysis framework of objects with spherical topology, described by sampled spherical harmonics SPHARM-PDM. In summary, the input of the proposed shape analysis is a set of binary segmentation of a single brain structure, such as the hippocampus or caudate. These segmentations are first processed to fill any interior holes and a minimal smoothing operation. The processed binary segmentations are converted to surface meshes, and a spherical parametrization is computed for the surface meshes using a area-preserving, distortion minimizing spherical mapping. The SPHARM description is computed from the mesh and its spherical parametrization. Using the first order ellipsoid from the spherical harmonic coefficients, the spherical parametrizations are aligned to establish correspondence across all surfaces. The SPHARM description is then sampled into a triangulated surfaces (SPHARM-PDM) via icosahedron subdivision of the spherical parametrization. These SPHARM-PDM surfaces are all spatially aligned using rigid Procrustes alignment. Group differences between groups of surfaces are computed using the standard robust Hotelling T^2 two sample metric. An alternative testing framework applies first a Generalized Linear Model and performs testing via a MANCOVA based test statistics. Statistical p-values, both raw and corrected for multiple comparisons, result in significance maps. Additional visualization of the group tests are provided via mean difference magnitude and vector maps, as well as maps of the group covariance information. The spherical parametrization allow also the calculation of the medial axis of the segmentations.<br />
<br />
The implementation has reached a stable framework and has been disseminated to several collaborating labs within NAMIC (BWH, GeorgiaTech, Utah) and many else outside of NAMIC.<br />
<br />
= Description =<br />
<br />
A considerable amount of work was spent on the development aspect of our shape analysis tools. The main visualization tool, KWMeshVisu, can be called directly from Slicer 3 for the overlay of scalar, vector and ellipsoid data onto surfaces (so-called attribution) and the application of a set of versatile colormaps. The display of a saved "attributed" surfaces is then again possible within Slicer 3 to close the loop. This lean visualization tool fills a niche and is also used in our cortical thickness analysis tool. <br />
<br />
<br />
The individual shape analysis components have also been integrated into Slicer 3 modules. While it is entirely possible to run all steps of our shape analysis pipeline by calling the individual modules, this is highly inefficient. As a result we have developed a separate shape module (ShapeAnalysisModule) to executed from within Slicer3. This tool creates a script for Batchmake to run the shape analysis pipeline as a distributed, background process. The module creates a set of MRML scenes for efficient quality control via visualizations in Slicer 3. The whole shape analysis pipeline thus becomes entirely encapsulated and accessible to the trained clinical collaborator.<br />
<br />
In addition, a novel [[ Projects:LocalStatisticalAnalysisViaPermutationTests | statistical analysis]] was incorporated that allows to control for patient covariates (such as gender, age etc) via a Generalized Linear Model and a MANCOVA based testing framework. This also enables testing of interaction between shape and continuous patient variables such as testing scores. <br />
<br />
It further noteworthy that the distribution ([http://www.nitrc.org/projects/spharm-pdm/ via NITRC]) contains open data for other researchers to evaluate novel shape analysis enhancements.<br />
<br />
Current modifications are focused on improving the Slicer visualizations, as well as enhancing the shape analysis pipeline to follow up SPHARM-PDM correspondence by a [[Projects:ParticlesForShapesAndComplexes |particle based entropy correspondence]]. The resulting surface are analyzed the exact same way as before, but with an improved correspondence.<br />
<br />
[[Image:QC_ShapeAnalysisModule_PhiColorMap.jpeg|thumb|center|900px|shapeAnalysisModule: quality control with phi colormap]]<br />
<br />
= UNC-Utah Shape Analysis Framework =<br />
<br />
[[Image:Spharm-particle.png|thumb|900px| a) SPHARM representation of a neonatal LV, color coded using the spherical parameterization b) Particle set computed using the SPHARM representation triangulated mesh as initialization]]<br />
<br />
The UNC-Utah shape analysis project uses a combined methodology of SPHARM-PDM and [[Projects:ParticlesForShapesAndComplexes | entropy-based particle correspondence]] in order to compute reliable correspondences in otherwise challenging biological shapes. SPHARM-PDM solves the correspondence problem by defining a first order ellipsoid aligned, uniform spherical parameterization for each object with correspondence established at equivalently parameterized points. However, SPHARM correspondence has shown to be inadequate for some biological shapes that are not well described by a uniform spherical parameterization. Entropy-based particle systems compute correspondence by representing surfaces as discrete point sets that does not rely in any inherent parameterization. However, they are sensitive to initialization and have little ability to recover from initial errors. The combined framework is implemented as a stand-alone Slicer3 module, which works as an end-to-end shape analysis module.<br />
<br />
= Key Investigators =<br />
* UNC Algorithms: Martin Styner, Ipek Oguz, Marc Niethammer, Beatriz Paniagua, Hongtu Zhu<br />
* Utah Algorithms: Guido Gerig<br />
<br />
= Publications =<br />
''In Print''<br />
* [http://www.na-mic.org/publications/pages/display/?search=Projects%3AShapeAnalysisFrameworkUsingSPHARMPDM NA-MIC Publications Database on Shape Analysis Framework using SPHARM-PDM]<br />
<br />
= Links =<br />
<br />
* [http://www.nitrc.org/projects/spharm-pdm NITRC SPHARM PDM page] <br />
* [[ Projects:LocalStatisticalAnalysisViaPermutationTests | Statistical shape testing framework]]<br />
* [[Engineering:Project:Shape_Analysis|Shape Analysis]]<br />
* [[Engineering:Project:UNC_Shape_AnalysisLONI_pipeline|Shape Analysis LONI pipeline]]<br />
* [[Engineering:Project:2006_AHM_Programming:MeshVisu|MeshVisu]]<br />
* [[AHM_2006:ProjectsUNCLoniShap|AHM2006 - LONI Shape]]<br />
* [[NA-MIC/Projects/Structural/Shape_Analysis/FemaleSPDCaudates|Female SPD Caudates]]<br />
* [[Algorithm:GATech:Multiscale_Shape_Analysis|UNC shape analysis with Spherical Wavelet Features]]<br />
<br />
Project Week Results: [[media:ProgWeek05ProjectDescShapeDesc.ppt|Jun 2005-1]], [[media:ProgWeek05ProjectDescStatShapeAnalFrame.ppt|Jun 2005-2]], [[media:ProgWeek05ProjectDescLONI.ppt|Jun 2005-3]], [[media:2006_AHM_Programming_Half_week_MeshVisu.ppt|Jan 2006-1]], [[media:2006_AHM_Programming_Half_week_UNCShapeLONI.ppt|Jan 2006-2]], [[media:2006_06_PW_female_SPD.ppt|Jun 2006]], [[media:2007_Project_Half_Week_ShapeAnalysis_WithSphericalWavelets.ppt|Jan 2007-1]], [[media:2007_AHM_Programming_Half_week_MeshVisu.ppt|Jan 2007-2]]<br />
<br />
[[Category:Shape Analysis]] [[Category:Slicer]]</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=Projects:ShapeAnalysisFrameworkUsingSPHARMPDM&diff=76681Projects:ShapeAnalysisFrameworkUsingSPHARMPDM2012-06-21T13:43:48Z<p>Jibberger: </p>
<hr />
<div> Back to [[NA-MIC_Internal_Collaborations:StructuralImageAnalysis|NA-MIC Collaborations]], [[Algorithm:UNC|UNC Algorithms]], [[Algorithm:Utah|Utah Algorithms]]<br />
__NOTOC__<br />
= Shape Analysis Framework using SPHARM-PDM =<br />
<br />
[[Image:UNCShape_OverviewAnalysis_MICCAI06.gif|thumb|300px|]]<br />
<br />
The UNC shape analysis is based on an analysis framework of objects with spherical topology, described by sampled spherical harmonics SPHARM-PDM. In summary, the input of the proposed shape analysis is a set of binary segmentation of a single brain structure, such as the hippocampus or caudate. These segmentations are first processed to fill any interior holes and a minimal smoothing operation. The processed binary segmentations are converted to surface meshes, and a spherical parametrization is computed for the surface meshes using a area-preserving, distortion minimizing spherical mapping. The SPHARM description is computed from the mesh and its spherical parametrization. Using the first order ellipsoid from the spherical harmonic coefficients, the spherical parametrizations are aligned to establish correspondence across all surfaces. The SPHARM description is then sampled into a triangulated surfaces (SPHARM-PDM) via icosahedron subdivision of the spherical parametrization. These SPHARM-PDM surfaces are all spatially aligned using rigid Procrustes alignment. Group differences between groups of surfaces are computed using the standard robust Hotelling T^2 two sample metric. An alternative testing framework applies first a Generalized Linear Model and performs testing via a MANCOVA based test statistics. Statistical p-values, both raw and corrected for multiple comparisons, result in significance maps. Additional visualization of the group tests are provided via mean difference magnitude and vector maps, as well as maps of the group covariance information. The spherical parametrization allow also the calculation of segmentations' medial axis.<br />
<br />
The implementation has reached a stable framework and has been disseminated to several collaborating labs within NAMIC (BWH, GeorgiaTech, Utah) and many else outside of NAMIC.<br />
<br />
= Description =<br />
<br />
A considerable amount of work was spent on the development aspect of our shape analysis tools. The main visualization tool, KWMeshVisu, can be called directly from Slicer 3 for the overlay of scalar, vector and ellipsoid data onto surfaces (so-called attribution) and the application of a set of versatile colormaps. The display of a saved "attributed" surfaces is then again possible within Slicer 3 to close the loop. This lean visualization tool fills a niche and is also used in our cortical thickness analysis tool. <br />
<br />
<br />
The individual shape analysis components have also been integrated into Slicer 3 modules. While it is entirely possible to run all steps of our shape analysis pipeline by calling the individual modules, this is highly inefficient. As a result we have developed a separate shape module (ShapeAnalysisModule) to executed from within Slicer3. This tool creates a script for Batchmake to run the shape analysis pipeline as a distributed, background process. The module creates a set of MRML scenes for efficient quality control via visualizations in Slicer 3. The whole shape analysis pipeline thus becomes entirely encapsulated and accessible to the trained clinical collaborator.<br />
<br />
In addition, a novel [[ Projects:LocalStatisticalAnalysisViaPermutationTests | statistical analysis]] was incorporated that allows to control for patient covariates (such as gender, age etc) via a Generalized Linear Model and a MANCOVA based testing framework. This also enables testing of interaction between shape and continuous patient variables such as testing scores. <br />
<br />
It further noteworthy that the distribution ([http://www.nitrc.org/projects/spharm-pdm/ via NITRC]) contains open data for other researchers to evaluate novel shape analysis enhancements.<br />
<br />
Current modifications are focused on improving the Slicer visualizations, as well as enhancing the shape analysis pipeline to follow up SPHARM-PDM correspondence by a [[Projects:ParticlesForShapesAndComplexes |particle based entropy correspondence]]. The resulting surface are analyzed the exact same way as before, but with an improved correspondence.<br />
<br />
[[Image:QC_ShapeAnalysisModule_PhiColorMap.jpeg|thumb|center|900px|shapeAnalysisModule: quality control with phi colormap]]<br />
<br />
= UNC-Utah Shape Analysis Framework =<br />
<br />
[[Image:Spharm-particle.png|thumb|900px| a) SPHARM representation of a neonatal LV, color coded using the spherical parameterization b) Particle set computed using the SPHARM representation triangulated mesh as initialization]]<br />
<br />
The UNC-Utah shape analysis project uses a combined methodology of SPHARM-PDM and [[Projects:ParticlesForShapesAndComplexes | entropy-based particle correspondence]] in order to compute reliable correspondences in otherwise challenging biological shapes. SPHARM-PDM solves the correspondence problem by defining a first order ellipsoid aligned, uniform spherical parameterization for each object with correspondence established at equivalently parameterized points. However, SPHARM correspondence has shown to be inadequate for some biological shapes that are not well described by a uniform spherical parameterization. Entropy-based particle systems compute correspondence by representing surfaces as discrete point sets that does not rely in any inherent parameterization. However, they are sensitive to initialization and have little ability to recover from initial errors. The combined framework is implemented as a stand-alone Slicer3 module, which works as an end-to-end shape analysis module.<br />
<br />
= Key Investigators =<br />
* UNC Algorithms: Martin Styner, Ipek Oguz, Marc Niethammer, Beatriz Paniagua, Hongtu Zhu<br />
* Utah Algorithms: Guido Gerig<br />
<br />
= Publications =<br />
''In Print''<br />
* [http://www.na-mic.org/publications/pages/display/?search=Projects%3AShapeAnalysisFrameworkUsingSPHARMPDM NA-MIC Publications Database on Shape Analysis Framework using SPHARM-PDM]<br />
<br />
= Links =<br />
<br />
* [http://www.nitrc.org/projects/spharm-pdm NITRC SPHARM PDM page] <br />
* [[ Projects:LocalStatisticalAnalysisViaPermutationTests | Statistical shape testing framework]]<br />
* [[Engineering:Project:Shape_Analysis|Shape Analysis]]<br />
* [[Engineering:Project:UNC_Shape_AnalysisLONI_pipeline|Shape Analysis LONI pipeline]]<br />
* [[Engineering:Project:2006_AHM_Programming:MeshVisu|MeshVisu]]<br />
* [[AHM_2006:ProjectsUNCLoniShap|AHM2006 - LONI Shape]]<br />
* [[NA-MIC/Projects/Structural/Shape_Analysis/FemaleSPDCaudates|Female SPD Caudates]]<br />
* [[Algorithm:GATech:Multiscale_Shape_Analysis|UNC shape analysis with Spherical Wavelet Features]]<br />
<br />
Project Week Results: [[media:ProgWeek05ProjectDescShapeDesc.ppt|Jun 2005-1]], [[media:ProgWeek05ProjectDescStatShapeAnalFrame.ppt|Jun 2005-2]], [[media:ProgWeek05ProjectDescLONI.ppt|Jun 2005-3]], [[media:2006_AHM_Programming_Half_week_MeshVisu.ppt|Jan 2006-1]], [[media:2006_AHM_Programming_Half_week_UNCShapeLONI.ppt|Jan 2006-2]], [[media:2006_06_PW_female_SPD.ppt|Jun 2006]], [[media:2007_Project_Half_Week_ShapeAnalysis_WithSphericalWavelets.ppt|Jan 2007-1]], [[media:2007_AHM_Programming_Half_week_MeshVisu.ppt|Jan 2007-2]]<br />
<br />
[[Category:Shape Analysis]] [[Category:Slicer]]</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=SPIE2012_Slicer&diff=73894SPIE2012 Slicer2012-02-01T16:00:24Z<p>Jibberger: </p>
<hr />
<div>Slicer4 binaries for the SPIE2012 course:<br />
<br />
*Mac OSX 10.7 (Lion) - Tested Jan 31 : [http://slicer.kitware.com/midas3/item/305 Download at Slicer MIDAS]<br />
*Windows 7 (VS 2008) : [http://slicer.kitware.com/midas3/item/310 Download at Slicer MIDAS]<br />
*Linux 64<br />
<br />
Tutorial list<br />
* DTIPrep module [[media:2012-SPIE-DTIQC.pptx | PPT]]<br />
* DICOM to NRRD conversion module [[media:2012-SPIE-DICOMToNRRDConversionTutorial.pptx | PPT ]]<br />
* FiberViewer Light module [[media:2012-SPIE-FiberViewerLightTutorial.pptx | PPT]]<br />
<br />
Timeline<br />
*Jan 20: Martin sends 1-2 slides to Sonia for overview session <br />
*Jan 20: Linux and Mac binaries ready<br />
*Jan 27: windows binaries ready<br />
*Jan 27: all draft presentations ready<br />
*Jan 31: all tutorials tested on all platforms</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=File:2012-SPIE-FiberViewerLightTutorial.pptx&diff=73893File:2012-SPIE-FiberViewerLightTutorial.pptx2012-02-01T15:59:02Z<p>Jibberger: </p>
<hr />
<div></div>Jibbergerhttps://www.na-mic.org/w/index.php?title=SPIE2012_Slicer&diff=73892SPIE2012 Slicer2012-02-01T15:27:50Z<p>Jibberger: </p>
<hr />
<div>Slicer4 binaries for the SPIE2012 course:<br />
<br />
*Mac OSX 10.7 (Lion) - Tested Jan 31 : [http://slicer.kitware.com/midas3/item/305 Download at Slicer MIDAS]<br />
*Windows 7 (VS 2008) : [http://slicer.kitware.com/midas3/item/310 Download at Slicer MIDAS]<br />
*Linux 64<br />
<br />
Tutorial list<br />
* DTIPrep module [[media:2012-SPIE-DTIQC.pptx | PPT]]<br />
* DICOM to NRRD conversion module [[media:2012-SPIE-DICOMToNRRDConversionTutorial.pptx | PPT ]]<br />
<br />
Timeline<br />
*Jan 20: Martin sends 1-2 slides to Sonia for overview session <br />
*Jan 20: Linux and Mac binaries ready<br />
*Jan 27: windows binaries ready<br />
*Jan 27: all draft presentations ready<br />
*Jan 31: all tutorials tested on all platforms</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=File:DICOMToNRRDConversionTutorial.pptx&diff=73850File:DICOMToNRRDConversionTutorial.pptx2012-01-26T20:25:24Z<p>Jibberger: uploaded a new version of "File:DICOMToNRRDConversionTutorial.pptx"</p>
<hr />
<div>Tutorial for conversion from DICOM files to Nrrd file.</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=SPIE2012_Slicer&diff=73846SPIE2012 Slicer2012-01-26T18:31:36Z<p>Jibberger: </p>
<hr />
<div>Slicer4 binaries for the SPIE2012 course:<br />
<br />
*Mac OSX 10.7 (Lion) - Tested Jan 23 : [http://slicer.kitware.com/midas3/item/285 Download at Slicer MIDAS]<br />
*Windows 7 (VS 2008)<br />
*Linux 64<br />
<br />
Tutorial list<br />
* DTIPrep module [[media:2012-SPIE-DTIQC.pptx | PPT]]<br />
* DICOM to NRRD conversion module [http://www.na-mic.org/Wiki/images/9/9d/DICOMToNRRDConversionTutorial.pptx PPT ]<br />
<br />
Timeline<br />
*Jan 20: Martin sends 1-2 slides to Sonia for overview session <br />
*Jan 20: Linux and Mac binaries ready<br />
*Jan 27: windows binaries ready<br />
*Jan 27: all draft presentations ready<br />
*Jan 31: all tutorials tested on all platforms</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=File:DICOMToNRRDConversionTutorial.pptx&diff=73845File:DICOMToNRRDConversionTutorial.pptx2012-01-26T18:29:43Z<p>Jibberger: Tutorial for conversion from DICOM files to Nrrd file.</p>
<hr />
<div>Tutorial for conversion from DICOM files to Nrrd file.</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=SPIE_2012_DTI_Workshop&diff=73800SPIE 2012 DTI Workshop2012-01-17T20:53:47Z<p>Jibberger: </p>
<hr />
<div>{| class="wikitable" border="1" cellpadding="8" cellspacing="1"<br />
| colspan="2" style="width:100px" |[[Image:spie2012.gif]]<br />
|-<br />
| style="width:50%" |[[Image:NAMIC.jpg]]<br />
| style="width:50%" |[[Image:Logo_nac.gif]]<br />
|}<br />
= Exploring Brain Connectivity in-vivo: from Theory to Practice - A hands-on analysis workshop on Diffusion MRI by the National Alliance for Medical Image Computing (NA-MIC) =<br />
<br />
'''Course Description''':<br />
[[Image:Spie2012 DTI course spujol.png|500px|right]]<br />
<br />
The development of Diffusion Tensor Magnetic Resonance Imaging (DT-MRI) has opened up the possibility of studying the complex organization of the brain's white matter in-vivo. By measuring the diffusion of water molecules in tissues, the technique gives insights into the structure and orientation of major white matter pathways, and DT-MRI findings have the potential to play a critical role in the extraction of meaningful information for diagnosis, prognosis and following of treatment response. <br />
The course will guide participants through the fundamental aspects of DT-MRI data analysis, as well as the challenges of transferring cutting-edge DT-MRI techniques to clinical routine. The format will include a series of hands-on sessions with the participants running DT-MRI analysis on their own laptops, to provide a practical experience of extracting useful clinical information from Diffusion MR images. The hands-on sessions will use DT-MRI tools from the NA-MIC toolkit, which include the 3DSlicer software, an open-source platform for medical image processing and 3D visualization used in biomedical and clinical research. Participants will be guided through an integrated workflow for exploring the brain white matter in a series of datasets that will be provided as part of the course. This event is part of the on-going effort of the NIH-funded National Alliance for Medical Image Computing (NA-MIC) to transfer the latest advances in biomedical image analysis to the scientific and clinical community.<br />
<br />
== Date and Location==<br />
The [http://spie.org/app/program/index.cfm?fuseaction=COURSE&export_id=x12534&ID=x12172&redir=x12172.xml&course_id=E0984213&event_id=896165 SC1065 course] will be held on Sunday February 5, 2012 from 1:30 pm to 5:30 pm at [http://spie.org/x12166.xml SPIE Medical Imaging 2012, San Diego, California].<br />
<br />
==Faculty ==<br />
*Sonia Pujol, Ph.D., Surgical Planning Laboratory, Brigham and Women’s Hospital, Harvard Medical School<br />
*Martin Styner, Ph.D.,Neuro Image Research and Analysis Laboratory, University of North Carolina<br />
*Guido Gerig, Ph.D., The Scientific Computing and Imaging Institute, University of Utah<br />
<br />
== Registration== <br />
To register for this course, please visit the [http://spie.org/x12166.xml SPIE 2012 conference website].<br />
<br />
== Learning Outcomes == <br />
This course will enable participants to:<br />
* identify the different components of a DT-MRI fiber tract analysis pipeline<br />
* perform DWI/DTI data quality control<br />
* visualize 3D tensor fields and diffusion-derived maps <br />
* generate 3D reconstructions of white matter tracts in a normal subject and pathological case <br />
* extract and visualize DTI fiber tract profiles <br />
* identify the current challenges inherent in using DT-MRI data in the clinics<br />
<br />
For questions related to the workshop, please send an e-mail to Sonia Pujol (spujol at bwh.harvard.edu).<br />
<br />
== Intended Audience == <br />
Scientists, engineers, and clinical researchers who are interested in learning how to use Diffusion Tensor MR Imaging for mapping the white matter of the human brain in health and disease. This course does not need any prior knwoledge, but it can ideally be combined with the course [http://spie.org/app/program/index.cfm?fuseaction=COURSE&export_id=x12534&ID=x12172&redir=x12172.xml&course_id=E0982442&event_id=896165 SC 1063: Diffusion Imaging].<br />
<br />
== Tentative Agenda ==<br />
<br />
*12:30-1:30 pm Pre-workshop installation of software and datasets<br />
*1:30-1:35 pm Introduction to the course (Sonia Pujol)<br />
*1:35-2:00 pm Fundamentals of DTI analysis (Guido Gerig)<br />
*2:00-2:10 pm Presentation of the hands-on DTI pipeline (Sonia Pujol)<br />
*2:10-2:40 pm Dicom conversion and DWI Quality Control (Martin Styner) (Dicom to Nrrd, DTIPrep)<br />
*2:40-3:45 pm General Tractography pipeline in Slicer (Sonia Pujol) (Tensor Estimation, Property computation computation, Glyphs, fiber tracking)<br />
*3:45-4:00 pm Coffee Break<br />
*4:00-4:20 pm DTI (pairwise) registration for clinical studies (Guido Gerig/Martin Styner)<br />
*4:20-4:45 pm DTI fiber profile processing and analysis (Martin Styner)<br />
*4:45-5:15 pm Towards DTI validation (Sonia Pujol)<br />
*5:15-5:30 pm Conclusion and Questions from the audience<br />
<br />
==Preparation for the hands-on sessions: Software and datasets ==<br />
The workshop combines oral presentations and instructor-led hands-on sessions with the participants working on their own laptop computers. <br />
All participants are required to come with their own laptop computer and install the software and datasets prior to the event. A minimum of 2 GB of RAM (4 GB is better) and a graphic accelerator with 256 MB (512MB is better) of on-board graphic memory are required. The 3DSlicer version 4.0 software and datasets to download will be posted a few weeks before the event on this website.<br />
<br />
The following OS will be supported: <br />
*MacOS X Lion <br />
*Windows 7 (VS 2008)<br />
*Linux 64<br />
<br />
== Slicer Community ==<br />
Participants are invited to join the [http://www.slicer.org/pages/Mailinglist Slicer user and Slicer developer community] prior to the workshop, for questions and feature requests related to the software.<br />
<br />
== Slicer4 Training Survey ==<br />
[http://www.surveymonkey.com/s/GZDXKXQ Click here to take the Slicer4 Training Survey]<br />
<br />
== Data ==<br />
[http://hdl.handle.net/1926/1759 SPIE Workshop Dataset]<br />
<br />
<br />
Back to [http://www.na-mic.org/Wiki/index.php/Events NA-MIC Events]</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=2012_Winter_Project_Week:DTIAFA&diff=736552012 Winter Project Week:DTIAFA2012-01-13T15:18:18Z<p>Jibberger: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]<br />
Image:DTIAFA1.jpg|DTIAtlasFiberAnalyzer - Top Screen<br />
Image:DTIAFA2.jpg|DTIAtlasFiberAnalyzer - Plot Window<br />
</gallery><br />
<br />
==Key Investigators==<br />
* UNC: Jean-Baptiste Berger, Benjamin Yvernault, Yundi Shi, Clement Vachet, Martin Styner<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
DTIAtlasFiberAnalyzer aims to map atlas fiber bundles to individual subjects, extract corresponding fiber profiles, gather and plot all related information (average FA map along fibers...). DTIAtlasFiberAnalyzer calls external applications, corresponding to individual steps or the framework, such as: dtitractstat, fiberprocess, and mergestatwithfiber. Once information are computed, each merged statistics on the fiber bundle can be displayed on 3D Slicer.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
Our plan for the project week is to test this tool on small datasets and meet with interested parties.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
* Test on two different group of subject<br />
* Noticing a bug on dtitractstat<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a<br />
<br />
#Slicer Module<br />
##Extension -- commandline<br />
##Extension -- loadable<br />
<br />
==References==<br />
<br />
</div></div>Jibbergerhttps://www.na-mic.org/w/index.php?title=2012_Winter_Project_Week:FVLight&diff=736542012 Winter Project Week:FVLight2012-01-13T15:16:58Z<p>Jibberger: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]<br />
Image:FV1.jpg|FiberViewerLight - Top Screen<br />
Image:FV2.jpg|FiberViewerLight - Length Screen with a plane<br />
</gallery><br />
<br />
==Key Investigators==<br />
* UNC: Jean-Baptiste Berger, Clement Vachet, Martin Styner<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
The main objective is to develop a light version of the existing tool FiberViewer. We will focus on the clustering part of Fiber Viewer such as Length, Gravity, Hausdorff, and Mean methods, but also a Normalized Cut algorithm. FiberViewerLight also provides 3D fibers visualization and 3D plane selection, for future FA analysis along fibers.<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
Our plan for the project week is to continue FiberVieweLight's development and improve its computing speed since it is a light version.<br />
<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
* Added an option to display only a percentage of a fiber bundle<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a<br />
<br />
#Slicer Module<br />
##Extension -- commandline<br />
##Extension -- loadable<br />
<br />
==References==<br />
<br />
</div></div>Jibbergerhttps://www.na-mic.org/w/index.php?title=2012_Winter_Project_Week:SPIEWorkshop&diff=736492012 Winter Project Week:SPIEWorkshop2012-01-13T15:12:31Z<p>Jibberger: </p>
<hr />
<div><gallery><br />
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]<br />
<br />
</gallery><br />
<br />
<br />
==Key Investigators==<br />
* UNC: Jean-Baptiste Berger, Clement Vachet, Martin Styner<br />
* BWH: Sonia Pujol<br />
* Utah: Guido Gerig<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
This pipeline goes from diffusion weighted images to cleaned diffusion tensor images with the possibility to highlights differences intra- or inter-subjects.<br />
We are currently preparing datasets and developing tools in order to test this pipeline. Tutorials will be made to guide users.<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
The pipeline follows those steps :<br />
* Processing of DWI images to DTI images and visualization through the current Slicer Module<br />
<br />
* DTI registration to Atlas thanks to DTI Reg<br />
<br />
* Tracking on Atlas<br />
<br />
* Cleaning fiber tracks with FiberViewer Light<br />
<br />
* Getting Statistical data with DTIAtlasFiberAnalyzer<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
* Gathering data for testing on Linux 64, Mac OS, and Windows 7 with Visual C++ 2008<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
</div><br />
<br />
<br />
==References==<br />
* [http://wiki.na-mic.org/Wiki/index.php/Projects:AtlasBasedDTIFiberAnalyzerFramework:Atlas Based DTI Fiber Analizer Framework]<br />
* [http://wiki.na-mic.org/Wiki/index.php/SPIE_2012_DTI_Workshop:SPIE 2012 DTI Workshop]</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=2012_Winter_Project_Week:SPIEWorkshop&diff=725032012 Winter Project Week:SPIEWorkshop2011-12-14T19:47:11Z<p>Jibberger: /* Key Investigators */</p>
<hr />
<div><gallery><br />
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]<br />
<br />
</gallery><br />
<br />
<br />
==Key Investigators==<br />
* UNC: Jean-Baptiste Berger, Sonia Pujol, Clement Vachet, Martin Styner<br />
* Utah: Guido Gerig<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
This pipeline goes from diffusion weighted images to cleaned diffusion tensor images with the possibility to highlights differences intra- or inter-subjects.<br />
We are currently preparing datasets and developing tools in order to test this pipeline. Tutorials will be made to guide users.<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
The pipeline follows those steps :<br />
* Processing of DWI images to DTI images and visualization through the current Slicer Module<br />
<br />
* DTI registration to Atlas thanks to DTI Reg<br />
<br />
* Tracking on Atlas<br />
<br />
* Cleaning fiber tracks with FiberViewer Light<br />
<br />
* Getting Statistical data with DTIAtlasFiberAnalyzer<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
</div><br />
<br />
<br />
==References==<br />
* [http://wiki.na-mic.org/Wiki/index.php/Projects:AtlasBasedDTIFiberAnalyzerFramework:Atlas Based DTI Fiber Analizer Framework]<br />
* [http://wiki.na-mic.org/Wiki/index.php/SPIE_2012_DTI_Workshop:SPIE 2012 DTI Workshop]</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=2012_Winter_Project_Week:SPIEWorkshop&diff=724862012 Winter Project Week:SPIEWorkshop2011-12-14T16:34:55Z<p>Jibberger: /* Key Investigators */</p>
<hr />
<div><gallery><br />
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]<br />
<br />
</gallery><br />
<br />
<br />
==Key Investigators==<br />
* UNC: Jean-Baptiste Berger, Sonia Pujol, Clement Vachet, Martin Styner<br />
* Utah: Guido Gerig<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
Pipeline to perform a quality control on DTI images, correcting motion or cleaning irrelevant fibers.<br />
Currently preparing data sets and developing tools in order to test the pipeline. Tutorials will be made to guide users.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
The pipeline follows those steps :<br />
* Processing of DWI images to DTI images and visualization through the current Slicer Module<br />
<br />
* DTI registration to Atlas thanks to DTI Reg<br />
<br />
* Tracking on Atlas<br />
<br />
* Cleaning fiber tracks with FiberViewer Light<br />
<br />
* Getting Statistical data with DTIAtlasFiberAnalyzer<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
</div><br />
<br />
<br />
==References==<br />
* [http://wiki.na-mic.org/Wiki/index.php/Projects:AtlasBasedDTIFiberAnalyzerFramework:Atlas Based DTI Fiber Analizer Framework]<br />
* [http://wiki.na-mic.org/Wiki/index.php/SPIE_2012_DTI_Workshop:SPIE 2012 DTI Workshop]</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=2012_Winter_Project_Week&diff=724852012 Winter Project Week2011-12-14T16:28:52Z<p>Jibberger: /* Predict Huntington's Disease DBP */</p>
<hr />
<div>Back to [[Project Events]], [[Events]]<br />
Back to [[Project Events]], [[AHM_2012]], [[Events]]<br />
<br />
__NOTOC__<br />
[[image:PW-SLC2012.png|300px]]<br />
<br />
== Dates.Venue.Registration ==<br />
<br />
Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.<br />
<br />
== Agenda==<br />
<br />
Please [[AHM_2012#Agenda|click here for the agenda for AHM 2012 and Project Week]].<br />
<br />
==Background==<br />
<br />
From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions. <br />
<br />
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. <br />
<br />
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.<br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
<br />
<br />
<br />
<br />
<br />
==Projects==<br />
<br />
===IGT===<br />
*Pelvic Registration (Mehdi Moradi UBC/BWH, Jan Egger, Andrey Fedorov)<br />
*iGyne (Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi)<br />
*[[2012_Winter_Project_Week:OpenIGTLink_Interface_for_Slicer4| OpenIGTLink interface for Slicer4]] (Junichi Tokuda, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)<br />
*Needle tracking (atushi yamada, radhika tibrewal, a needle navigation person)<br />
*[[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen)<br />
*[[2012_Winter_Project_Week:OsteoPlan|Surgical Planning for facial osteotomy (OsteoPlan)]] (Laurent, Noby)<br />
*Generating a hybrid MR Spectroscopic Dataset under Slicer (Isaiah Norton, Jan Egger, Tina Kapur)<br />
<br />
===Traumatic Brain Injury DBP===<br />
<br />
* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Segmentation of Serial MRI of TBI patients <br />
using Personalized Atlas Construction]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)<br />
* [[2012_Winter_Project_Week:TBIDTIAnalysis|Registration and analysis of white matter tract changes in TBI]] (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig, Martin Styner, Danielle Pace, Stephen Aylward)<br />
* [[2012_Winter_Project_Week:TBIValidation|Validation, visualization and analysis of segmentation for TBI]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)<br />
*Geometric Metamorphosis for TBI (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Danielle Pace, Stephen Aylward)<br />
* [[2012_Winter_Project_Week:TBIRegistration|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa, Danielle Pace, Stephen Aylward)<br />
* [[2012_Winter_Project_Week:TBIRegistration|Integration of unscented Kalman filter (UKF) based multi-tensor tractography in Slicer]] (Christian Baumgartner, Yogesh Rathi, Carl-Fredrik Westin)<br />
<br />
===Predict Huntington's Disease DBP===<br />
* [[2012_Winter_Project_Week:SPIEWorkshop|SPIE DTI Workshop Preparation: Perform DTI Quality Control]] (Jean-Baptiste Berger, Sonia Pujol, Guido Gerig, Clement Vachet, Martin Styner)<br />
* [[2012_Winter_Project_Week:DWIPhantom|DTI tractography phantom: a software for evaluating tractography algorithms]] (Gwendoline Roger,Yundi Shi, Clement Vachet, Martin Styner, Sylvain Gouttard)<br />
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)<br />
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)<br />
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)<br />
* [[2012_Winter_Project_Week:ShapeAnalysisSubcorticalStructuresHD|Morphometric analysis in subcortical structures in HD]] (Beatriz Paniagua, Clement Vachet, Hans Johnson, Martin Styner)<br />
* [[2012_Winter_Project_Week:DTI pipeline|Applying our DTI pipeline to analyse HD data]] (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)<br />
* [[2012_Winter_Project_Week: DTI Change Modeling | Longitudinal change modeling of fiber tracts in serial HD DTI data]] (Anuja Sharma, Hans Johnson, Guido Gerig)<br />
* [[2012_Winter_Project_Week: Continuous 4D shapes | Continuous 4d shape models from time-discrete data: Subcortical structures in HD]] (James Fishbaugh, Hans Johnson, Guido Gerig)<br />
<br />
===Atrial fibrillation DBP===<br />
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)<br />
* [[2012_Winter_Project_Week:LAWallRegistration|Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)<br />
* [[2012_Winter_Project_Week:PVRegistration|Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)<br />
* [[2012_Winter_Project_Week:RealTime|OpenIGT for realtime MRI-guided RF ablation]] (Gene Payne, Rob MacLeod, and Junichi Tokuda)<br />
<br />
===Head and Neck Cancer DBP===<br />
* A patch-based approach to the segmentation of organs of risk (Christian Wachinger, Polina Golland)<br />
* RT dose comparison tool for Slicer (Nadya Shusharina, Greg Sharp)<br />
* [[2012_Winter_Project_Week:InteractiveSegmentation|Interactive editing tools for segmentation]] (Greg Sharp, Steve Pieper)<br />
<br />
===Radiation therapy===<br />
* [[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)<br />
* [[2012_Winter_Project_Week:RTSS|RT structure set data representation]] (Greg Sharp, Andras Lasso, Steve Pieper, etc.)<br />
<br />
===Musculoskeletal System===<br />
* [[2012_Winter_Project_Week:Radnostics|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)<br />
<br />
===Registration===<br />
* [[2012_Winter_Project_Week:CMFreg|Framework for Cranio-Maxillo Facial registration in Slicer3]] (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)<br />
* [[2012_Winter_Project_Week:SlidingOrgans|Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)]]<br />
* [[2012_Winter_Project_Week:GeometricMetamorphosis|Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)]]<br />
<br />
===Shape Analysis===<br />
* [[2012_Winter_Project_Week:PNSnormals|Principal Nested Spheres Normal Consistency in ShapeWorks]] (Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)<br />
* [[2012_Winter_Project_Week:GeomIndicesSlicer4|Porting of White Matter Geometric Indices Module to Slicer4]] (Peter Savadjiev)<br />
<br />
===NA-MIC Kit Internals===<br />
*Slicer4 release (Jean-Christophe Fillion-Robin (JC), and Julien Finet (J2))<br />
*Slicer4 extensions (JC)<br />
*Slicer4 documentation (JC)<br />
*Slicer4 GUI Testing (Benjamin Long, J2, JC)<br />
*Slicer4 data on MIDAS (Josh Cates, Patrick Reynolds)<br />
*Slicer4 extension: Slicer4 Scene Views Module (Nicole Aucoin)<br />
*Slicer4 Annotations Module<br />
** File format refactor (Nicole Aucoin)<br />
** QT 3D Text rendering proof of concept (Julien Finet, Steve Pieper, Nicole Aucoin)<br />
*[[2012_Project_Week:DICOM|DICOM Networking, Database, and Slicer Integration]] (Steve, Andrey, Andras)<br />
*[[2012_Project_Week:EditorExtensions|Editor Extension Examples and Debugging]] (Steve, Andrey, Jc, Hans, Satra)<br />
*[[2012_Project_Week:ViewerControls|Redesign of the slice viewer control panels]] (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)<br />
* [[2012_Project_Week:AutomatedTesting |Automated Testing (Sonia Pujol, Steve Pieper, Jc, Benjamin)]]<br />
* Remove legacy code from slicer4 (itk, modules, build scripts) (Hans, Jim, Steve, J2, JC)<br />
*[[2012_Project_Week:BatchProcessing|Batch Processing with Slicer Modules]] (Steve, Andrey, JC, Hans, Satra)<br />
*[[2012_Project_Week:4DImageSlicer4|Support for 4D Images in Slicer4]] (Andrey, Steve, Junichi, Alex)<br />
* AIM, DICOM SR and Slicer annotations (Andrey, Steve, Nicole, Jayashree)<br />
<br />
=== Preparation ===<br />
<br />
#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] <br />
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:<br />
#*October 27: MGH DBP<br />
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics<br />
#*November 10: Utah Atrial Fibrillation DBP<br />
#*November 17: UCLA TBI DBP<br />
#*November 24: No call. thanksgiving.<br />
#*December 1: <br />
#*December 8: <br />
#*December 15:Finalize Projects <br />
#*January 5: Loose Ends<br />
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br />
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br />
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]<br />
##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)<br />
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br />
##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)<br />
#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...</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=2012_Winter_Project_Week:SPIEWorkshop&diff=724842012 Winter Project Week:SPIEWorkshop2011-12-14T16:22:41Z<p>Jibberger: </p>
<hr />
<div><gallery><br />
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]<br />
<br />
</gallery><br />
<br />
<br />
==Key Investigators==<br />
* UNC: Jean-Baptiste Berger, Sonia Pujol, Clement Vachet, Martin Styner<br />
* Utah: Guido Gerig<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
Pipeline to perform a quality control on DTI images, correcting motion or cleaning irrelevant fibers.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
The pipeline follows those steps :<br />
* Processing of DWI images to DTI images and visualization through the current Slicer Module<br />
<br />
* DTI registration to Atlas thanks to DTI Reg<br />
<br />
* Tracking on Atlas<br />
<br />
* Cleaning fiber tracks with FiberViewer Light<br />
<br />
* Getting Statistical data with DTIAtlasFiberAnalyzer<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
</div><br />
<br />
<br />
==References==<br />
* [http://wiki.na-mic.org/Wiki/index.php/Projects:AtlasBasedDTIFiberAnalyzerFramework:Atlas Based DTI Fiber Analizer Framework]<br />
* [http://wiki.na-mic.org/Wiki/index.php/SPIE_2012_DTI_Workshop:SPIE 2012 DTI Workshop]</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=2012_Winter_Project_Week&diff=724832012 Winter Project Week2011-12-14T16:16:58Z<p>Jibberger: /* Predict Huntington's Disease DBP */</p>
<hr />
<div>Back to [[Project Events]], [[Events]]<br />
Back to [[Project Events]], [[AHM_2012]], [[Events]]<br />
<br />
__NOTOC__<br />
[[image:PW-SLC2012.png|300px]]<br />
<br />
== Dates.Venue.Registration ==<br />
<br />
Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.<br />
<br />
== Agenda==<br />
<br />
Please [[AHM_2012#Agenda|click here for the agenda for AHM 2012 and Project Week]].<br />
<br />
==Background==<br />
<br />
From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions. <br />
<br />
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. <br />
<br />
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.<br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
<br />
<br />
<br />
<br />
<br />
==Projects==<br />
<br />
===IGT===<br />
*Pelvic Registration (Mehdi Moradi UBC/BWH, Jan Egger, Andrey Fedorov)<br />
*iGyne (Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi)<br />
*[[2012_Winter_Project_Week:OpenIGTLink_Interface_for_Slicer4| OpenIGTLink interface for Slicer4]] (Junichi Tokuda, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)<br />
*Needle tracking (atushi yamada, radhika tibrewal, a needle navigation person)<br />
*[[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen)<br />
*[[2012_Winter_Project_Week:OsteoPlan|Surgical Planning for facial osteotomy (OsteoPlan)]] (Laurent, Noby)<br />
*Generating a hybrid MR Spectroscopic Dataset under Slicer (Isaiah Norton, Jan Egger, Tina Kapur)<br />
<br />
===Traumatic Brain Injury DBP===<br />
<br />
* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Segmentation of Serial MRI of TBI patients <br />
using Personalized Atlas Construction]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)<br />
* [[2012_Winter_Project_Week:TBIDTIAnalysis|Registration and analysis of white matter tract changes in TBI]] (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig, Martin Styner, Danielle Pace, Stephen Aylward)<br />
* [[2012_Winter_Project_Week:TBIValidation|Validation, visualization and analysis of segmentation for TBI]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)<br />
*Geometric Metamorphosis for TBI (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Danielle Pace, Stephen Aylward)<br />
* [[2012_Winter_Project_Week:TBIRegistration|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa, Danielle Pace, Stephen Aylward)<br />
* [[2012_Winter_Project_Week:TBIRegistration|Integration of unscented Kalman filter (UKF) based multi-tensor tractography in Slicer]] (Christian Baumgartner, Yogesh Rathi, Carl-Fredrik Westin)<br />
<br />
===Predict Huntington's Disease DBP===<br />
* [[2012_Winter_Project_Week:SPIEWorkshop|SPIE Workshop: Perform DTI Quality Control]] (Jean-Baptiste Berger, Sonia Pujol, Guido Gerig, Clement Vachet, Martin Styner)<br />
* [[2012_Winter_Project_Week:DWIPhantom|DTI tractography phantom: a software for evaluating tractography algorithms]] (Gwendoline Roger,Yundi Shi, Clement Vachet, Martin Styner, Sylvain Gouttard)<br />
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)<br />
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)<br />
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)<br />
* [[2012_Winter_Project_Week:ShapeAnalysisSubcorticalStructuresHD|Morphometric analysis in subcortical structures in HD]] (Beatriz Paniagua, Clement Vachet, Hans Johnson, Martin Styner)<br />
* [[2012_Winter_Project_Week:DTI pipeline|Applying our DTI pipeline to analyse HD data]] (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)<br />
* [[2012_Winter_Project_Week: DTI Change Modeling | Longitudinal change modeling of fiber tracts in serial HD DTI data]] (Anuja Sharma, Hans Johnson, Guido Gerig)<br />
* [[2012_Winter_Project_Week: Continuous 4D shapes | Continuous 4d shape models from time-discrete data: Subcortical structures in HD]] (James Fishbaugh, Hans Johnson, Guido Gerig)<br />
<br />
===Atrial fibrillation DBP===<br />
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)<br />
* [[2012_Winter_Project_Week:LAWallRegistration|Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)<br />
* [[2012_Winter_Project_Week:PVRegistration|Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)<br />
* [[2012_Winter_Project_Week:RealTime|OpenIGT for realtime MRI-guided RF ablation]] (Gene Payne, Rob MacLeod, and Junichi Tokuda)<br />
<br />
===Head and Neck Cancer DBP===<br />
* A patch-based approach to the segmentation of organs of risk (Christian Wachinger, Polina Golland)<br />
* RT dose comparison tool for Slicer (Nadya Shusharina, Greg Sharp)<br />
* [[2012_Winter_Project_Week:InteractiveSegmentation|Interactive editing tools for segmentation]] (Greg Sharp, Steve Pieper)<br />
<br />
===Radiation therapy===<br />
* [[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)<br />
* [[2012_Winter_Project_Week:RTSS|RT structure set data representation]] (Greg Sharp, Andras Lasso, Steve Pieper, etc.)<br />
<br />
===Musculoskeletal System===<br />
* [[2012_Winter_Project_Week:Radnostics|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)<br />
<br />
===Registration===<br />
* [[2012_Winter_Project_Week:CMFreg|Framework for Cranio-Maxillo Facial registration in Slicer3]] (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)<br />
* [[2012_Winter_Project_Week:SlidingOrgans|Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)]]<br />
* [[2012_Winter_Project_Week:GeometricMetamorphosis|Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)]]<br />
<br />
===Shape Analysis===<br />
* [[2012_Winter_Project_Week:PNSnormals|Principal Nested Spheres Normal Consistency in ShapeWorks]] (Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)<br />
* [[2012_Winter_Project_Week:GeomIndicesSlicer4|Porting of White Matter Geometric Indices Module to Slicer4]] (Peter Savadjiev)<br />
<br />
===NA-MIC Kit Internals===<br />
*Slicer4 release (Jean-Christophe Fillion-Robin (JC), and Julien Finet (J2))<br />
*Slicer4 extensions (JC)<br />
*Slicer4 documentation (JC)<br />
*Slicer4 GUI Testing (Benjamin Long, J2, JC)<br />
*Slicer4 data on MIDAS (Josh Cates, Patrick Reynolds)<br />
*Slicer4 extension: Slicer4 Scene Views Module (Nicole Aucoin)<br />
*Slicer4 Annotations Module<br />
** File format refactor (Nicole Aucoin)<br />
** QT 3D Text rendering proof of concept (Julien Finet, Steve Pieper, Nicole Aucoin)<br />
*[[2012_Project_Week:DICOM|DICOM Networking, Database, and Slicer Integration]] (Steve, Andrey, Andras)<br />
*[[2012_Project_Week:EditorExtensions|Editor Extension Examples and Debugging]] (Steve, Andrey, Jc, Hans, Satra)<br />
*[[2012_Project_Week:ViewerControls|Redesign of the slice viewer control panels]] (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)<br />
* [[2012_Project_Week:AutomatedTesting |Automated Testing (Sonia Pujol, Steve Pieper, Jc, Benjamin)]]<br />
* Remove legacy code from slicer4 (itk, modules, build scripts) (Hans, Jim, Steve, J2, JC)<br />
*[[2012_Project_Week:BatchProcessing|Batch Processing with Slicer Modules]] (Steve, Andrey, JC, Hans, Satra)<br />
*[[2012_Project_Week:4DImageSlicer4|Support for 4D Images in Slicer4]] (Andrey, Steve, Junichi, Alex)<br />
* AIM, DICOM SR and Slicer annotations (Andrey, Steve, Nicole, Jayashree)<br />
<br />
=== Preparation ===<br />
<br />
#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] <br />
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:<br />
#*October 27: MGH DBP<br />
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics<br />
#*November 10: Utah Atrial Fibrillation DBP<br />
#*November 17: UCLA TBI DBP<br />
#*November 24: No call. thanksgiving.<br />
#*December 1: <br />
#*December 8: <br />
#*December 15:Finalize Projects <br />
#*January 5: Loose Ends<br />
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br />
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br />
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]<br />
##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)<br />
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br />
##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)<br />
#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...</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=2012_Winter_Project_Week:SPIEWorkshop&diff=724822012 Winter Project Week:SPIEWorkshop2011-12-14T16:16:03Z<p>Jibberger: /* Key Investigators */</p>
<hr />
<div><gallery><br />
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]<br />
<br />
</gallery><br />
<br />
<br />
==Key Investigators==<br />
* UNC: Jean-Baptiste Berger, Sonia Pujol, Clement Vachet, Martin Styner<br />
* Utah: Guido Gerig<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
Pipeline to perform a quality control on DTI images, correcting motion or cleaning irrelevant fibers.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
The pipeline follows those steps :<br />
* Processing of DWI images to DTI images and visualization through the current Slicer Module<br />
<br />
* DTI registration to Atlas thanks to DTI Reg<br />
<br />
* Tracking on Atlas<br />
<br />
* Cleaning fiber tracks with FiberViewer Light<br />
<br />
* Getting Statistical data with DTIAtlasFiberAnalyzer<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
</div><br />
<br />
<br />
==References==</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=2012_Winter_Project_Week:SPIEWorkshop&diff=724812012 Winter Project Week:SPIEWorkshop2011-12-14T16:03:26Z<p>Jibberger: Created page with '<gallery> Image:PW-SLC2012.png|Projects List </gallery> ==Key Investigators== * UNC: Sonia Pujol, Jean-Baptiste Berger, Clement Vachet, M…'</p>
<hr />
<div><gallery><br />
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]<br />
<br />
</gallery><br />
<br />
<br />
==Key Investigators==<br />
* UNC: Sonia Pujol, Jean-Baptiste Berger, Clement Vachet, Martin Styner<br />
* Utah: Guido Gerig<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
Pipeline to perform a quality control on DTI images, correcting motion or cleaning irrelevant fibers.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
The pipeline follows those steps :<br />
* Processing of DWI images to DTI images and visualization through the current Slicer Module<br />
<br />
* DTI registration to Atlas thanks to DTI Reg<br />
<br />
* Tracking on Atlas<br />
<br />
* Cleaning fiber tracks with FiberViewer Light<br />
<br />
* Getting Statistical data with DTIAtlasFiberAnalyzer<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
</div><br />
<br />
<br />
==References==</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=2012_Winter_Project_Week&diff=724802012 Winter Project Week2011-12-14T14:47:53Z<p>Jibberger: /* Predict Huntington's Disease DBP */</p>
<hr />
<div>Back to [[Project Events]], [[Events]]<br />
Back to [[Project Events]], [[AHM_2012]], [[Events]]<br />
<br />
__NOTOC__<br />
[[image:PW-SLC2012.png|300px]]<br />
<br />
== Dates.Venue.Registration ==<br />
<br />
Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.<br />
<br />
== Agenda==<br />
<br />
Please [[AHM_2012#Agenda|click here for the agenda for AHM 2012 and Project Week]].<br />
<br />
==Background==<br />
<br />
From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions. <br />
<br />
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. <br />
<br />
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.<br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
<br />
<br />
<br />
<br />
<br />
==Projects==<br />
<br />
===IGT===<br />
*Pelvic Registration (Mehdi Moradi UBC/BWH, Jan Egger, Andrey Fedorov)<br />
*iGyne (Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi)<br />
*[[2012_Winter_Project_Week:OpenIGTLink_Interface_for_Slicer4| OpenIGTLink interface for Slicer4]] (Junichi Tokuda, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)<br />
*Needle tracking (atushi yamada, radhika tibrewal, a needle navigation person)<br />
*[[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen)<br />
*[[2012_Winter_Project_Week:OsteoPlan|Surgical Planning for facial osteotomy (OsteoPlan)]] (Laurent, Noby)<br />
*Generating a hybrid MR Spectroscopic Dataset under Slicer (Isaiah Norton, Jan Egger, Tina Kapur)<br />
<br />
===Traumatic Brain Injury DBP===<br />
<br />
* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Segmentation of Serial MRI of TBI patients <br />
using Personalized Atlas Construction]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)<br />
* [[2012_Winter_Project_Week:TBIDTIAnalysis|Registration and analysis of white matter tract changes in TBI]] (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig, Martin Styner, Danielle Pace, Stephen Aylward)<br />
* [[2012_Winter_Project_Week:TBIValidation|Validation, visualization and analysis of segmentation for TBI]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)<br />
*Geometric Metamorphosis for TBI (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Danielle Pace, Stephen Aylward)<br />
* [[2012_Winter_Project_Week:TBIRegistration|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa, Danielle Pace, Stephen Aylward)<br />
* [[2012_Winter_Project_Week:TBIRegistration|Integration of unscented Kalman filter (UKF) based multi-tensor tractography in Slicer]] (Christian Baumgartner, Yogesh Rathi, Carl-Fredrik Westin)<br />
<br />
===Predict Huntington's Disease DBP===<br />
* [[2012_Winter_Project_Week:SPIEWorkshop|SPIE Workshop: Perform DTI Quality Control]] (Sonia Pujol, Jean-Baptiste Berger, Guido Gerig, Clement Vachet, Martin Styner)<br />
* [[2012_Winter_Project_Week:DWIPhantom|DTI tractography phantom: a software for evaluating tractography algorithms]] (Gwendoline Roger,Yundi Shi, Clement Vachet, Martin Styner, Sylvain Gouttard)<br />
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)<br />
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)<br />
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)<br />
* [[2012_Winter_Project_Week:ShapeAnalysisSubcorticalStructuresHD|Morphometric analysis in subcortical structures in HD]] (Beatriz Paniagua, Clement Vachet, Hans Johnson, Martin Styner)<br />
* [[2012_Winter_Project_Week:DTI pipeline|Applying our DTI pipeline to analyse HD data]] (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)<br />
* [[2012_Winter_Project_Week: DTI Change Modeling | Longitudinal change modeling of fiber tracts in serial HD DTI data]] (Anuja Sharma, Hans Johnson, Guido Gerig)<br />
* [[2012_Winter_Project_Week: Continuous 4D shapes | Continuous 4d shape models from time-discrete data: Subcortical structures in HD]] (James Fishbaugh, Hans Johnson, Guido Gerig)<br />
<br />
===Atrial fibrillation DBP===<br />
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)<br />
* [[2012_Winter_Project_Week:LAWallRegistration|Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)<br />
* [[2012_Winter_Project_Week:PVRegistration|Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)<br />
* [[2012_Winter_Project_Week:RealTime|OpenIGT for realtime MRI-guided RF ablation]] (Gene Payne, Rob MacLeod, and Junichi Tokuda)<br />
<br />
===Head and Neck Cancer DBP===<br />
* A patch-based approach to the segmentation of organs of risk (Christian Wachinger, Polina Golland)<br />
* RT dose comparison tool for Slicer (Nadya Shusharina, Greg Sharp)<br />
* [[2012_Winter_Project_Week:InteractiveSegmentation|Interactive editing tools for segmentation]] (Greg Sharp, Steve Pieper)<br />
<br />
===Radiation therapy===<br />
* [[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)<br />
* [[2012_Winter_Project_Week:RTSS|RT structure set data representation]] (Greg Sharp, Andras Lasso, Steve Pieper, etc.)<br />
<br />
===Musculoskeletal System===<br />
* [[2012_Winter_Project_Week:Radnostics|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)<br />
<br />
===Registration===<br />
* [[2012_Winter_Project_Week:CMFreg|Framework for Cranio-Maxillo Facial registration in Slicer3]] (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)<br />
* [[2012_Winter_Project_Week:SlidingOrgans|Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)]]<br />
* [[2012_Winter_Project_Week:GeometricMetamorphosis|Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)]]<br />
<br />
===Shape Analysis===<br />
* [[2012_Winter_Project_Week:PNSnormals|Principal Nested Spheres Normal Consistency in ShapeWorks]] (Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)<br />
* [[2012_Winter_Project_Week:GeomIndicesSlicer4|Porting of White Matter Geometric Indices Module to Slicer4]] (Peter Savadjiev)<br />
<br />
===NA-MIC Kit Internals===<br />
*Slicer4 release (Jean-Christophe Fillion-Robin (JC), and Julien Finet (J2))<br />
*Slicer4 extensions (JC)<br />
*Slicer4 documentation (JC)<br />
*Slicer4 GUI Testing (Benjamin Long, J2, JC)<br />
*Slicer4 data on MIDAS (Josh Cates, Patrick Reynolds)<br />
*Slicer4 extension: Slicer4 Scene Views Module (Nicole Aucoin)<br />
*Slicer4 Annotations Module<br />
** File format refactor (Nicole Aucoin)<br />
** QT 3D Text rendering proof of concept (Julien Finet, Steve Pieper, Nicole Aucoin)<br />
*[[2012_Project_Week:DICOM|DICOM Networking, Database, and Slicer Integration]] (Steve, Andrey, Andras)<br />
*[[2012_Project_Week:EditorExtensions|Editor Extension Examples and Debugging]] (Steve, Andrey, Jc, Hans, Satra)<br />
*[[2012_Project_Week:ViewerControls|Redesign of the slice viewer control panels]] (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)<br />
* [[2012_Project_Week:AutomatedTesting |Automated Testing (Sonia Pujol, Steve Pieper, Jc, Benjamin)]]<br />
* Remove legacy code from slicer4 (itk, modules, build scripts) (Hans, Jim, Steve, J2, JC)<br />
*[[2012_Project_Week:BatchProcessing|Batch Processing with Slicer Modules]] (Steve, Andrey, JC, Hans, Satra)<br />
*[[2012_Project_Week:4DImageSlicer4|Support for 4D Images in Slicer4]] (Andrey, Steve, Junichi, Alex)<br />
* AIM, DICOM SR and Slicer annotations (Andrey, Steve, Nicole, Jayashree)<br />
<br />
=== Preparation ===<br />
<br />
#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] <br />
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:<br />
#*October 27: MGH DBP<br />
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics<br />
#*November 10: Utah Atrial Fibrillation DBP<br />
#*November 17: UCLA TBI DBP<br />
#*November 24: No call. thanksgiving.<br />
#*December 1: <br />
#*December 8: <br />
#*December 15:Finalize Projects <br />
#*January 5: Loose Ends<br />
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br />
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br />
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]<br />
##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)<br />
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br />
##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)<br />
#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...</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=Projects:AtlasBasedDTIFiberAnalyzerFramework&diff=71995Projects:AtlasBasedDTIFiberAnalyzerFramework2011-11-22T15:56:14Z<p>Jibberger: /* Description */</p>
<hr />
<div> Back to [[Algorithm:UNC|UNC Algorithms]]<br />
__NOTOC__<br />
<br />
= Atlas Based DTI FIber Analyzer Framework =<br />
<br />
This projects gather some tools aiming at completing each step required to build an Atlas. Concerning the first step as the creation and the mapping of the Atlas, DWI QC will be the appropriate tool. Then comes the tractography followed by a postprocessing step easily done by FiberViewer Light. Finally we will gather statistics thanks to DTI Atlas Fiber Analyzer.<br />
<br />
= Description =<br />
[[Image:AtlasBuilderLogo.jpg|thumb|300px|Length analysis of Cingulum tractography. Colors go from red to blue where red ones are the longest and blue ones are the shortest]]<br />
As regards the post-processing step, We developped FiberViewer Light. It includes every clustering methods of the full version FiberViewer such as : Length, Gravity, Hausdorff, and Mean methods but also a Normalized Cut algorithm. As in the full version you can also display a plane on the fiber. This tool works faster than the full version due to simplified visualizations.<br />
Finally, DTI Atlas Fiber Analyzer allows users to gather every information about a fiber by calling FiberProcess or DtiTractStat. Besides you can plot every statistical data such as FA or MD. Then, thanks to the tool MergeStatWithFiber you can insert those statistics on the original Fiber File in order to display it on Slicer.<br />
<br />
= Publications =<br />
<br />
= Key Investigators =<br />
* UNC Algorithms: Jean-Baptiste Berger, Benjamin Yvernault, Clement Vachet, Yundi Shi, Martin Styner<br />
<br />
= Links =<br />
<br />
[[Category: Diffusion MRI]]</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=Projects:AtlasBasedDTIFiberAnalyzerFramework&diff=71974Projects:AtlasBasedDTIFiberAnalyzerFramework2011-11-21T16:03:24Z<p>Jibberger: Created page with ' Back to UNC Algorithms __NOTOC__ = Atlas Based DTI FIber Analyzer Framework = This projects gather some tools aiming at completing each step required to bui…'</p>
<hr />
<div> Back to [[Algorithm:UNC|UNC Algorithms]]<br />
__NOTOC__<br />
<br />
= Atlas Based DTI FIber Analyzer Framework =<br />
<br />
This projects gather some tools aiming at completing each step required to build an Atlas. Concerning the first step as the creation and the mapping of the Atlas, DWI QC will be the appropriate tool. Then comes the tractography followed by a postprocessing step easily done by FiberViewer Light. Finally we will gather statistics thanks to DTI Atlas Fiber Analyzer.<br />
<br />
= Description =<br />
[[Image:AtlasBuilderLogo.jpg|thumb|300px|Length analysis of Cingulum tractography. Colors go from red to blue where red ones are the longest and blue ones are the shortest]]<br />
As regards post-processing step, We developped FiberViewer Light. It includes every clustering methods of the full version FiberViewer such as : Lenght, Gravity, Hausdorff, and Mean methods but also a Normalized Cut algorithm. As in the full version you can also display a plane on the fiber. This tool works faster than the full version due to simplified visualizations.<br />
Finally, DTI Atlas Fiber Analyzer allows users to gather every information about a fiber by calling FiberProcess or DtiTractStat. Besides you can plot every statistical data such as FA or MD. Then, thanks to the tool MergeStatWithFiber you can insert those statistics on the original Fiber File in order to display it on Slicer.<br />
<br />
= Publications =<br />
<br />
= Key Investigators =<br />
* UNC Algorithms: Jean-Baptiste Berger, Benjamin Yvernault, Clement Vachet, Yundi Shi, Martin Styner<br />
<br />
= Links =<br />
<br />
[[Category: Diffusion MRI]]</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=Algorithm:UNC&diff=71972Algorithm:UNC2011-11-21T15:48:08Z<p>Jibberger: </p>
<hr />
<div> Back to [[Algorithm:Main|NA-MIC Algorithms]]<br />
__NOTOC__<br />
= Overview of UNC Algorithms (PI: Martin Styner) =<br />
<br />
At UNC, we are interested in a range of algorithms and solutions for the surface based analysis of brain structures and the cortex. We pioneered the use of spherical harmonics based shape analysis for comparing brain structures across objects. We has also worked on incorporating various data sources for correspondence computation on surfaces of different complexity (ranging from simple brain structures to the highly folded cortical surface). A current topic includes the use of diffusion tensor imaging for connectivity analysis in pathological settings. Finally, investigating quality control, validation and evaluation methodology is another important topic of our NA-MIC research.<br />
<br />
= UNC Projects =<br />
<br />
<br />
{| cellpadding="10" style="text-align:left;"<br />
<br />
| style="width:15%" |[[Image:AtlasBuilderLogo.jpg|200px]]<br />
| style="width:85%" |<br />
<br />
== [[Projects:AtlasBasedDTIFiberAnalyzerFramework| Atlas Based DTI Fiber Analyzer Framework]] ==<br />
This projects gather some tools aiming at completing each step required to build an Atlas. Concerning the first step as the creation and the mapping of the Atlas, DWI QC will be the appropriate tool. Then comes the tractography followed by a postprocessing step easily done by FiberViewer Light. Finally we will gather statistics thanks to DTI Atlas Fiber Analyzer.[[Projects:AtlasBasedDTIFiberAnalyzerFramework|More...]]<br />
<br />
|-<br />
<br />
| style="width:15%" |[[Image:UNC_longitudinalAtlasEx1.png|200px]]<br />
| style="width:85%" |<br />
<br />
== [[Projects:LongitudinalAtlasBuilding| Longitudinal Atlas Building]] ==<br />
As part of the longitudinal intra- and interpatient analysis theme within NA-MIC, we are working on a deformable, longitudinal DTI atlas method. Our longitudinal framework explicitly accounts for temporal dependencies via iterative subject-specific statistical growth modeling, and cross-sectional atlas-building. To effectively account for measurements sparse in time, a continuous-discrete statistical growth model is proposed incorporating also patient co-variates[[Projects:LongitudinalAtlasBuilding|More...]]<br />
<br />
<br />
<font color="red">'''New: '''</font> Gabe Hart, Yundi Shi , Hongtu Zhu, Mar Sanchez, Martin Styner, Marc Niethammer. DTI Longitudinal Atlas Construction as an Average of Growth Models. Workshop on Spatio-Temporal Image Analysis for Longitudinal and Time-Series Image Data, MICCAI 2010 Aug.;<br />
<br />
|-<br />
<br />
| style="width:15%" |[[Image:UNC_dwiatlas.png|200px]]<br />
| style="width:85%" |<br />
<br />
== [[Projects:DWIAtlas|Diffusion Weighted Atlas Construction via model-based transformation and averaging of signal]] == <br />
This project investigated a method for model-based averaging of sets of diffusion weighted magnetic resonance images (DW-MRI) under space transformations (resulting for example from registration methods). A robust weighted least squares method is developed. Synthetic validation experiments show the improvement of the proposed estimation method in comparison to standard least squares estimation. The developed method is applied to construct an atlas of {\it diffusion weighted images} for a set of macaques, allowing for a more flexible representation of average diffusion information compared to standard diffusion tensor atlases.<br />
[[Projects:DWIAtlas|More...]]<br />
<br />
<br />
<font color="red">'''New: '''</font> Y. Shi, S. Benzaid, M. Sanchez, M. Styner, M. Niethammer. Diffusion Weighted Atlas Construction via robust model-based transformation. NeuroImage, in preparation.<br />
<br />
<font color="red">'''New: '''</font> M. Niethammer, Y. Shi, S. Benzaid, M. Sanchez, and M. Styner. Robust model-based transformation and averaging of diffusion weighted images applied to diffusion weighted atlas construction. MICCAI, Workshop on Computational Diffusion MRI, 2010.<br />
<br />
|-<br />
<br />
| style="width:15%" |[[Image:UNC_GraphbasedConnectivity_Ex1.png|200px]]<br />
| style="width:85%" |<br />
<br />
== [[Projects:DiffusionGraphBasedConnectivity|Diffusion Imaging based Connectivity]] ==<br />
<br />
This project focuses on connectivity measurements derived from diffusion imaging datasets in order to better understand cortical and subcortical white matter connectivity. Our research employs a novel, multi-directional graph propagation method that performs a fully deterministic, efficient and stable connectivity computation. The method handles crossing fibers and deals well with multiple seed regions. In addition to the analysis of these connectivity measures in describing brain pathology, they can also be used as scalar maps for use in DTI registration.<br />
[[Projects:DiffusionGraphBasedConnectivity|More...]]<br />
<br />
<br />
<font color="red">'''New: '''</font> Alexis Boucharin, Ipek Oguz, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner. Efficient, graph-based white matter connectivity from orientation distribution functions via multi-directional graph propagation. Medical Imaging 2011: Image Processing (2011) vol. 7962 (1) pp. 79620S<br />
<br />
|-<br />
<br />
| style="width:15%" |[[Image:DTIPrep_example1.png|200px]]<br />
| style="width:85%" |<br />
<br />
== [[Projects:DTI_DWI_QualityControl|DWI and DTI Quality Control]] ==<br />
<br />
DWI data suffers from inherent low SNR, overall long scanning time of multiple directional encoding with correspondingly large risk to encounter several kinds of artifacts. These artifacts can be too severe for a correct and stable estimation of the diffusion tensor. Thus, a quality control (QC) procedure is absolutely necessary for DTI studies. We are developing a framework for automatic DWI and DTI quality assessment and correction. We developed a tool called DTIPrep which pipelines the QC steps with designated protocol use and report generation. [[Projects:DTI_DWI_QualityControl|More...]]<br />
<br />
<font color="red">'''New: '''</font> DTIPrep first full version on [http://www.nitrc.org/projects/dtiprep/ NITRC ]<br />
<br />
<font color="red">'''New: '''</font> Zhexing Liu, Casey Goodlett, Guido Gerig, Martin Styner. Evaluation of DTI property maps as basis of DTI atlas building. Medical Imaging 2010: Image Processing (2010) vol. 7623 (1) pp. 762325<br />
<br />
<font color="red">'''New: '''</font> Zhexing Liu, Yi Wang, Guido Gerig, Sylvain Gouttard, Ran Tao, Thomas Fletcher, Martin Styner. Quality control of diffusion weighted images. Medical Imaging 2010: Advanced PACS-based Imaging Informatics and Therapeutic Applications (2010) vol. 7628 (1) pp. 76280J<br />
<br />
<br />
|-<br />
<br />
| style="width:15%" |[[Image:Sulcaldepth.png|200px]]<br />
| style="width:85%" |<br />
<br />
== [[Projects:CorticalCorrespondenceWithParticleSystem|Cortical Correspondence using Particle System]] ==<br />
<br />
In this project, we want to compute cortical correspondence on populations, using various features such as cortical structure, DTI connectivity, vascular structure, and functional data (fMRI). This presents a challenge because of the highly convoluted surface of the cortex, as well as because of the different properties of the data features we want to incorporate together. This correspondence method has been included in our NAMIC cortical thickness framework GAMBIT [[Projects:CorticalCorrespondenceWithParticleSystem|More...]]<br />
<br />
<font color="red">'''New: '''</font> Vachet, C., Hazlett, H., Niethammer, M., Oguz, I., Cates, J., Whitaker, R., Piven, J., Styner, M., “Group-wise automatic mesh-based analysis of cortical thickness“. Medical Imaging 2011: Image Processing (2011) vol. 7962 (1) pp. 796227 1 - 10<br />
<br />
<font color="red">'''New: '''</font> Lee J, Ehlers C, Crews F, Niethammer M, Budin F, Paniagua B, Sulik K, Johns J, Styner M, Oguz I. Automatic cortical thickness analysis on rodent brain. Medical Imaging 2011: Image Processing (2011) vol. 7962 (1) pp. 796248<br />
<br />
|-<br />
<br />
<br />
| | [[Image:UNCShape_OverviewAnalysis_MICCAI06.gif|200px]]<br />
| |<br />
<br />
== [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|UNC-Utah Shape Analysis Framework]] ==<br />
<br />
The UNC shape analysis is based on an analysis framework of objects with spherical topology, described mainly by sampled spherical harmonics SPHARM-PDM. The input of the shape analysis framework is a set of binary segmentations of a single brain structure, such as the hippocampus or caudate. These segmentations are converted into a shape description (SPHARM-PDM) with correspondence and tested via statistical point-wise analysis. Additionally, the SPHARM correspondences can be improved with Entropy-based particle systems, by using an integration module recently added to the pipeline. [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|More...]]<br />
<br />
* SPHARM-Particle Shape Analysis Toolkit disseminated on [http://www.nitrc.org/projects/spharm-pdm NITRC SPHARM PDM page]. All tools are Slicer compatible.<br />
* Single Slicer 3 module for whole shape analysis pipeline with automatic generation of Slicer MRML scenes for result visualization<br />
<br />
<font color="red">'''New: '''</font> Mark Walterfang, Jeffrey Chee Leong Looi, Martin Styner, Ruth H Walker, Adrian Danek, Marc Neithammer, Andrew Evans, Katya Kotschet, Guilherme R Rodrigues, Andrew Hughes, Dennis Velakoulis. Shape alterations in the striatum in chorea-acanthocytosis. Psychiatry research (2011) vol. 192 (1), pp. 29-36<br />
<br />
<font color="red">'''New: '''</font> Beatriz Paniagua, Lucia Cevidanes, David Walker, Hongtu Zhu, Ruixin Guo, Martin Styner. Clinical application of SPHARM-PDM to quantify temporomandibular joint osteoarthritis. Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society (2011) vol. 35(5), pp. 345-352<br />
<br />
<font color="red">'''New: '''</font> Beatriz Paniagua, Lucia Cevidanes, Hongtu Zhu, Martin Styner. Outcome quantification using SPHARM-PDM toolbox in orthognathic surgery. International journal of computer assisted radiology and surgery (2011) vol. 6 (5) pp. 617-626<br />
<br />
<font color="red">'''New: '''</font> Jeffrey Chee Leong Looi, Mark Walterfang, Martin Styner, Leif Svensson, Olof Lindberg, Per Ostberg, Lisa Botes, Eva Orndahl, Phyllis Chua, Rajeev Kumar, Dennis Velakoulis, Lars-Olof Wahlund. Shape analysis of the neostriatum in frontotemporal lobar degeneration, Alzheimer's disease, and controls. Neuroimage (2010) vol. 51 (3) pp. 970-86<br />
<br />
<font color="red">'''New: '''</font> Maltbie E, Bhatt K, Paniagua B, Smith RG, Graves MM, Mosconi MW, Peterson S, White S, Blocher J, El-Sayed M, Hazlett HC, Styner M. Asymmetric bias in user guided segmentations of brain structures. NeuroImage 2011 Aug. [Epub ahead of print]<br />
<br />
<font color="red">'''New: '''</font> Datar M, Gur Y, Paniagua B, Styner M, Whitaker R. Geometric Correspondence for Ensembles of. MICCAI 2011, Part II 2011 Aug.;6892:368–375.<br />
<br />
<font color="red">'''New: '''</font> Looi JCL, Macfarlane MD, Walterfang M, Styner M, Velakoulis D, Lätt J, van Westen D, Nilsson C. Morphometric analysis of subcortical structures in progressive supranuclear palsy: In vivo evidence of neostriatal and mesencephalic atrophy. Psychiatry Research: Neuroimaging 2011 Sep.;:1–13<br />
<br />
|-<br />
<br />
| | [[Image:UNCShape_ShapeCorrespondence.png|200px]]<br />
| |<br />
<br />
== [[Projects:LocalStatisticalAnalysisViaPermutationTests|Local Statistical Analysis via Permutation Tests]] ==<br />
<br />
We have further developed a set of statistical testing methods that allow the analysis of local shape differences via group differences tests as well interaction tests. Resulting significance maps (both raw and corrected for multiple comparisons) are easily visualized. Additional visualization of the group tests are provided via mean difference magnitude and vector maps, as well as maps of the group covariance information. Additional visualization of the interaction tests include Pearson and Spearman correlation maps. [[Projects:LocalStatisticalAnalysisViaPermutationTests|More...]]<br />
<br />
<font color="red">'''New: '''</font> User-friendly GUI interface and statistical result visualization via automatically generated Slicer MRML scenes<br />
<br />
<font color="red">'''New: '''</font> Available on NITRC either [http://www.nitrc.org/projects/shape_mancova separately (ShapeAnalysisMANCOVA)] or as part of the [http://www.nitrc.org/projects/spharm-pdm SPHARM-PDM shape analysis package]<br />
<br />
* Paniagua B., Styner M., Macenko M., Pantazis D., Niethammer M, Local Shape Analysis using MANCOVA, Insight Journal, 2009 July-December, http://hdl.handle.net/10380/3124<br />
<br />
<br />
|-<br />
| | [[Image:Cause07Competition.gif|200px]]<br />
| |<br />
<br />
== [[Projects:MethodEvaluationValidation|Evaluation and Comparison of Medical Image Analysis Methods]] ==<br />
<br />
In this project, we want to focus on the evaluation of medical image analysis methods for specific clinical applications in respect to development of evaluation methodology and the organization of venues promoting such comparison and validation studies.<br />
<br />
<font color="red">'''New: '''</font> [[Events:_DTI_Tractography_Challenge_MICCAI_2011 | DTI fiber tractography challenge]] at MICCAI 2011<br />
<br />
|-<br />
<br />
<br />
| | [[Image:UNCShape_CaudatePval_MICCAI06.png|200px]]<br />
| |<br />
<br />
== [[Projects:PopulationBasedCorrespondence|Population Based Correspondence]] ==<br />
<br />
We are developing methodology to automatically find dense point correspondences between a collection of polygonal genus 0 meshes. The advantage of this method is independence from indivisual templates, as well as enhanced modeling properties. The method is based on minimizing a cost function that describes the goodness of correspondence. Apart from a cost function derived from the description length of the model, we also employ a cost function working with arbitrary local features. We extended the original methods to use surface curvature measurements, which are independent to differences of object aligment. [[Projects:PopulationBasedCorrespondence|More...]]<br />
<br />
* Styner M., Oguz I., Heimann T., Gerig G. Minimum description length with local geometry. Proceedings of the 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2008; 1283-1286<br />
* Software available as part of UNC Neurolib open source ([http://www.ia.unc.edu/dev website])<br />
<br />
|-<br />
<br />
<br />
|}</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=File:AtlasBuilderLogo.jpg&diff=71971File:AtlasBuilderLogo.jpg2011-11-21T15:45:54Z<p>Jibberger: </p>
<hr />
<div></div>Jibbergerhttps://www.na-mic.org/w/index.php?title=2012_Winter_Project_Week:DTIAFA&diff=718722012 Winter Project Week:DTIAFA2011-11-10T20:04:23Z<p>Jibberger: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:DTIAFA1.jpg|DTIAtlasFiberAnalyzer - Top Screen<br />
Image:DTIAFA2.jpg|DTIAtlasFiberAnalyzer - Plot Window<br />
</gallery><br />
<br />
==Key Investigators==<br />
* UNC: Yundi Shi, Benjamin Yvernault, Jean-Baptiste Berger, Clement Vachet, Martin Styner<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
DTIAtlasFiberAnalyzer aims to applies an atlas fiber to all datasets, extracts the fiber profiles, gathers and plot all the information.<br />
This tool calls some others such as : dtitractstat, fiberprocess, and mergestatwithfiber. Once informations are computed, each merged statistics on the fiber can be watched on slicer.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
Our plan for the project week is to try out this tool.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a<br />
<br />
#Slicer Module<br />
##Extension -- commandline<br />
##Extension -- loadable<br />
<br />
==References==<br />
<br />
</div></div>Jibbergerhttps://www.na-mic.org/w/index.php?title=2012_Winter_Project_Week:FVLight&diff=718712012 Winter Project Week:FVLight2011-11-10T20:02:20Z<p>Jibberger: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:FV1.jpg|FiberViewerLight - Top Screen<br />
Image:FV2.jpg|FiberViewerLight - Length Screen with a plane<br />
</gallery><br />
<br />
==Key Investigators==<br />
* UNC: Jean-Baptiste Berger, Clement Vachet, Martin Styner<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
The goal is to developp a light version of the existing tool Fiber Viewer. We will only developp the clustering part of Fiber Viewer such as : the Lenght, Gravity, Hausdorff, and Mean methods but also a Normalized Cut algorithm and a plane display on a fiber.<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
Our plan for the project week is to try out this light version and improve its computing speed since it is a light version.<br />
<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a<br />
<br />
#Slicer Module<br />
##Extension -- commandline<br />
##Extension -- loadable<br />
<br />
==References==<br />
<br />
</div></div>Jibbergerhttps://www.na-mic.org/w/index.php?title=2012_Winter_Project_Week:DTIAFA&diff=718552012 Winter Project Week:DTIAFA2011-11-10T19:24:44Z<p>Jibberger: Created page with '__NOTOC__ <gallery> Image:PW-SLC2011.png|Projects List Image:DTIAFA1.jpg|DTIAtlasFiberAnalyzer - Top Screen Image:DTIAFA2.jpg|DTIAtlasFiberA…'</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:DTIAFA1.jpg|DTIAtlasFiberAnalyzer - Top Screen<br />
Image:DTIAFA2.jpg|DTIAtlasFiberAnalyzer - Plot Window<br />
</gallery><br />
<br />
==Key Investigators==<br />
* UNC: Martin Styner, Clement Vachet, Yundi Shi, Benjamin Yvernault, Jean-Baptiste Berger<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
DTIAtlasFiberAnalyzer aims to applies an atlas fiber to all datasets, extracts the fiber profiles, gathers and plot all the information.<br />
This tool calls some others such as : dtitractstat, fiberprocess, and mergestatwithfiber. Once informations are computed, each merged statistics on the fiber can be watched on slicer.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
Our plan for the project week is to try out this tool.<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a<br />
<br />
#Slicer Module<br />
##Extension -- commandline<br />
##Extension -- loadable<br />
<br />
==References==<br />
<br />
</div></div>Jibbergerhttps://www.na-mic.org/w/index.php?title=File:DTIAFA2.jpg&diff=71854File:DTIAFA2.jpg2011-11-10T19:23:43Z<p>Jibberger: DTIAtlasFiberAnalyzer - Plot Window</p>
<hr />
<div>DTIAtlasFiberAnalyzer - Plot Window</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=File:DTIAFA1.jpg&diff=71853File:DTIAFA1.jpg2011-11-10T19:23:18Z<p>Jibberger: DTIAtlasFiberAnalyzer - Top Screen</p>
<hr />
<div>DTIAtlasFiberAnalyzer - Top Screen</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=2012_Winter_Project_Week&diff=718522012 Winter Project Week2011-11-10T18:59:54Z<p>Jibberger: /* Predict Huntington's Disease DBP */</p>
<hr />
<div>Back to [[Project Events]], [[Events]]<br />
Back to [[Project Events]], [[AHM_2012]], [[Events]]<br />
<br />
__NOTOC__<br />
[[image:PW-SLC2012.png|300px]]<br />
<br />
== Dates.Venue.Registration ==<br />
<br />
Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.<br />
<br />
== Agenda==<br />
<br />
Please [[AHM_2012#Agenda|click here for the agenda for AHM 2012 and Project Week]].<br />
<br />
==Background==<br />
<br />
From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions. <br />
<br />
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. <br />
<br />
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.<br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
<br />
<br />
<br />
<br />
<br />
==Projects==<br />
Please list projects here.<br />
<br />
===IGT===<br />
*MR guided laser ablation for neurosurgery (Dan Orringer, MD BWH, Jason Stafford, MD Anderson, Isaiah Norton BWH)<br />
*Pelvic Registration (Sandy Wells, Firdaus Janoos, Mehdi Moradi UBC/BWH, jan egger, andrey fedorov)<br />
*openIGTLink interface for Slicer4(Junichi, Clif Burdette/Jack Blevins, Tamas, Andras)<br />
*needle tracking (atushi yamada, radhika tibrewal, a needle navigation person)<br />
*?mr susceptability (clare poynton, mr physics person?)<br />
<br />
===Predict Huntington's Disease DBP===<br />
* [[2012_Winter_Project_Week:FVLight|Fiber Clustering]] (Martin Styner, Clement Vachet, Jean-Baptiste Berger)<br />
* [[2012_Winter_Project_Week:DTIAFA|Atlas Builder]] (Martin Styner, Clement Vachet, Yundi Shi, Benjamin Yvernault, Jean-Baptiste Berger)<br />
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration]] (Clement Vachet, Hans Johnson, Martin Styner)<br />
<br />
===Atrial fibrillation DBP===<br />
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Gregory Phillip Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)<br />
<br />
===NA-MIC Kit Internals===<br />
*Slicer4 Scene Views Module (Nicole Aucoin)<br />
*Slicer4 Annotations Module<br />
** File format refactor (Nicole Aucoin)<br />
** QT 3D Text rendering proof of concept (Julien Finet, Steve Pieper, Nicole Aucoin)<br />
* Editor Extension Examples and Debugging (Steve Pieper)<br />
<br />
=== Preparation ===<br />
<br />
#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] <br />
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:<br />
#*October 27: MGH DBP<br />
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics<br />
#*November 10: Utah Atrial Fibrillation DBP<br />
#*November 17: UCLA TBI DBP<br />
#*November 24: No call. thanksgiving.<br />
#*December 1: <br />
#*December 8: <br />
#*December 15:Finalize Projects <br />
#*January 5: Loose Ends<br />
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br />
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br />
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]<br />
##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)<br />
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br />
##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)<br />
#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...</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=2012_Winter_Project_Week:FVLight&diff=718512012 Winter Project Week:FVLight2011-11-10T18:58:01Z<p>Jibberger: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:FV1.jpg|FiberViewerLight - Top Screen<br />
Image:FV2.jpg|FiberViewerLight - Length Screen with a plane<br />
</gallery><br />
<br />
==Key Investigators==<br />
* UNC: Martin Styner, Clement Vachet, Jean-Baptiste Berger<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
The goal is to developp a light version of the existing tool Fiber Viewer. We will only developp the clustering part of Fiber Viewer such as : the Lenght, Gravity, Hausdorff, and Mean methods but also a Normalized Cut algorithm and a plane display on a fiber.<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
Our plan for the project week is to try out this light version and improve its computing speed since it is a light version.<br />
<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a<br />
<br />
#Slicer Module<br />
##Extension -- commandline<br />
##Extension -- loadable<br />
<br />
==References==<br />
<br />
</div></div>Jibbergerhttps://www.na-mic.org/w/index.php?title=2012_Winter_Project_Week&diff=718502012 Winter Project Week2011-11-10T18:57:49Z<p>Jibberger: /* Predict Huntington's Disease DBP */</p>
<hr />
<div>Back to [[Project Events]], [[Events]]<br />
Back to [[Project Events]], [[AHM_2012]], [[Events]]<br />
<br />
__NOTOC__<br />
[[image:PW-SLC2012.png|300px]]<br />
<br />
== Dates.Venue.Registration ==<br />
<br />
Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.<br />
<br />
== Agenda==<br />
<br />
Please [[AHM_2012#Agenda|click here for the agenda for AHM 2012 and Project Week]].<br />
<br />
==Background==<br />
<br />
From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions. <br />
<br />
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. <br />
<br />
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.<br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
<br />
<br />
<br />
<br />
<br />
==Projects==<br />
Please list projects here.<br />
<br />
===IGT===<br />
*MR guided laser ablation for neurosurgery (Dan Orringer, MD BWH, Jason Stafford, MD Anderson, Isaiah Norton BWH)<br />
*Pelvic Registration (Sandy Wells, Firdaus Janoos, Mehdi Moradi UBC/BWH, jan egger, andrey fedorov)<br />
*openIGTLink interface for Slicer4(Junichi, Clif Burdette/Jack Blevins, Tamas, Andras)<br />
*needle tracking (atushi yamada, radhika tibrewal, a needle navigation person)<br />
*?mr susceptability (clare poynton, mr physics person?)<br />
<br />
===Predict Huntington's Disease DBP===<br />
* [[2012_Winter_Project_Week:FVLight|Fiber Viewer Light]](Martin Styner, Clement Vachet, Jean-Baptiste Berger)<br />
* [[2012_Winter_Project_Week:DTIAFA|DTI Atlas Fiber Analyzer]]<br />
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration]] (Clement Vachet, Hans Johnson, Martin Styner)<br />
<br />
===Atrial fibrillation DBP===<br />
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Gregory Phillip Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)<br />
<br />
===NA-MIC Kit Internals===<br />
*Slicer4 Scene Views Module (Nicole Aucoin)<br />
*Slicer4 Annotations Module<br />
** File format refactor (Nicole Aucoin)<br />
** QT 3D Text rendering proof of concept (Julien Finet, Steve Pieper, Nicole Aucoin)<br />
* Editor Extension Examples and Debugging (Steve Pieper)<br />
<br />
=== Preparation ===<br />
<br />
#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] <br />
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:<br />
#*October 27: MGH DBP<br />
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics<br />
#*November 10: Utah Atrial Fibrillation DBP<br />
#*November 17: UCLA TBI DBP<br />
#*November 24: No call. thanksgiving.<br />
#*December 1: <br />
#*December 8: <br />
#*December 15:Finalize Projects <br />
#*January 5: Loose Ends<br />
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br />
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br />
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]<br />
##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)<br />
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br />
##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)<br />
#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...</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=2012_Winter_Project_Week:FVLight&diff=718492012 Winter Project Week:FVLight2011-11-10T18:56:58Z<p>Jibberger: Created page with '__NOTOC__ <gallery> Image:PW-SLC2011.png|Projects List Image:FV1.jpg|FiberViewerLight - Top Screen Image:FV2.jpg|FiberViewerLight - Length S…'</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]<br />
Image:FV1.jpg|FiberViewerLight - Top Screen<br />
Image:FV2.jpg|FiberViewerLight - Length Screen with a plane<br />
</gallery><br />
<br />
==Key Investigators==<br />
* UNC: Martyn Styner, Clement Vachet, Jean-Baptiste Berger<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
The goal is to developp a light version of the existing tool Fiber Viewer. We will only developp the clustering part of Fiber Viewer such as : the Lenght, Gravity, Hausdorff, and Mean methods but also a Normalized Cut algorithm and a plane display on a fiber.<br />
<br />
<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
Our plan for the project week is to try out this light version and improve its computing speed since it is a light version.<br />
<br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will be delivered to the NA-MIC Kit as a<br />
<br />
#Slicer Module<br />
##Extension -- commandline<br />
##Extension -- loadable<br />
<br />
==References==<br />
<br />
</div></div>Jibbergerhttps://www.na-mic.org/w/index.php?title=File:FV2.jpg&diff=71848File:FV2.jpg2011-11-10T18:54:32Z<p>Jibberger: Length screen with plane FiberViewerLight</p>
<hr />
<div>Length screen with plane FiberViewerLight</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=File:FV1.jpg&diff=71847File:FV1.jpg2011-11-10T18:50:07Z<p>Jibberger: uploaded a new version of "File:FV1.jpg"</p>
<hr />
<div>Top Screen FiberViewerLight</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=File:FV1.jpg&diff=71846File:FV1.jpg2011-11-10T18:47:42Z<p>Jibberger: Top Screen FiberViewerLight</p>
<hr />
<div>Top Screen FiberViewerLight</div>Jibbergerhttps://www.na-mic.org/w/index.php?title=2012_Winter_Project_Week&diff=718422012 Winter Project Week2011-11-10T18:21:58Z<p>Jibberger: </p>
<hr />
<div>Back to [[Project Events]], [[Events]]<br />
Back to [[Project Events]], [[AHM_2012]], [[Events]]<br />
<br />
__NOTOC__<br />
[[image:PW-SLC2012.png|300px]]<br />
<br />
== Dates.Venue.Registration ==<br />
<br />
Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.<br />
<br />
== Agenda==<br />
<br />
Please [[AHM_2012#Agenda|click here for the agenda for AHM 2012 and Project Week]].<br />
<br />
==Background==<br />
<br />
From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions. <br />
<br />
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. <br />
<br />
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.<br />
<br />
A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].<br />
<br />
<br />
<br />
<br />
<br />
==Projects==<br />
Please list projects here.<br />
<br />
===IGT===<br />
*MR guided laser ablation for neurosurgery (Dan Orringer, MD BWH, Jason Stafford, MD Anderson, Isaiah Norton BWH)<br />
*Pelvic Registration (Sandy Wells, Firdaus Janoos, Mehdi Moradi UBC/BWH, jan egger, andrey fedorov)<br />
*openIGTLink interface for Slicer4(Junichi, Clif Burdette/Jack Blevins, Tamas, Andras)<br />
*needle tracking (atushi yamada, radhika tibrewal, a needle navigation person)<br />
*?mr susceptability (clare poynton, mr physics person?)<br />
<br />
===Predict Huntington's Disease DBP===<br />
* [[2012_Winter_Project_Week:FVLight|Fiber Viewer Light]]<br />
* [[2012_Winter_Project_Week:DTIAFA|DTI Atlas Fiber Analyzer]]<br />
<br />
===Atrial fibrillation DBP===<br />
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Gregory Phillip Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)<br />
<br />
===NA-MIC Kit Internals===<br />
*Slicer4 Scene Views Module (Nicole Aucoin)<br />
*Slicer4 Annotations Module<br />
** File format refactor (Nicole Aucoin)<br />
** QT 3D Text rendering proof of concept (Julien Finet, Steve Pieper, Nicole Aucoin)<br />
* Editor Extension Examples and Debugging (Steve Pieper)<br />
<br />
=== Preparation ===<br />
<br />
#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] <br />
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:<br />
#*October 27: MGH DBP<br />
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics<br />
#*November 10: Utah Atrial Fibrillation DBP<br />
#*November 17: UCLA TBI DBP<br />
#*November 24: No call. thanksgiving.<br />
#*December 1: <br />
#*December 8: <br />
#*December 15:Finalize Projects <br />
#*January 5: Loose Ends<br />
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br />
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br />
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]<br />
##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)<br />
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br />
##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)<br />
#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...</div>Jibberger