NAMIC Wiki - User contributions [en]

Algorithm:UNC

2011-11-02T17:17:15Z

Wendyuu:

Back to [[Algorithm:Main|NA-MIC Algorithms]]
__NOTOC__
= Overview of UNC Algorithms (PI: Martin Styner) =

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.

= UNC Projects =

{| cellpadding="10" style="text-align:left;"

| style="width:15%" |[[Image:UNC_longitudinalAtlasEx1.png|200px]]
| style="width:85%" |

== [[Projects:LongitudinalAtlasBuilding| Longitudinal Atlas Building]] ==
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...]]

<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.;

|-

| style="width:15%" |[[Image:UNC_dwiatlas.png‎|200px]]
| style="width:85%" |

== [[Projects:DWIAtlas|Diffusion Weighted Atlas Construction via model-based transformation and averaging of signal]] ==
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.
[[Projects:DWIAtlas|More...]]

<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.

<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.

|-

| style="width:15%" |[[Image:UNC_GraphbasedConnectivity_Ex1.png‎|200px]]
| style="width:85%" |

== [[Projects:DiffusionGraphBasedConnectivity|Diffusion Imaging based Connectivity]] ==

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.
[[Projects:DiffusionGraphBasedConnectivity|More...]]

<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

|-

| style="width:15%" |[[Image:DTIPrep_example1.png|200px]]
| style="width:85%" |

== [[Projects:DTI_DWI_QualityControl|DWI and DTI Quality Control]] ==

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...]]

<font color="red">'''New: '''</font> DTIPrep first full version on [http://www.nitrc.org/projects/dtiprep/ NITRC ]

<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

<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

|-

| style="width:15%" |[[Image:Sulcaldepth.png|200px]]
| style="width:85%" |

== [[Projects:CorticalCorrespondenceWithParticleSystem|Cortical Correspondence using Particle System]] ==

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...]]

<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

<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

|-

| | [[Image:UNCShape_OverviewAnalysis_MICCAI06.gif|200px]]
| |

== [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|UNC-Utah Shape Analysis Framework]] ==

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...]]

* SPHARM-Particle Shape Analysis Toolkit disseminated on [http://www.nitrc.org/projects/spharm-pdm NITRC SPHARM PDM page]. All tools are Slicer compatible.
* Single Slicer 3 module for whole shape analysis pipeline with automatic generation of Slicer MRML scenes for result visualization

<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

<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

<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

<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

<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]

<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.

<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

|-

| | [[Image:UNCShape_ShapeCorrespondence.png|200px]]
| |

== [[Projects:LocalStatisticalAnalysisViaPermutationTests|Local Statistical Analysis via Permutation Tests]] ==

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...]]

<font color="red">'''New: '''</font> User-friendly GUI interface and statistical result visualization via automatically generated Slicer MRML scenes

<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]

* 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

|-
| | [[Image:Cause07Competition.gif|200px]]
| |

== [[Projects:MethodEvaluationValidation|Evaluation and Comparison of Medical Image Analysis Methods]] ==

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.

<font color="red">'''New: '''</font> [[Events:_DTI_Tractography_Challenge_MICCAI_2011 | DTI fiber tractography challenge]] at MICCAI 2011

|-

| | [[Image:UNCShape_CaudatePval_MICCAI06.png|200px]]
| |

== [[Projects:PopulationBasedCorrespondence|Population Based Correspondence]] ==

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...]]

* 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
* Software available as part of UNC Neurolib open source ([http://www.ia.unc.edu/dev website])

|-

|}

Projects:DWIAtlas

2011-11-02T17:14:14Z

Wendyuu: Created page with ' Back to UNC Algorithms __NOTOC__ = Longitudinal atlas building = As part of the longitudinal intra- and interpatient analysis theme within NA-MIC, we are wo…'

Back to [[Algorithm:UNC|UNC Algorithms]]
__NOTOC__

= Longitudinal atlas building =

As part of the longitudinal intra- and interpatient analysis theme within NA-MIC, we are working on a deformable, longitudinal DTI atlas method. Our initial approach is based on intensity calibrated images assuming homogenous intensity across the time scale. This 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

= Description =

[[Image:UNC_longitudinalAtlasEx1.png|thumb|300px|Longitudinal macaque developmental DTI atlas from postnatal day 14 to 180 as visualized on a center axial slice. Top row: Reconstructed atlas image at each age pulled back to day 14. The high quality of the longitudinal modeling is visible through the close similarity of the pulled-back atlas images. Middle row: Estimated change in FA between time points displaying major change occurring in the first 60 days (overshadowing the magnitude of later changes). Bottom row: Jacobian determinant of the pull-back deformation field. Cyan = no change, dark blue = growth (most of white matter), yellow-red = shrinkage (here seen on the 3rd ventricle in the center of the image) ]]

The initial longitudinal framework explicitly accounts for temporal dependencies via iterative subject-specific statistical growth modeling , and cross-sectional atlas-building using a deformable LDDMM based registration approach. To effectively account for measurements sparse in time, a continuous-discrete statistical growth model is proposed incorporating also patient co-variates. This initial approach is based on intensity calibrated images assuming homogenous intensity across the time scale.

Currently we are working on incorporating the intra and inter-subject registration jointly, as well as modeling longitudinal changes both in shape as well as intensity.

= Publications =

* [http://www.na-mic.org/publications/pages/display?search=Projects%3ALongitudinalAtlasBuilding NA-MIC Publication Database on Longitudinal Atlas Building]

= Key Investigators =
* UNC Algorithms: Marc Niethammer, Istvan Csapo, Yundi Shi, Martin Styner

= Links =

[[Category: Diffusion MRI]]

Algorithm:UNC

2011-11-02T17:13:30Z

Wendyuu: /* Diffusion Weighted Atlas Construction via model-based transformation and averaging of signal */

Back to [[Algorithm:Main|NA-MIC Algorithms]]
__NOTOC__
= Overview of UNC Algorithms (PI: Martin Styner) =

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.

= UNC Projects =

{| cellpadding="10" style="text-align:left;"

| style="width:15%" |[[Image:UNC_longitudinalAtlasEx1.png|200px]]
| style="width:85%" |

== [[Projects:LongitudinalAtlasBuilding| Longitudinal Atlas Building]] ==
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...]]

<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.;

|-

| style="width:15%" |[[Image:UNC_dwiatlas.png‎|200px]]
| style="width:85%" |

== [[Projects:DWIAtlas|Diffusion Weighted Atlas Construction via model-based transformation and averaging of signal]] == 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.
[[Projects:DWIAtlas|More...]]

<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.

<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.

|-

| style="width:15%" |[[Image:UNC_GraphbasedConnectivity_Ex1.png‎|200px]]
| style="width:85%" |

== [[Projects:DiffusionGraphBasedConnectivity|Diffusion Imaging based Connectivity]] ==

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.
[[Projects:DiffusionGraphBasedConnectivity|More...]]

<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

|-

| style="width:15%" |[[Image:DTIPrep_example1.png|200px]]
| style="width:85%" |

== [[Projects:DTI_DWI_QualityControl|DWI and DTI Quality Control]] ==

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...]]

<font color="red">'''New: '''</font> DTIPrep first full version on [http://www.nitrc.org/projects/dtiprep/ NITRC ]

<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

<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

|-

| style="width:15%" |[[Image:Sulcaldepth.png|200px]]
| style="width:85%" |

== [[Projects:CorticalCorrespondenceWithParticleSystem|Cortical Correspondence using Particle System]] ==

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...]]

<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

<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

|-

| | [[Image:UNCShape_OverviewAnalysis_MICCAI06.gif|200px]]
| |

== [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|UNC-Utah Shape Analysis Framework]] ==

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...]]

* SPHARM-Particle Shape Analysis Toolkit disseminated on [http://www.nitrc.org/projects/spharm-pdm NITRC SPHARM PDM page]. All tools are Slicer compatible.
* Single Slicer 3 module for whole shape analysis pipeline with automatic generation of Slicer MRML scenes for result visualization

<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

<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

<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

<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

<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]

<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.

<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

|-

| | [[Image:UNCShape_ShapeCorrespondence.png|200px]]
| |

== [[Projects:LocalStatisticalAnalysisViaPermutationTests|Local Statistical Analysis via Permutation Tests]] ==

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...]]

<font color="red">'''New: '''</font> User-friendly GUI interface and statistical result visualization via automatically generated Slicer MRML scenes

<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]

* 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

|-
| | [[Image:Cause07Competition.gif|200px]]
| |

== [[Projects:MethodEvaluationValidation|Evaluation and Comparison of Medical Image Analysis Methods]] ==

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.

<font color="red">'''New: '''</font> [[Events:_DTI_Tractography_Challenge_MICCAI_2011 | DTI fiber tractography challenge]] at MICCAI 2011

|-

| | [[Image:UNCShape_CaudatePval_MICCAI06.png|200px]]
| |

== [[Projects:PopulationBasedCorrespondence|Population Based Correspondence]] ==

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...]]

* 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
* Software available as part of UNC Neurolib open source ([http://www.ia.unc.edu/dev website])

|-

|}

Algorithm:UNC

2011-10-17T16:22:07Z

Wendyuu: /* Diffusion Weighted Atlas Construction via model-based transformation and averaging of signal */

Back to [[Algorithm:Main|NA-MIC Algorithms]]
__NOTOC__
= Overview of UNC Algorithms (PI: Martin Styner) =

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.

= UNC Projects =

{| cellpadding="10" style="text-align:left;"

| style="width:15%" |[[Image:UNC_longitudinalAtlasEx1.png|200px]]
| style="width:85%" |

== [[Projects:LongitudinalAtlasBuilding| Longitudinal Atlas Building]] ==
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...]]

<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.;

|-

| style="width:15%" |[[Image:UNC_dwiatlas.png‎|200px]]
| style="width:85%" |

== [[Projects:DWIAtlas|Diffusion Weighted Atlas Construction via model-based transformation and averaging of signal]] ==

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.
[[Projects:DWIAtlas|More...]]

<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.

<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.

|-

| style="width:15%" |[[Image:UNC_GraphbasedConnectivity_Ex1.png‎|200px]]
| style="width:85%" |

== [[Projects:DiffusionGraphBasedConnectivity|Diffusion Imaging based Connectivity]] ==

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.
[[Projects:DiffusionGraphBasedConnectivity|More...]]

<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

|-

| style="width:15%" |[[Image:DTIPrep_example1.png|200px]]
| style="width:85%" |

== [[Projects:DTI_DWI_QualityControl|DWI and DTI Quality Control]] ==

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...]]

<font color="red">'''New: '''</font> DTIPrep first full version on [http://www.nitrc.org/projects/dtiprep/ NITRC ]

<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

<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

|-

| style="width:15%" |[[Image:Sulcaldepth.png|200px]]
| style="width:85%" |

== [[Projects:CorticalCorrespondenceWithParticleSystem|Cortical Correspondence using Particle System]] ==

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...]]

<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

<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

|-

| | [[Image:UNCShape_OverviewAnalysis_MICCAI06.gif|200px]]
| |

== [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|Shape Analysis Framework using SPHARM-PDM]] ==

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. [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|More...]]

* Shape Analysis Toolkit disseminated on [http://www.nitrc.org/projects/spharm-pdm NITRC SPHARM PDM page]. All tools are Slicer compatible.
* Single Slicer 3 module for whole shape analysis pipeline

<font color="red">'''New: '''</font> automatic generation of Slicer MRML scenes for result visualization

<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) preprint online

<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) preprint online.

<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) preprint online

<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

|-

| | [[Image:UNCShape_ShapeCorrespondence.png|200px]]
| |

== [[Projects:LocalStatisticalAnalysisViaPermutationTests|Local Statistical Analysis via Permutation Tests]] ==

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...]]

<font color="red">'''New: '''</font> User-friendly GUI interface and statistical result visualization via automatically generated Slicer MRML scenes

<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]

* 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

|-
| | [[Image:Cause07Competition.gif|200px]]
| |

== [[Projects:MethodEvaluationValidation|Evaluation and Comparison of Medical Image Analysis Methods]] ==

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.

<font color="red">'''New: '''</font> [[Events:_DTI_Tractography_Challenge_MICCAI_2011 | DTI fiber tractography challenge]] at MICCAI 2011

|-

| | [[Image:UNCShape_CaudatePval_MICCAI06.png|200px]]
| |

== [[Projects:PopulationBasedCorrespondence|Population Based Correspondence]] ==

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...]]

* 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
* Software available as part of UNC Neurolib open source ([http://www.ia.unc.edu/dev website])

|-

|}

File:UNC dwiatlas.png

2011-10-17T16:21:05Z

Wendyuu:

Algorithm:UNC

2011-10-17T16:20:42Z

Wendyuu:

Back to [[Algorithm:Main|NA-MIC Algorithms]]
__NOTOC__
= Overview of UNC Algorithms (PI: Martin Styner) =

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.

= UNC Projects =

{| cellpadding="10" style="text-align:left;"

| style="width:15%" |[[Image:UNC_longitudinalAtlasEx1.png|200px]]
| style="width:85%" |

== [[Projects:LongitudinalAtlasBuilding| Longitudinal Atlas Building]] ==
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...]]

<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.;

|-

| style="width:15%" |[[Image:UNC_dwiatlas.png‎|200px]]
| style="width:85%" |

== [[Projects:DWIAtlas|Diffusion Weighted Atlas Construction via model-based transformation and averaging of signal]] ==

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.
[[Projects:DWIAtlas|More...]]

<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 revision.
<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.

|-

| style="width:15%" |[[Image:UNC_GraphbasedConnectivity_Ex1.png‎|200px]]
| style="width:85%" |

== [[Projects:DiffusionGraphBasedConnectivity|Diffusion Imaging based Connectivity]] ==

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.
[[Projects:DiffusionGraphBasedConnectivity|More...]]

<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

|-

| style="width:15%" |[[Image:DTIPrep_example1.png|200px]]
| style="width:85%" |

== [[Projects:DTI_DWI_QualityControl|DWI and DTI Quality Control]] ==

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...]]

<font color="red">'''New: '''</font> DTIPrep first full version on [http://www.nitrc.org/projects/dtiprep/ NITRC ]

<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

<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

|-

| style="width:15%" |[[Image:Sulcaldepth.png|200px]]
| style="width:85%" |

== [[Projects:CorticalCorrespondenceWithParticleSystem|Cortical Correspondence using Particle System]] ==

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...]]

<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

<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

|-

| | [[Image:UNCShape_OverviewAnalysis_MICCAI06.gif|200px]]
| |

== [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|Shape Analysis Framework using SPHARM-PDM]] ==

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. [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|More...]]

* Shape Analysis Toolkit disseminated on [http://www.nitrc.org/projects/spharm-pdm NITRC SPHARM PDM page]. All tools are Slicer compatible.
* Single Slicer 3 module for whole shape analysis pipeline

<font color="red">'''New: '''</font> automatic generation of Slicer MRML scenes for result visualization

<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) preprint online

<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) preprint online.

<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) preprint online

<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

|-

| | [[Image:UNCShape_ShapeCorrespondence.png|200px]]
| |

== [[Projects:LocalStatisticalAnalysisViaPermutationTests|Local Statistical Analysis via Permutation Tests]] ==

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...]]

<font color="red">'''New: '''</font> User-friendly GUI interface and statistical result visualization via automatically generated Slicer MRML scenes

<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]

* 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

|-
| | [[Image:Cause07Competition.gif|200px]]
| |

== [[Projects:MethodEvaluationValidation|Evaluation and Comparison of Medical Image Analysis Methods]] ==

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.

<font color="red">'''New: '''</font> [[Events:_DTI_Tractography_Challenge_MICCAI_2011 | DTI fiber tractography challenge]] at MICCAI 2011

|-

| | [[Image:UNCShape_CaudatePval_MICCAI06.png|200px]]
| |

== [[Projects:PopulationBasedCorrespondence|Population Based Correspondence]] ==

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...]]

* 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
* Software available as part of UNC Neurolib open source ([http://www.ia.unc.edu/dev website])

|-

|}

2011 Summer Project Week re-parameterize fiber

2011-06-22T21:04:48Z

Wendyuu: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:Tracts Pval.png | P value of changes in diffusion properties visualized along fiber tracts
</gallery>

'''Full Title of Project'''

==Key Investigators==
* UNC-Chapel Hill: Yundi(Wendy) Shi, Clement Vachet, Benjamin Yvernault, Martin Styner
* University of Utah: Anuja Sharma

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

<h3>Objective</h3>


The dti_tract_stats tool is a command line tool developed to provide statistical information of white matter diffusion properties along fiber tracts, and therefore complements geometric information obtained by tractography with white matter integrity measurements. It calculates statistics on parametrized fiber tract data, represented as sets of streamlines. The goal of this project week is to add the functionality of 1) re-parametrizing fibers that allows visualizing further generated statistics along the stream lines. 2) Make the tool compatible with Slicer using GenerateCLP

</div>

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

<h3>Approach, Plan</h3>


* Add functionality to the original source code
* Make the tool Slicer compatible
* Use the tool for primate dataset
</div>

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

<h3>Progress</h3>


* Bugs are fixed in the tool and GenerateCLP is used to make it a slicer command line module
* Code is committed to the svn repository on NITRC
* The tool has the functions now to sample a fiber file (vtk) and generate a profile of FA/MD/AD/RD/l2/l3/GA/FRO along the fibers with different noise model (Gaussian or Beta). Sampling step size and kernel size used in the noise model could be changed.

USAGE:

dtitractstatCLP [--returnparameterfile <std::string>]
[--processinformationaddress <std::string>] [--xml]
[--echo] [--quantile_percentage <double>] [--stat_type
<mean|mode|quantile>] [--noise_model <gaussian|beta>]
[--parameter_list <std::vector<std::string>>]
[--bandwidth <double>] [--window <int>] [--step_size
<double>] [--image_space] [--window_file <std::string>]
[--plane_file <std::string>] [-o <std::string>] [-i
<std::string>] [--] [--version] [-h]

Where:

--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--quantile_percentage <double>
Quantile percentage [0,100] (default value: 50) (default: 50)

--stat_type <mean|mode|quantile>
type of maximum likelihood estimate at each point (default: mean)

--noise_model <gaussian|beta>
noise model used (gaussian or beta) (default: gaussian)

--parameter_list <std::vector<std::string>>
the list of scalar diffusion properties that are calculated. It can be
one or multiple of the following: fa,md,fro,ad,rd,l2,l3,ga (default:
"fa","md","fro","ad","rd","l2","l3","ga")

--bandwidth <double>
bandwidth or standard deviation for the kernel used in modeling noise
(default value: 1 unit) It needs to be larger than 0.1 (default: 1)

--window <int>
window (default value: -1 (no window chosen for visualization)), the
window value lies in range [0,max_number_of_kernel_windows] where
max_number_of_kernel_windows depends on the stepsize chosen and
available arc length range (default: -1)

--step_size <double>
Step size used for sampling the fiber file. It needs to be larger than
0.1 (default: 1)

--image_space
The fiber file is in default in world coordinate space. This argument
changes it to image space (default: 0)

--window_file <std::string>
csv file containing the histogram values for the chosen kernel window

--plane_file <std::string>
File that specifies the plane

-o <std::string>, --ouput_stats_file <std::string>
Ouput statistics file in .fvp format that has the statistics along the
fiber

-i <std::string>, --input_fiber_file <std::string>
input fiber file that needs to be in .vtk format

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

</div>
</div>

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

==References==



==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
http://www.nitrc.org/projects/dti_tract_stat/

2011 Summer Project Week re-parameterize fiber

2011-06-22T21:03:58Z

Wendyuu: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:Tracts Pval.png | P value of changes in diffusion properties visualized along fiber tracts
</gallery>

'''Full Title of Project'''

==Key Investigators==
* UNC-Chapel Hill: Yundi(Wendy) Shi, Clement Vachet, Benjamin Yvernault, Martin Styner
* University of Utah: Anuja Sharma

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

<h3>Objective</h3>


The dti_tract_stats tool is a command line tool developed to provide statistical information of white matter diffusion properties along fiber tracts, and therefore complements geometric information obtained by tractography with white matter integrity measurements. It calculates statistics on parametrized fiber tract data, represented as sets of streamlines. The goal of this project week is to add the functionality of 1) re-parametrizing fibers that allows visualizing further generated statistics along the stream lines. 2) Make the tool compatible with Slicer using GenerateCLP

</div>

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

<h3>Approach, Plan</h3>


* Add functionality to the original source code
* Make the tool Slicer compatible
* Use the tool for primate dataset
</div>

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

<h3>Progress</h3>


Bugs are fixed in the tool and GenerateCLP is used to make it a slicer command line module
Code is committed to the svn repository on NITRC
The tool has the functions now to sample a fiber file (vtk) and generate a profile of FA/MD/AD/RD/l2/l3/GA/FRO along the fibers with different noise model (Gaussian or Beta). Sampling step size and kernel size used in the noise model could be changed.

USAGE:

dtitractstatCLP [--returnparameterfile <std::string>]
[--processinformationaddress <std::string>] [--xml]
[--echo] [--quantile_percentage <double>] [--stat_type
<mean|mode|quantile>] [--noise_model <gaussian|beta>]
[--parameter_list <std::vector<std::string>>]
[--bandwidth <double>] [--window <int>] [--step_size
<double>] [--image_space] [--window_file <std::string>]
[--plane_file <std::string>] [-o <std::string>] [-i
<std::string>] [--] [--version] [-h]

Where:

--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--quantile_percentage <double>
Quantile percentage [0,100] (default value: 50) (default: 50)

--stat_type <mean|mode|quantile>
type of maximum likelihood estimate at each point (default: mean)

--noise_model <gaussian|beta>
noise model used (gaussian or beta) (default: gaussian)

--parameter_list <std::vector<std::string>>
the list of scalar diffusion properties that are calculated. It can be
one or multiple of the following: fa,md,fro,ad,rd,l2,l3,ga (default:
"fa","md","fro","ad","rd","l2","l3","ga")

--bandwidth <double>
bandwidth or standard deviation for the kernel used in modeling noise
(default value: 1 unit) It needs to be larger than 0.1 (default: 1)

--window <int>
window (default value: -1 (no window chosen for visualization)), the
window value lies in range [0,max_number_of_kernel_windows] where
max_number_of_kernel_windows depends on the stepsize chosen and
available arc length range (default: -1)

--step_size <double>
Step size used for sampling the fiber file. It needs to be larger than
0.1 (default: 1)

--image_space
The fiber file is in default in world coordinate space. This argument
changes it to image space (default: 0)

--window_file <std::string>
csv file containing the histogram values for the chosen kernel window

--plane_file <std::string>
File that specifies the plane

-o <std::string>, --ouput_stats_file <std::string>
Ouput statistics file in .fvp format that has the statistics along the
fiber

-i <std::string>, --input_fiber_file <std::string>
input fiber file that needs to be in .vtk format

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

</div>
</div>

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

==References==



==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
http://www.nitrc.org/projects/dti_tract_stat/

2011 Summer Project Week re-parameterize fiber

2011-06-20T18:52:22Z

Wendyuu: /* Key Investigators */

2011 Summer Project Week re-parameterize fiber

2011-06-20T18:35:33Z

Wendyuu: /* Key Investigators */

2011 Summer Project Week

2011-06-20T18:35:08Z

Wendyuu: /* Projects */

Back to [[Events]]

[[image:PW-MIT2011.png|right|204px]]

[[image:Panorama-summer-2011.png|left|thumb|200px|[http://360.io/Afjepd Interactive Panorama of Project Week] (Works on chrome, maybe not on other browsers)]]

*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT ([http://whereis.mit.edu/?go=34 Grier Rooms Location on MIT Campus Map])

==Preliminary Agenda==
==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 20
!style="width:18%" |Tuesday, June 21
!style="width:18%" |Wednesday, June 22
!style="width:18%" |Thursday, June 23
!style="width:18%" |Friday, June 24
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-11am:''' Slicer4 Extension Writing Tutorial (Finet, Fillion-Robin)
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> [[2011 Summer Project Week Breakout Session Slicer4 Annotation|Slicer4 Annotations]] (Nicole Aucoin)<br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:15pm''' Slicer4 Developers Guided Tour (Pieper) ([[media:2011 Summer-Slicer4.ppt|Slides]]). <br>---<br>'''4:15-5:00pm''' [[2011 Project Week Breakout Session: Slicer4|Slicer 4 Core Modules Usability Review]]''' [[MIT_Project_Week_Rooms#Star|Star Room]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:MultiVolumeContainer#Summer_2011_Project_Week_Breakout_Session Slicer4 MultiVolume Containers] (Nicole Aucoin)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[Summer_2011_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' [[2011 Summer Project Week Breakout Session VTKCharts|VTK Charts]] (Marcus Hanwell)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2011|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2011_Summer_Project_Week_Breakout_Session_EMRegistration|Inter-subject Registration for EM segmenter]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''1-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

* Please make a link for your project to a new page based on the [[2011_Summer_Project_Week_Template| 2011 Summer Project Page Template]]

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

#[[2011_Summer_Project_Week_Segmentation_TBI|Segmentation of Longitudinal TBI data]] (Bo Wang, Jack Van Horn, Andrei Irimia, Marcel Prastawa, Guido Gerig)
#[[Multimodality Image Registration for TBI]] (Yifei Lou, Danielle Pace, Jack Van Horn, Micah Chambers)
#[[2011_Summer_Project_Week_White_Matter_Laterality|White Matter Laterality in Python/Slicer4]] (Lauren O'Donnell)
#[[2011_Summer_Project_Week_Intraoperative_Brain_Shift_Monitor|Intraoperative Brain Shift Monitor]] (Jason White, Alex Golby, Steve Pieper, Junichi Tokuda)
#[[2011_Summer_Project_Week_GBM_Masks|Obtaining and Evaluation of Glioblastoma Multiforme (GBM) Segmentation Masks]] (Jan Egger,Tina Kapur, Andriy Fedorov, Rivka Colen, Ron Kikinis, Alex Golby, Christopher Nimsky)
#[[2011_Summer_Project_Week_NerveSeg|Segmentation of Nerve and Nerve Ganglia in the Spine]] (Adrian Dalca, Giovanna Danagoulian, Ron Kikinis, Ehud Schmidt, Polina Golland)
#[[2011_Summer_Project_Week_Spine_Segmentation_And_Osteoporosis_Screening_CT|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)
#[[2011_Summer_Project_Week_Quantitative_Magnetic_Susceptibility_Mapping|Quantitative Magnetic Susceptibility Mapping ]] (Clare Poynton)

'''Radiation Therapy'''
#[[2011_Summer Project Week_Non-rigid_inter-patient_registration_of_bone_masks_derived_from_CT_for_Head_and_Neck_Cancer_Radiation_Therapy|Non-rigid, inter-patient registration of bone masks derived from CT for Head and Neck Cancer Radiation Therapy]] (Ivan Kolesov, Yi Gao, Gregory Sharp,Xiaodong Tao,Nadya Shusharina, Jan Egger, and Allen Tannenbaum)
#[[2011_Summer_Project_Week_Contouring_Gyne_Structures|Contouring of Anatomy Structures like Tumor, Bladder, Rectum and Sigmoid for Gynecological Brachytherapy]] (Tina Kapur, Akila Viswanathan, Jan Egger)
#[[2011_Summer_Project_Week_Slicer_DICOM_RT_Brachytherapy|Visualization of DICOM RT Planning Contours and Dose Distributions for Prostate and Gynecologic Brachytherapy in Slicer]] (Firdaus Janoos, Jan Egger, Greg Sharp, Andriy Fedorov, Tina Kapur)
#[[2011_Summer_Project__Week_DVH|Dose volume histograms in Slicer]] (Greg Sharp, Nadya Shusharina, Steve Pieper, Csaba Pinter, Tina Kapur)
#[[2011_Summer_Project__Week_DICOM_RT|Synthetic images, vector fields, RT structures and RT doses in Slicer and ITK]]. (Nadya Shusharina, Greg Sharp, Luis Ibanez, Steve Pieper)

'''Huntington's Disease'''
#[[2011_Summer_Project_Week_normal_consistency_particles|Normal consistency in particle correspondence computation using great circles in principal spheres - Huntington's Disease]], (Beatriz Paniagua, Martin Styner, Sungkyu Jung, Mark Scully)
#[[2011_Summer_Project__Week_Shape_Analysis_UNC |SPHARM & particles shape analysis - Huntington's Disease]] (Lucile Bompard, Clement Vachet, Beatriz Paniagua, Martin Styner
#[[2011_Summer_Project_Week_long_shape_regression|Longitudinal Shape Regression - Huntington's Disease]] (James Fishbaugh, Marcel Prastawa, Guido Gerig, Hans Johnson)
#[[2011_Summer_Project_Week_DTIPrep|DTIPrep - "Study-specific Protocol" based automatic DWI/DTI quality control and preparation]] - Huntington's Disease (Mashid Farzinfar, Clement Vachet, Joy Matsui, Martin Styner)
#[[2011_Summer_Project_Week_DTI_PairWise_Registration|DTI pair-wise registration module]] - Huntington's Disease (Clement Vachet, Joy Matsui, Mark Scully, Martin Styner)
#[[2011_Summer_Project_Week_DTI analysis_for_Huntington's_disease | DTI analysis for Huntington's disease]] (Gopal Veni, Ross Whitaker)

'''Atrial Fibrillation'''
#[[2011_Summer_Project_Week_RSS_for_AFib_Ablation|Robust Statistical Segmentation (RSS) for the Atrial Fibrillation Ablation Therapy]] (Yi Gao, Kedar Patwardhan, Steve Pieper, Wassim Haddad, and Allen Tannenbaum, Rob MacLeod, Josh Blauer, and Josh Cates)
#[[2011_Summer_Project_Week_Watersheds|Interactive Watersheds Segmentation Module for Slicer for Atrial Fibrillation and HN Cancer]] (Josh Cates, Ross Whitaker, Steve Pieper, Jim Miller, Nadya)

'''Device Integration with Slicer and General Image Guided Therapy'''
#[[2011_Summer_Project__Week_Wireless_Joystick|Wireless joystick controlling medical devices and software (e.g. Slicer4) in the operating room]] (Szymon Kostrzewski)
#[[2011_Summer_Project__Week_Live_Tracked_Ultrasound|Live Tracked Ultrasound with Slicer4 (Tamas Heffter)]]
#[http://wiki.na-mic.org/Wiki/index.php/Survey_stealthlink_openigtlink Surveying research teams interested in Open IGT Link support of Stealth Station (Nobuhiko Hata, Ron Kikinis)]
#[[2011_Summer_Project_Week_Needle_Detection_to_Control_Scanner_for_Prostate_Biopsy | Needle Detection to Control Scanner for Prostate Biopsy ]] (Atsushi Yamada, Loïc Cadour, Junichi Tokuda and Nobuhiko Hata)
#[[2011_Summer_Project_Week_Segementation_Reconstruction_Pericardial_Sac]] (Mohsen Mahvash, Noby Hata, Ron Kikinis)
#[[2011_Summer_Project_Week_4DUltrasound_HybridProbe_OsteoPlan|4D Ultrasound / Hybrid Probe / OsteoPlan]] (Laurent Chauvin, Noby Hata)
#[[2011_Summer_Project_Week_AMIGO|AMIGO]] (Mallika Winsor, Vivian He, Dan Kacher, Tina Kapur)

'''General Segmentation'''
#[[2011_Summer_Project_Week_Integrate_BRAINSCut_into_Slicer3]](Regina Kim, ... )
#[[2011_Summer_Project_Week_EMSegmentation_in_3D_Slicer4|EM Segmentation in 3D Slicer 4]] (Daniel Haehn, Dominique Belhachemi, Kilian Pohl)
#[[2011_Summer_Project_Week_Customizing_EMSegmenter_pipelines_for_brain_lesions | Customizing EMSegmenter pipelines for brain lesions]] (Dominique Belhachemi, Alexander Zaitsev, Kilian Pohl)
#[[2011_Summer_Project_Week_Plastimatch_for_EMSegmenter | Integrating Plastimatch into the EMSegmenter]] (Dominique Belhachemi, Kilian Pohl, Greg Sharp, Daniel Haehn)
#[[2011_Summer_Project_Week_Slicer_Extension_for_GLISTR | Slicer extension for GLiome Image SegmenTation and Registration (GLISTR)]] (Andreas Schuh, Daniel Haehn, Kilian Pohl)

'''General Registration'''
#[[2011_Summer_Project_Week__BRAINSFit_new_features_integration|Integrate new features into BRAINSFit]] (Andrey Fedorov, Hans Johnson, Mark Scully)
#[[2011_Summer_Project_Week__LANDWARP_integration|Integration of LANDWARP into interactive registration module]] (Andrey Fedorov, Greg Sharp, Nadya Shusharina)
#[[2011_Summer_Project_Week_Registration_of_mouse_brains|Registration of mouse brains]] (Francois Budin)
#[[NonRigidRegistrationThatAccommodatesResection|Demons Based Non-Rigid Registration that Accommodates Resection in 3D Slicer]] (Petter Risholm, Sandy Wells)
#[[2011_Summer_Project_Week_SlidingOrganRegistrationFED|Integrate Fast Explicit Diffusion into Sliding Organ Registration module]] (Danielle Pace)
#[[2011_Summer_Project_Week_Image_Manifold_Learning_with_Spectral_Embedding_and_Laplacian_Eigenmaps|Image Manifold Learning with Spectral Embedding and Laplacian Eigenmaps]] (Ramesh Sridharan, Polina Golland)

'''General Diffusion Tractography'''
#[[2011_Summer_Project_Week_WMGeometry_Slicer4 | White matter geometry measures in Slicer 4]] (Peter Savadjiev)
#[[2011_Summer_Project_Week_re-parameterize_fiber|Re-parametrize fiber tracts for fiber statistics analysis]] (Yundi Shi, Clement Vachet, Benjamin Yvernault, Anuja Sharma, Martin Styner)
#[[2011_Summer_Project_Week_ODF_though_Fiber_Counting | ODF computation through fiber counting]] (Yinpeng Li, Ipek Oguz, Martin Styner)
#[[2011_Summer_Project_Week_Nifti_Support_for_Diffusion_Tensor_Images|Nifti Support for Diffusion Tensor Images]] (Demian)
#[[2011_Summer_Project_Week_Finishing_details_on_the_workflows_DICOM_full_brain_tractography_peritumoral|Finishing details on the workflows: DICOM->Full brain tractography / peritumoral]] (Demian)
#[[Summer_project_week_2011_Finsler_Streamlines|Adding streamlined tractography to the Finsler front propagation tractography toolkit]] (Antonio Tristán-Vega)
#[[2011_Summer_Project_Week_Slicer4_Tractography_Interaction_and_Display|Tractography Bundle/Cluster Interaction and Display in Slicer4]] (Lauren O'Donnell, Isaiah, Demian)
#[[2011_Summer_Project_Week_DTI_Volumetric_Tractography | DTI Volumetric Tractography]] (Steve Callahan, Mark Scully, Jim Miller)
#[[2011_Summer_Project_Week_DWI_Atlas | Slicer module for building an average population DWI Atlas]] (Ryan Eckbo, Sylvain Bouix)
#[[2011_Summer_Project_Week_DTI_Volumetric_Segmentation_for_Group_studies | DTI Volumetric Segmentation for Group studies]] (Gopal Veni, Ross Whitaker)

'''Vessels'''
#[[2011_Summer_Project_Week_SlicerVmtk4|The Vascular Modeling Toolkit in 3D Slicer 4]] (Daniel Haehn, Luca Antiga, Steve Pieper, Kilian Pohl, Ron Kikinis)
#[[2011_Summer_Project__Week_Stenosis_Detector|Stenosis Detector in 3D Slicer 4]] (Suares Tamekue, Daniel Haehn, Luca Antiga, Ron Kikinis)

'''Infrastructure'''
#[[2011_Summer_Project_Week_Annotation_Module|Annotation Module in Slicer4]] (Nicole Aucoin, Daniel Haehn)
#[[2011_Summer_Project_Week_RECIST|RECIST Slicer4 module]] (Nicole Aucoin)
#[[2011_Summer_Project_Week_Dicom2Nrrd|DicomToNrrdConverter refactoring]] ( Xiaodong Tao, Mark Scully)
#[[Summer_project_week_2011_Workflows_SOA|Workflows and Service Oriented Architecture Modules for Slicer4 as Extensions]] (Alexander Zaitsev, Wendy Plesniak, Ron Kikinis)
#[[2011_Summer_Project__Week_DICOM_Networking|DICOM Networking interface for Slicer4]] (Steve Pieper, Nicole Aucoin, Noby Hata)
#[[2011_Summer_Project_Week_Automated_GUI_Testing| Automated GUI Testing (Sonia Pujol, Steve Pieper, Dave Partyka, Jean-Christophe Fillion-Robin, Xiaodong Tao)]]
#[[2011_Summer_Project_Week_FetchMI:_Slicer_integration_with_XNAT |FetchMI: Slicer integration with XNAT 1.5]] (Misha Milchenko, Wendy Plesniak)
#[[2011_Summer_Project_Week_Internationalization_of_Slicer|Internationalization of Slicer]] (Luping Fang, Steve Pieper, Daniel Haehn, Suares Tamekue, Jean-Christophe Fillion-Robin, Julien Finet, Yiming Ge, Ping Cao)

==Background==

We are pleased to announce the 13th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 28th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

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

== Logistics ==
*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please register [http://guest.cvent.com/d/sdqy0l/4W here]. Payment must be made by credit card.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' Boston Marriott Cambridge, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. Group rate is $199/night plus tax. Book [http://www.marriott.com/hotels/travel/boscb?groupCode=jrbjrba&app=resvlink&fromDate=6/19/11&toDate=6/24/11 here] or call 1-617-494-6600 and mention that you are booking in the MIT Room Block. '''All reservations must be made by May 29, 2011 to receive the discounted rate.'''

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 28, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 12, all participants to add a one line title of their project to #Projects
#By 3pm ET on Thursday June 9, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 16: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Registrants==

Do not add your name to this list- it is maintained by the organizers based on your paid registration (see Logistics for link)
# Peter Anderson, Retired
# Nicole Aucoin, Brigham and Women's Hospital
# Dominique Belhachemi, University of Pennsylvania
# Anthony Blumfiled, Radnostics
# Lucile Bompard, UNC NIRAL
# Sylvain Bouix, Brigham and Women's Hospital
# Francois Budin, UNC NIRAL
# Steve Callahan, University of Utah
# Joshua Cates, University of Utah
# Micah Chambers, Laboratory of NeuroImaging
# Laurent Chauvin, Brigham and Women's Hospital
# Rivka Colen, Brigham and Women's Hospital
# Nikos Chrisochoides, Old Dominion University
# Adrian Dalca, Massachusetts Institute of Technology
# Manasi Datar, University of Utah
# Colin Davey
# Ryan Eckbo, Brigham and Women's Hospital
# Jan Egger, University Hospital of Marburg
# Luping Fang, Zhejiang University of Technology, China
# Mahshid Farzinfar, University of North Carolina at Chapel Hill
# Andriy Fedorov, Brigham and Women's Hospital
# Jean-Christophe Fillion-Robin, Kitware, Inc.
# Julien Finet, Kitware, Inc.
# James Fishbaugh, University of Utah
# Yi Gao, Georgia Institute of Technology
# Greg Gardner, University of Utah
# Ronen Globinsky, Yale University
# Vivian He, Brigham and Women's Hospital
# Maged Goubran, Robarts Research Institute
# Daniel Haehn, University of Pennsylvania
# Mike Halle, Brigham and Women's Hospital
# Marcus Hanwell, Kitware, Inc.
# Firdaus Janoos, Brigham and Women's Hospital
# Noby Hata, Brigham and Women's Hospital
# Tamas Heffter, Queen's University
# Nicholas Herlambang, AZE, Ltd.
# Luis Ibanez, Kitware, Inc.
# Andrei Irimia, University of California, Los Angeles
# Hans Johnson, University of Iowa
# Ilknur Kabul, Kitware, Inc.
# Tina Kapur, Brigham and Women's Hospital
# Peter Karasev, Georgia Institute of Technology
# Ron Kikinis, Brigham and Women's Hospital
# Regina Kim, University of Iowa
# Ivan Kolesov, Georgia Institute of Technology
# Szymon Kostrzewski, Ecole Polytechnique Federale de Lausanne EPFL
# Dillon Lee, University of Utah
# Yinpeng Li, UNC-NIRAL
# Yifei Lou, Georgia Institute of Technology
# Mohsen Mahvash, Harvard Medical School (BWH and VA)
# Nikos Makris, Massachusetts General Hospital
# Katie Mastrogiacomo, Brigham and Women's Hospital
# Joy Matsui, University of Iowa
# Dominik Meier, Brigham and Women's Hospital
# Mikhail Milchenko, Washington University in St. Louis
# James Miller, GE Research
# Zach Mullen, Kitware, Inc.
# Isaiah Norton, Brigham and Women's Hospital
# Lauren O'Donnell, Brigham and Women's Hospital
# Danielle Pace, Kitware, Inc.
# Beatriz Paniagua, University of North Carolina at Chapel Hill
# Xenophon Papademetris, Yale University
# Kedar Patwardhan, GE Global Research
# Steve Pieper, Isomics, Inc.
# Csaba Pinter, Queen's University
# Wendy Plesniak, Brigham and Women's Hospital
# Kilian Pohl, University of Pennsylvania
# Marcel Prastawa, University of Utah
# Sonia Pujol, Brigham and Women's Hospital
# Martin Rajchl, Robarts Research Institute
# Ramesh Sridharan, Massachusetts Institute of Technology
# Petter Risholm, Brigham and Women's Hospital
# Peter Savadjiev, Brigham and Women's Hospital
# Will Schroeder, Kitware, Inc.
# Andreas Schuh, University of Pennsylvania
# Mark Scully, University of Iowa
# Gregory Sharp, Massachusetts General Hospital
# Junichi Tokuda, Brigham and Women's Hospital
# Yundi Shi, University of North Carolina at Chapel Hill
# Matthew Toews, Brigham and Women's Hospital
# Nadya Shusharina, Massachusetts General Hospital
# Hao Su, Worcester Polytechnic Institute
# Suares Tamekue, Brigham and Women's Hospital
# Xiaodong Tao, GE Research
# Clement Vachet, UNC Chapel Hill
# Antonio Vega, Brigham and Women's Hospital
# Gopal Veni, University of Utah
# Bo Wang, University of Utah
# Andrew Wassam, CoSMo Software Inc.
# Demian Wassermann, Brigham and Women's Hospital
# Sandy Wells, Brigham and Women's Hospital
# Jason White, Brigham and Women's Hospital
# Mallika Winsor, Brigham and Women's Hospital
# Atsushi Yamada, Brigham and Women's Hospital
# Alexander Yarmarkovich, Isomics, Inc.
# Alexander Zaitsev, Brigham and Women's Hospital
# Ming Zhao, Sun Yat-Sen University Cancer Center, GuangZhou, China

2011 Summer Project Week

2011-06-20T17:58:19Z

Wendyuu: /* Projects */

Back to [[Events]]

[[image:PW-MIT2011.png|right|200px]]

[[image:Panorama-summer-2011.png]] [http://360.io/Afjepd Interactive Panorama of Project Week] (Works on chrome, maybe not on other browsers)

*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT ([http://whereis.mit.edu/?go=34 Grier Rooms Location on MIT Campus Map])

==Preliminary Agenda==
==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 20
!style="width:18%" |Tuesday, June 21
!style="width:18%" |Wednesday, June 22
!style="width:18%" |Thursday, June 23
!style="width:18%" |Friday, June 24
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-11am:''' [[2011 Project Week Breakout Session: Slicer4|Slicer 4 Core Modules Usability Review]]''' [[MIT_Project_Week_Rooms#Star|Star Room]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> [[2011 Summer Project Week Breakout Session Slicer4 Annotation|Slicer4 Annotations]] (Nicole Aucoin)<br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-5:00pm: NA-MIC Kit Update''' Slicer4 Developers Guided Tour (Pieper) ([[media:2011 Summer-Slicer4.ppt|Slides]]), Slicer4 Extension Writing Tutorial (Finet, Fillion-Robin)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:MultiVolumeContainer#Summer_2011_Project_Week_Breakout_Session Slicer4 MultiVolume Containers] (Nicole Aucoin)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[Summer_2011_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' [[2011 Summer Project Week Breakout Session VTKCharts|VTK Charts]] (Marcus Hanwell)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2011|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2011_Summer_Project_Week_Breakout_Session_EMRegistration|Inter-subject Registration for EM segmenter]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''1-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

* Please make a link for your project to a new page based on the [[2011_Summer_Project_Week_Template| 2011 Summer Project Page Template]]

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

#[[2011_Summer_Project_Week_Segmentation_TBI|Segmentation of Longitudinal TBI data]] (Bo Wang, Jack Van Horn, Andrei Irimia, Marcel Prastawa, Guido Gerig)
#[[Multimodality Image Registration for TBI]] (Yifei Lou, Danielle Pace, Jack Van Horn, Micah Chambers)
#[[2011_Summer_Project_Week_White_Matter_Laterality|White Matter Laterality in Python/Slicer4]] (Lauren O'Donnell)
#[[2011_Summer_Project_Week_Intraoperative_Brain_Shift_Monitor|Intraoperative Brain Shift Monitor]] (Jason White, Alex Golby, Steve Pieper, Junichi Tokuda)
#[[2011_Summer_Project_Week_GBM_Masks|Obtaining and Evaluation of Glioblastoma Multiforme (GBM) Segmentation Masks]] (Jan Egger,Tina Kapur, Andriy Fedorov, Rivka Colen, Ron Kikinis, Alex Golby, Christopher Nimsky)
#[[2011_Summer_Project_Week_NerveSeg|Segmentation of Nerve and Nerve Ganglia in the Spine]] (Adrian Dalca, Giovanna Danagoulian, Ron Kikinis, Ehud Schmidt, Polina Golland)
#[[2011_Summer_Project_Week_Spine_Segmentation_And_Osteoporosis_Screening_CT|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)
#[[2011_Summer_Project_Week_Quantitative_Magnetic_Susceptibility_Mapping|Quantitative Magnetic Susceptibility Mapping ]] (Clare Poynton)

'''Radiation Therapy'''
#[[2011_Summer Project Week_Non-rigid_inter-patient_registration_of_bone_masks_derived_from_CT_for_Head_and_Neck_Cancer_Radiation_Therapy|Non-rigid, inter-patient registration of bone masks derived from CT for Head and Neck Cancer Radiation Therapy]] (Ivan Kolesov, Yi Gao, Gregory Sharp, and Allen Tannenbaum)
#[[2011_Summer_Project_Week_Contouring_Gyne_Structures|Contouring of Anatomy Structures like Tumor, Bladder, Rectum and Sigmoid for Gynecological Brachytherapy]] (Tina Kapur, Akila Viswanathan, Jan Egger)
#[[2011_Summer_Project_Week_Slicer_DICOM_RT_Brachytherapy|Visualization of DICOM RT Planning Contours and Dose Distributions for Prostate and Gynecologic Brachytherapy in Slicer]] (Firdaus Janoos, Jan Egger, Greg Sharp, Andriy Fedorov, Tina Kapur)
#[[2011_Summer_Project__Week_DVH|Dose volume histograms in Slicer]] (Greg Sharp, Nadya Shusharina, Steve Pieper, Csaba Pinter, Tina Kapur)
#[[2011_Summer_Project__Week_DICOM_RT|Synthetic images, vector fields, RT structures and RT doses in Slicer and ITK]]. (Nadya Shusharina, Greg Sharp, Luis Ibanez, Steve Pieper)

'''Huntington's Disease'''
#[[2011_Summer_Project_Week_normal_consistency_particles|Normal consistency in particle correspondence computation using great circles in principal spheres - Huntington's Disease]], (Beatriz Paniagua, Martin Styner, Sungkyu Jung, Mark Scully)
#[[2011_Summer_Project__Week_Shape_Analysis_UNC |SPHARM & particles shape analysis - Huntington's Disease]] (Lucile Bompard, Clement Vachet, Beatriz Paniagua, Martin Styner
#[[2011_Summer_Project_Week_long_shape_regression|Longitudinal Shape Regression - Huntington's Disease]] (James Fishbaugh, Marcel Prastawa, Guido Gerig, Hans Johnson)
#[[2011_Summer_Project_Week_DTIPrep|DTIPrep - "Study-specific Protocol" based automatic DWI/DTI quality control and preparation]] - Huntington's Disease (Mashid Farzinfar, Clement Vachet, Joy Matsui, Martin Styner)
#[[2011_Summer_Project_Week_DTI_PairWise_Registration|DTI pair-wise registration module]] - Huntington's Disease (Clement Vachet, Joy Matsui, Mark Scully, Martin Styner)
#[[2011_Summer_Project_Week_DTI analysis_for_Huntington's_disease | DTI analysis for Huntington's disease]] (Gopal Veni, Ross Whitaker)

'''Atrial Fibrillation'''
#[[2011_Summer_Project_Week_RSS_for_AFib_Ablation|Robust Statistical Segmentation (RSS) for the Atrial Fibrillation Ablation Therapy]] (Yi Gao, Kedar Patwardhan, Wassim Haddad, and Allen Tannenbaum, Rob MacLeod, Josh Blauer, and Josh Cates)
#[[2011_Summer_Project_Week_Watersheds|Interactive Watersheds Segmentation Module for Slicer for Atrial Fibrillation and HN Cancer]] (Josh Cates, Ross Whitaker, Steve Pieper, Jim Miller, Nadya)

'''Device Integration with Slicer and General Image Guided Therapy'''
#[[2011_Summer_Project__Week_Wireless_Joystick|Wireless joystick controlling medical devices and software (e.g. Slicer4) in the operating room]] (Szymon Kostrzewski)
#[[2011_Summer_Project__Week_Live_Tracked_Ultrasound|Live Tracked Ultrasound with Slicer4 (Tamas Heffter)]]
#[http://wiki.na-mic.org/Wiki/index.php/Survey_stealthlink_openigtlink Surveying research teams interested in Open IGT Link support of Stealth Station (Nobuhiko Hata, Ron Kikinis)]
#[[2011_Summer_Project_Week_Needle_Detection_to_Control_Scanner_for_Prostate_Biopsy | Needle Detection to Control Scanner for Prostate Biopsy ]] (Atsushi Yamada, Loïc Cadour, Junichi Tokuda and Nobuhiko Hata)
#[[2011_Summer_Project_Week_Segementation_Reconstruction_Pericardial_Sac]] (Mohsen Mahvash, Noby Hata, Ron Kikinis)
#[[2011_Summer_Project_Week_4DUltrasound_HybridProbe_OsteoPlan|4D Ultrasound / Hybrid Probe / OsteoPlan]] (Laurent Chauvin, Noby Hata)
#[[2011_Summer_Project_Week_AMIGO|AMIGO]] (Mallika Winsor, Vivian He, Dan Kacher, Tina Kapur)

'''General Segmentation'''
#[[2011_Summer_Project_Week_Integrate_BRAINSCut_into_Slicer3]](Regina Kim, ... )
#[[2011_Summer_Project_Week_EMSegmentation_in_3D_Slicer4|EM Segmentation in 3D Slicer 4]] (Daniel Haehn, Dominique Belhachemi, Kilian Pohl)
#[[2011_Summer_Project_Week_Customizing_EMSegmenter_pipelines_for_brain_lesions | Customizing EMSegmenter pipelines for brain lesions]] (Dominique Belhachemi, Alexander Zaitsev, Kilian Pohl)
#[[2011_Summer_Project_Week_Plastimatch_for_EMSegmenter | Integrating Plastimatch into the EMSegmenter]] (Dominique Belhachemi, Kilian Pohl, Greg Sharp, Daniel Haehn)
#[[2011_Summer_Project_Week_Slicer_Extension_for_GLISTR | Slicer extension for GLiome Image SegmenTation and Registration (GLISTR)]] (Andreas Schuh, Daniel Haehn, Kilian Pohl)

'''General Registration'''
#[[2011_Summer_Project_Week__BRAINSFit_new_features_integration|Integrate new features into BRAINSFit]] (Andrey Fedorov, Hans Johnson, Mark Scully)
#[[2011_Summer_Project_Week__LANDWARP_integration|Integration of LANDWARP into interactive registration module]] (Andrey Fedorov, Greg Sharp, Nadya Shusharina)
#[[2011_Summer_Project_Week_Registration_of_mouse_brains|Registration of mouse brains]] (Francois Budin)
#[[NonRigidRegistrationThatAccommodatesResection|Demons Based Non-Rigid Registration that Accommodates Resection in 3D Slicer]] (Petter Risholm, Sandy Wells)
#[[2011_Summer_Project_Week_SlidingOrganRegistrationFED|Integrate Fast Explicit Diffusion into Sliding Organ Registration module]] (Danielle Pace)
#[[2011_Summer_Project_Week_Image_Manifold_Learning_with_Spectral_Embedding_and_Laplacian_Eigenmaps|Image Manifold Learning with Spectral Embedding and Laplacian Eigenmaps]] (Ramesh Sridharan, Polina Golland)

'''General Diffusion Tractography'''
#[[2011_Summer_Project_Week_WMGeometry_Slicer4 | White matter geometry measures in Slicer 4]] (Peter Savadjiev)
#[[2011_Summer_Project_Week_re-parameterize_fiber|Re-parametrize fiber tracts for fiber statistics analysis]] (Yundi Shi, Benjamin Yvernault, Clement Vachet, Anuja Sharma, Martin Styner)
#[[2011_Summer_Project_Week_ODF_though_Fiber_Counting | ODF computation through fiber counting]] (Yinpeng Li, Ipek Oguz, Martin Styner)
#[[2011_Summer_Project_Week_Nifti_Support_for_Diffusion_Tensor_Images|Nifti Support for Diffusion Tensor Images]] (Demian)
#[[2011_Summer_Project_Week_Finishing_details_on_the_workflows_DICOM_full_brain_tractography_peritumoral|Finishing details on the workflows: DICOM->Full brain tractography / peritumoral]] (Demian)
#[[Summer_project_week_2011_Finsler_Streamlines|Adding streamlined tractography to the Finsler front propagation tractography toolkit]] (Antonio Tristán-Vega)
#[[2011_Summer_Project_Week_Slicer4_Tractography_Interaction_and_Display|Tractography Bundle/Cluster Interaction and Display in Slicer4]] (Lauren O'Donnell, Isaiah, Demian)
#[[2011_Summer_Project_Week_DTI_Volumetric_Tractography | DTI Volumetric Tractography]] (Steve Callahan, Mark Scully, Jim Miller)
#[[2011_Summer_Project_Week_DWI_Atlas | Slicer module for building an average population DWI Atlas]] (Ryan Eckbo, Sylvain Bouix)
#[[2011_Summer_Project_Week_DTI_Volumetric_Segmentation_for_Group_studies | DTI Volumetric Segmentation for Group studies]] (Gopal Veni, Ross Whitaker)

'''Vessels'''
#[[2011_Summer_Project_Week_SlicerVmtk4|The Vascular Modeling Toolkit in 3D Slicer 4]] (Daniel Haehn, Luca Antiga, Steve Pieper, Kilian Pohl, Ron Kikinis)
#[[2011_Summer_Project__Week_Stenosis_Detector|Stenosis Detector in 3D Slicer 4]] (Suares Tamekue, Daniel Haehn, Luca Antiga, Ron Kikinis)

'''Infrastructure'''
#[[2011_Summer_Project_Week_Annotation_Module|Annotation Module in Slicer4]] (Nicole Aucoin, Daniel Haehn)
#[[2011_Summer_Project_Week_RECIST|RECIST Slicer4 module]] (Nicole Aucoin)
#[[2011_Summer_Project_Week_Dicom2Nrrd|DicomToNrrdConverter refactoring]] ( Xiaodong Tao, Mark Scully)
#[[Summer_project_week_2011_Workflows_SOA|Workflows and Service Oriented Architecture Modules for Slicer4 as Extensions]] (Alexander Zaitsev, Wendy Plesniak, Ron Kikinis)
#[[2011_Summer_Project__Week_DICOM_Networking|DICOM Networking interface for Slicer4]] (Steve Pieper, Nicole Aucoin, Noby Hata)
#[[2011_Summer_Project_Week_Automated_GUI_Testing| Automated GUI Testing (Sonia Pujol, Steve Pieper, Dave Partyka, Jean-Christophe Fillion-Robin, Xiaodong Tao)]]
#[[2011_Summer_Project_Week_FetchMI:_Slicer_integration_with_XNAT |FetchMI: Slicer integration with XNAT 1.5]] (Misha Milchenko, Wendy Plesniak)
#[[2011_Summer_Project_Week_Internationalization_of_Slicer|Internationalization of Slicer]] (Luping Fang, Steve Pieper, Daniel Haehn, Suares Tamekue, Jean-Christophe Fillion-Robin, Julien Finet, Yiming Ge, Ping Cao)

==Background==

We are pleased to announce the 13th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 28th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

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

== Logistics ==
*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please register [http://guest.cvent.com/d/sdqy0l/4W here]. Payment must be made by credit card.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' Boston Marriott Cambridge, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. Group rate is $199/night plus tax. Book [http://www.marriott.com/hotels/travel/boscb?groupCode=jrbjrba&app=resvlink&fromDate=6/19/11&toDate=6/24/11 here] or call 1-617-494-6600 and mention that you are booking in the MIT Room Block. '''All reservations must be made by May 29, 2011 to receive the discounted rate.'''

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 28, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 12, all participants to add a one line title of their project to #Projects
#By 3pm ET on Thursday June 9, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 16: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Registrants==

Do not add your name to this list- it is maintained by the organizers based on your paid registration (see Logistics for link)
# Peter Anderson, Retired
# Nicole Aucoin, Brigham and Women's Hospital
# Dominique Belhachemi, University of Pennsylvania
# Anthony Blumfiled, Radnostics
# Lucile Bompard, UNC NIRAL
# Sylvain Bouix, Brigham and Women's Hospital
# Francois Budin, UNC NIRAL
# Steve Callahan, University of Utah
# Joshua Cates, University of Utah
# Micah Chambers, Laboratory of NeuroImaging
# Laurent Chauvin, Brigham and Women's Hospital
# Rivka Colen, Brigham and Women's Hospital
# Nikos Chrisochoides, Old Dominion University
# Adrian Dalca, Massachusetts Institute of Technology
# Manasi Datar, University of Utah
# Colin Davey
# Ryan Eckbo, Brigham and Women's Hospital
# Jan Egger, University Hospital of Marburg
# Luping Fang, Zhejiang University of Technology, China
# Mahshid Farzinfar, University of North Carolina at Chapel Hill
# Andriy Fedorov, Brigham and Women's Hospital
# Jean-Christophe Fillion-Robin, Kitware, Inc.
# Julien Finet, Kitware, Inc.
# James Fishbaugh, University of Utah
# Yi Gao, Georgia Institute of Technology
# Greg Gardner, University of Utah
# Ronen Globinsky, Yale University
# Vivian He, Brigham and Women's Hospital
# Maged Goubran, Robarts Research Institute
# Daniel Haehn, University of Pennsylvania
# Mike Halle, Brigham and Women's Hospital
# Marcus Hanwell, Kitware, Inc.
# Firdaus Janoos, Brigham and Women's Hospital
# Noby Hata, Brigham and Women's Hospital
# Tamas Heffter, Queen's University
# Nicholas Herlambang, AZE, Ltd.
# Luis Ibanez, Kitware, Inc.
# Andrei Irimia, University of California, Los Angeles
# Hans Johnson, University of Iowa
# Ilknur Kabul, Kitware, Inc.
# Tina Kapur, Brigham and Women's Hospital
# Peter Karasev, Georgia Institute of Technology
# Ron Kikinis, Brigham and Women's Hospital
# Regina Kim, University of Iowa
# Ivan Kolesov, Georgia Institute of Technology
# Szymon Kostrzewski, Ecole Polytechnique Federale de Lausanne EPFL
# Dillon Lee, University of Utah
# Yinpeng Li, UNC-NIRAL
# Yifei Lou, Georgia Institute of Technology
# Mohsen Mahvash, Harvard Medical School (BWH and VA)
# Nikos Makris, Massachusetts General Hospital
# Katie Mastrogiacomo, Brigham and Women's Hospital
# Joy Matsui, University of Iowa
# Dominik Meier, Brigham and Women's Hospital
# Mikhail Milchenko, Washington University in St. Louis
# James Miller, GE Research
# Zach Mullen, Kitware, Inc.
# Isaiah Norton, Brigham and Women's Hospital
# Lauren O'Donnell, Brigham and Women's Hospital
# Danielle Pace, Kitware, Inc.
# Beatriz Paniagua, University of North Carolina at Chapel Hill
# Xenophon Papademetris, Yale University
# Kedar Patwardhan, GE Global Research
# Steve Pieper, Isomics, Inc.
# Csaba Pinter, Queen's University
# Wendy Plesniak, Brigham and Women's Hospital
# Kilian Pohl, University of Pennsylvania
# Marcel Prastawa, University of Utah
# Sonia Pujol, Brigham and Women's Hospital
# Martin Rajchl, Robarts Research Institute
# Ramesh Sridharan, Massachusetts Institute of Technology
# Petter Risholm, Brigham and Women's Hospital
# Peter Savadjiev, Brigham and Women's Hospital
# Will Schroeder, Kitware, Inc.
# Andreas Schuh, University of Pennsylvania
# Mark Scully, University of Iowa
# Gregory Sharp, Massachusetts General Hospital
# Junichi Tokuda, Brigham and Women's Hospital
# Yundi Shi, University of North Carolina at Chapel Hill
# Matthew Toews, Brigham and Women's Hospital
# Nadya Shusharina, Massachusetts General Hospital
# Hao Su, Worcester Polytechnic Institute
# Suares Tamekue, Brigham and Women's Hospital
# Xiaodong Tao, GE Research
# Clement Vachet, UNC Chapel Hill
# Antonio Vega, Brigham and Women's Hospital
# Gopal Veni, University of Utah
# Bo Wang, University of Utah
# Andrew Wassam, CoSMo Software Inc.
# Demian Wasserman, Brigham and Women's Hospital
# Sandy Wells, Brigham and Women's Hospital
# Jason White, Brigham and Women's Hospital
# Mallika Winsor, Brigham and Women's Hospital
# Atsushi Yamada, Brigham and Women's Hospital
# Alexander Yarmarkovich, Isomics, Inc.
# Alexander Zaitsev, Brigham and Women's Hospital
# Ming Zhao, Sun Yat-Sen University Cancer Center, GuangZhou, China

2011 Summer Project Week re-parameterize fiber

2011-06-20T17:57:47Z

Wendyuu: /* Key Investigators */

2011 Summer Project Week

2011-06-20T02:46:46Z

Wendyuu:

Back to [[Events]]

[[image:PW-MIT2011.png|right|200px]]

*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT

==Preliminary Agenda==
==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 20
!style="width:18%" |Tuesday, June 21
!style="width:18%" |Wednesday, June 22
!style="width:18%" |Thursday, June 23
!style="width:18%" |Friday, June 24
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-11am:''' [[2011 Project Week Breakout Session: Slicer4|Slicer 4 Core Modules Usability Review]]''' [[MIT_Project_Week_Rooms#Star|Star Room]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> [[2011 Summer Project Week Breakout Session Slicer4 Annotation|Slicer4 Annotations]] (Nicole Aucoin)<br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-5:00pm: NA-MIC Kit Update''' Slicer4 Developers Guided Tour (Pieper) ([[media:2011 Summer-Slicer4.ppt|Draft Slides]]), Slicer4 Extension Writing Tutorial (Finet, Fillion-Robin)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:MultiVolumeContainer#Summer_2011_Project_Week_Breakout_Session Slicer4 MultiVolume Containers] (Nicole Aucoin)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[Summer_2011_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' [[2011 Summer Project Week Breakout Session VTKCharts|VTK Charts]] (Marcus Hanwell)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2011|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2011_Summer_Project_Week_Breakout_Session_EMRegistration|Inter-subject Registration for EM segmenter]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''1-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

* Please make a link for your project to a new page based on the [[2011_Summer_Project_Week_Template| 2011 Summer Project Page Template]]

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

#[[2011_Summer_Project_Week_Segmentation_TBI|Segmentation of Longitudinal TBI data]] (Bo Wang, Jack Van Horn, Andrei Irimia, Marcel Prastawa, Guido Gerig)
#[[2011_Summer_Project_Week_Slicer4_Tractography_Interaction_and_Display|Tractography Bundle/Cluster Interaction and Display in Slicer4]] (Lauren O'Donnell, Isaiah, Demian)
#[[2011_Summer_Project_Week_White_Matter_Laterality|White Matter Laterality in Python/Slicer4]] (Lauren O'Donnell)
#[[Multimodality Image Registration for TBI]] (Yifei Lou, Danielle Pace, Jack Van Horn?, Marcel Prastawa?)
#[[2011_Summer_Project_Week_Intraoperative_Brain_Shift_Monitor|Intraoperative Brain Shift Monitor]] (Jason White, Alex Golby, Steve Pieper)
#[[2011_Summer_Project_Week_GBM_Masks|Obtaining and Evaluation of Glioblastoma Multiforme (GBM) Segmentation Masks]] (Jan Egger,Tina Kapur, Andriy Fedorov, Rivka Colen, Ron Kikinis, Alex Golby, Christopher Nimsky)
#[[2011_Summer_Project_Week_NerveSeg|Segmentation of Nerve and Nerve Ganglia in the Spine]] (Adrian Dalca, Giovanna Danagoulian, Ron Kikinis, Ehud Schmidt, Polina Golland)
#[[2011_Summer_Project_Week_Spine_Segmentation_And_Osteoporosis_Screening_CT|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)

'''Radiation Therapy'''
#[[2011_Summer Project Week_Non-rigid_inter-patient_registration_of_bone_masks_derived_from_CT_for_Head_and_Neck_Cancer_Radiation_Therapy|Non-rigid, inter-patient registration of bone masks derived from CT for Head and Neck Cancer Radiation Therapy]] (Ivan Kolesov, Yi Gao, Gregory Sharp, and Allen Tannenbaum)
#[[2011_Summer_Project_Week_Contouring_Gyne_Structures|Contouring of Anatomy Structures like Tumor, Bladder, Rectum and Sigmoid for Gynecological Brachytherapy]] (Tina Kapur, Akila Viswanathan, Jan Egger)
#[[2011_Summer_Project_Week_Slicer_DICOM_RT_Brachytherapy|Visualization of DICOM RT Planning Contours and Dose Distributions for Prostate and Gynecologic Brachytherapy in Slicer]] (Firdaus Janoos, Jan Egger, Greg Sharp, Andriy Fedorov, Tina Kapur)
#[[2011_Summer_Project__Week_DVH|Dose volume histograms in Slicer]] (Greg Sharp, Nadya Shusharina, Steve Pieper, Csaba Pinter, Tina Kapur)
#[[2011_Summer_Project__Week_DICOM_RT|Synthetic images, vector fields, RT structures and RT doses in Slicer and ITK]]. (Nadya Shusharina, Greg Sharp, Luis Ibanez, Steve Pieper)

'''Huntington's Disease'''
#[[2011_Summer_Project_Week_normal_consistency_particles|Normal consistency in particle correspondence computation using great circles in principal spheres - Huntington's Disease]], (Beatriz Paniagua, Martin Styner, Sungkyu Jung, Mark Scully)
#[[2011_Summer_Project__Week_Shape_Analysis_UNC |SPHARM & particles shape analysis - Huntington's Disease]] (Lucile Bompard, Clement Vachet, Beatriz Paniagua, Martin Styner
#[[2011_Summer_Project_Week_long_shape_regression|Longitudinal Shape Regression - Huntington's Disease]] (James Fishbaugh, Guido Gerig)
#[[2011_Summer_Project_Week_DTIPrep|DTIPrep - "Study-specific Protocol" based automatic DWI/DTI quality control and preparation]] - Huntington's Disease (Mashid Farzinfar, Clement Vachet, Joy Matsui, Martin Styner)
#[[2011_Summer_Project_Week_DTI_PairWise_Registration|DTI pair-wise registration module]] - Huntington's Disease (Clement Vachet, Joy Matsui, Mark Scully, Martin Styner)
#[[2011_Summer_Project_Week_DTI analysis_for_Huntington's_disease | DTI analysis for Huntington's disease]] (Gopal Veni, Ross Whitaker)

'''Atrial Fibrillation'''
#[[2011_Summer_Project_Week_RSS_for_AFib_Ablation|Robust Statistical Segmentation (RSS) for the Atrial Fibrillation Ablation Therapy]] (Yi Gao, Kedar Patwardhan, Wassim Haddad, and Allen Tannenbaum, Rob MacLeod, Josh Blauer, and Josh Cates)
#[[2011_Summer_Project_Week_Watersheds|Interactive Watersheds Segmentation Module for Slicer for Atrial Fibrillation and HN Cancer]] (Josh Cates, Ross Whitaker, Steve Pieper, Jim Miller, Nadya)

'''Vessels'''
#[[2011_Summer_Project_Week_SlicerVmtk4|The Vascular Modeling Toolkit in 3D Slicer 4]] (Daniel Haehn, Luca Antiga, Steve Pieper, Kilian Pohl, Ron Kikinis)
#[[2011_Summer_Project__Week_Stenosis_Detector|Stenosis Detector in 3D Slicer 4]] (Suares Tamekue, Daniel Haehn, Luca Antiga)

'''Device Integration with Slicer and General Image Guided Therapy'''
#[[2011_Summer_Project__Week_Wireless_Joystick|Wireless joystick controlling medical devices and software (e.g. Slicer4) in the operating room]] (Szymon Kostrzewski)
#[[2011_Summer_Project__Week_Live_Tracked_Ultrasound|Live Tracked Ultrasound with Slicer4 (Tamas Heffter)]]
#[http://wiki.na-mic.org/Wiki/index.php/Survey_stealthlink_openigtlink Surveying research teams interested in Open IGT Link support of Stealth Station (Nobuhiko Hata, Ron Kikinis)]
#[[2011_Summer_Project_Week_Needle_Detection_to_Control_Scanner_for_Prostate_Biopsy | Needle Detection to Control Scanner for Prostate Biopsy ]] (Atsushi Yamada, Loïc Cadour, Junichi Tokuda and Nobuhiko Hata)
#[[2011_Summer_Project_Week_4DUltrasound_HybridProbe_OsteoPlan|4D Ultrasound / Hybrid Probe / OsteoPlan]] (Laurent Chauvin, Noby Hata)
#[[2011_Summer_Project_Week_AMIGO|AMIGO]] (Mallika Winsor, Vivian He, Dan Kacher, Tina Kapur)

'''General Segmentation'''
#[[2011_Summer_Project_Week_Integrate_BRAINSCut_into_Slicer3]](Regina Kim, ... )
#[[2011_Summer_Project_Week_EMSegmentation_in_3D_Slicer4|EM Segmentation in 3D Slicer 4]] (Daniel Haehn, Dominique Belhachemi, Kilian Pohl)
#[[2011_Summer_Project_Week_Customizing_EMSegmenter_pipelines_for_brain_lesions | Customizing EMSegmenter pipelines for brain lesions]] (Dominique Belhachemi, Alexander Zaitsev, Kilian Pohl)
#[[2011_Summer_Project_Week_Plastimatch_for_EMSegmenter | Integrating Plastimatch into the EMSegmenter]] (Dominique Belhachemi, Kilian Pohl, Greg Sharp, Daniel Haehn)
#[[2011_Summer_Project_Week_Slicer_Extension_for_GLISTR | Slicer extension for GLiome Image SegmenTation and Registration (GLISTR)]] (Andreas Schuh, Daniel Haehn, Kilian Pohl)
#[[2011_Summer_Project_Week_DTI_Volumetric_Segmentation_for_Group_studies | DTI Volumetric Segmentation for Group studies]] (Gopal Veni, Ross Whitaker)
#[[2011_Summer_Project_Week_Segementation_Reconstruction_Pericardial_Sac]] (Mohasen)

'''General Registration'''
#[[2011_Summer_Project_Week__BRAINSFit_new_features_integration|Integrate new features into BRAINSFit]] (Andrey Fedorov, Hans Johnson, Mark Scully)
#[[2011_Summer_Project_Week__LANDWARP_integration|Integration of LANDWARP into interactive registration module]] (Andrey Fedorov, Greg Sharp, Nadya Shusharina)
#[[2011_Summer_Project_Week_Registration_of_mouse_brains|Registration of mouse brains]] (Francois Budin)
#[[NonRigidRegistrationThatAccommodatesResection|Demons Based Non-Rigid Registration that Accommodates Resection in 3D Slicer]] (Petter Risholm, Sandy Wells)

'''General Atlas'''
#[[2011_Summer_Project_Week_DWI_Atlas | Slicer module for building an average population DWI Atlas]] (Ryan Eckbo, Sylvain Bouix)
#[[2011_Summer_Project_Week_Image_Manifold_Learning_with_Spectral_Embedding_and_Laplacian_Eigenmaps|Image Manifold Learning with Spectral Embedding and Laplacian Eigenmaps]] (Ramesh Sridharan, Polina Golland)

'''General Diffusion Tractography'''
#[[2011_Summer_Project_Week_WMGeometry_Slicer4 | White matter geometry measures in Slicer 4]] (Peter Savadjiev)
#[[2011_Summer_Project_Week_re-parameterize_fiber|Re-parametrize fiber tracts for fiber statistics analysis]] (Yundi Shi, Benjamin Yvernault, Anuja Sharma, Martin Styner)
#[[2011_Summer_Project_Week_ODF_though_Fiber_Counting | ODF computation through fiber counting]] (Yinpeng Li, Ipek Oguz, Martin Styner)
#[[2011_Summer_Project_Week_Nifti_Support_for_Diffusion_Tensor_Images|Nifti Support for Diffusion Tensor Images]] (Demian)
#[[2011_Summer_Project_Week_Finishing_details_on_the_workflows_DICOM_full_brain_tractography_peritumoral|Finishing details on the workflows: DICOM->Full brain tractography / peritumoral]] (Demian)
#[[Summer_project_week_2011_Finsler_Streamlines|Adding streamlined tractography to the Finsler front propagation tractography toolkit]] (Antonio Tristán-Vega)

'''Infrastructure'''
#[[2011_Summer_Project_Week_Annotation_Module|Annotation Module in Slicer4]] (Nicole Aucoin, Daniel Haehn)
#[[2011_Summer_Project_Week_RECIST|RECIST Slicer4 module]] (Nicole Aucoin)
#[[2011_Summer_Project_Week_Dicom2Nrrd|DicomToNrrdConverter refactoring]] ( Xiaodong Tao, Mark Scully)
#[[Summer_project_week_2011_Workflows_SOA|Workflows and Service Oriented Architecture Modules for Slicer4 as Extensions]] (Alexander Zaitsev, Wendy Plesniak, Ron Kikinis)
#[[2011_Summer_Project__Week_DICOM_Networking|DICOM Networking interface for Slicer4]] (Steve Pieper, Nicole Aucoin, Noby Hata)
#[[2011_Summer_Project_Week_Automated_GUI_Testing| Automated GUI Testing (Sonia Pujol, Steve Pieper, Dave Partyka, Jean-Christophe Fillion-Robin, Xiaodong Tao)]]
#[[2011_Summer_Project_Week_FetchMI:_Slicer_integration_with_XNAT |FetchMI: Slicer integration with XNAT 1.5]] (Misha Milchenko, Wendy Plesniak)
#[[2011_Summer_Project_Week_Internationalization_of_Slicer|Internationalization of Slicer]] (Luping Fang, Steve Pieper, Daniel Haehn, Suares Tamekue, Jean-Christophe Fillion-Robin, Julien Finet, Yiming Ge, Ping Cao)

==Background==

We are pleased to announce the 13th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 28th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

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

== Logistics ==
*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please register [http://guest.cvent.com/d/sdqy0l/4W here]. Payment must be made by credit card.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' Boston Marriott Cambridge, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. Group rate is $199/night plus tax. Book [http://www.marriott.com/hotels/travel/boscb?groupCode=jrbjrba&app=resvlink&fromDate=6/19/11&toDate=6/24/11 here] or call 1-617-494-6600 and mention that you are booking in the MIT Room Block. '''All reservations must be made by May 29, 2011 to receive the discounted rate.'''

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 28, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 12, all participants to add a one line title of their project to #Projects
#By 3pm ET on Thursday June 9, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 16: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Registrants==

Do not add your name to this list- it is maintained by the organizers based on your paid registration (see Logistics for link)
# Peter Anderson , retired
# Nicole Aucoin , Brigham and Women's Hospital
# Dominique Belhachemi , University of Pennsylvania
# Anthony Blumfiled , Radnostics
# Lucile Bompard , UNC NIRAL
# Sylvain Bouix , Brigham and Women's Hospital
# Francois Budin , UNC NIRAL
# Steve Callahan , University of Utah
# Joshua Cates , University of Utah
# Micah Chambers , Laboratory of NeuroImaging
# Laurent Chauvin , Brigham and Women's Hospital
# Rivka Colen, Brigham and Women's Hospital
# Nikos Chrisochoides, ODU
#Adrian Dalca, MIT
# Manasi Datar , University of Utah
# Colin Davey ,
# Ryan Eckbo , Brigham and Women's Hospital
# Jan Egger , University Hospital of Marburg
# Luping Fang , Zhejiang University of Technology, China
# mahshid farzinfar , UNC
# Andriy Fedorov , Brigham and Women's Hospital
# Jean-Christophe Fillion-Robin , Kitware, Inc.
# Julien Finet , Kitware, Inc.
# James Fishbaugh , University of Utah
# Yi Gao , Georgia Tech
# Greg Gardner , University of Utah
# Ronen Globinsky , Yale University
# Maged Goubran , Robarts Research Institute
# Daniel Haehn , University of Pennsylvania
# Mike Halle , Brigham and Women's Hospital
# Marcus Hanwell , Kitware, Inc.
# Noby Hata , Brigham and Women's Hospital
# Tamas Heffter , Queen's University
# Nicholas Herlambang , AZE, Ltd.
# Vivian Hu, Brigham and Women's Hospital
# Luis Ibanez , Kitware, Inc.
# Andrei Irimia , University of California, Los Angeles
#Firdaus Janoos, Brigham and Women's Hospital
# Hans Johnson , University of Iowa
# Ilknur Kabul , Kitware, Inc.
# Tina Kapur , Brigham and Women's Hospital
# Peter Karasev , Georgia Institute of Technology
# Ron Kikinis , Brigham and Women's Hospital; Harvard Medical School
# Regina Kim , University of Iowa
# Ivan Kolesov , Ga Tech
# Szymon Kostrzewski , Ecole Polytechnique Federale de Lausanne EPFL
# Dillon Lee , University of Utah
# Yinpeng Li , UNC-NIRAL
# Yifei Lou , Georgia Institute of Technology
# mohsen mahvash , Harvard Medical School (BWH and VA)
# Katie Mastrogiacomo , Brigham and Women's Hospital
# Joy Matsui , University of Iowa
# Dominik Meier , BWH
# Mikhail Milchenko , Washington University in St. Louis
# James Miller , GE Research
# Zach Mullen , Kitware, Inc.
# Isaiah Norton , Brigham and Women's Hospital
# Lauren O'Donnell , Brigham and Women's Hospital
# Danielle Pace , Kitware, Inc.
# Beatriz Paniagua , University of North Carolina at Chapel Hill
# Xenophon Papademetris , Yale University
# Kedar Patwardhan , GE Global Research
# Steve Pieper , Isomics, Inc.
# Csaba Pinter , Queen's University
# Wendy Plesniak , Brigham and Women's Hospital
# Kilian Pohl , UPenn
# Marcel Prastawa , University of Utah
# Sonia Pujol , Brigham and Women's Hospital
# Martin Rajchl , Robarts Research Institute
# Petter Risholm , Brigham and Women's Hospital
# Peter Savadjiev , Brigham and Women's Hospital
# Andreas Schuh , University of Pennsylvania
# Mark Scully , University of Iowa
# Gregory Sharp , MGH
# Yundi Shi , UNC-Chapel Hill
# Nadya Shusharina , MGH
#Ramesh Sridharan, MIT
# Hao Su , WPI
# Suarez Tamekue , Brigham and Women's Hospital
# Xiaodong Tao , GE Research
#Junichi Tokuda, Brigham and Women's Hospital
#Matthew Toews, Brigham and Women's Hospital
# Clement Vachet , UNC Chapel Hill
# Antonio Vega , Brigham and Women's Hospital
# Gopal Veni , University of Utah
# Bo Wang , University of Utah
# Demian Wasserman , Brigham and Women's Hospital
# Sandy Wells , Brigham and Women's Hospital
# Jason White , Brigham and Women's Hospital
# Mallika Winsor , Brigham and Women's Hospital
# Atsushi Yamada , Brigham and Women's Hospital
# Alexander Yarmarkovich , Isomics
# Alexander Zaitsev , Brigham and Women's Hospital

2011 Summer Project Week re-parameterize fiber

2011-06-20T02:25:17Z

Wendyuu: /* Key Investigators */

2011 Summer Project Week re-parameterize fiber

2011-06-20T02:24:31Z

Wendyuu: /* Key Investigators */

2011 Summer Project Week re-parameterize fiber

2011-06-20T02:18:50Z

Wendyuu:

2011 Summer Project Week re-parameterize fiber

2011-06-20T02:18:00Z

Wendyuu:

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

'''Full Title of Project'''

==Key Investigators==
* UNC-Chapel Hill: Yundi Shi, Benjamin Yvernault, Martin Styner
* University of Utah: Anuja Sharma

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

<h3>Objective</h3>



</div>

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

<h3>Approach, Plan</h3>



</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==



==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
http://www.nitrc.org/projects/dti_tract_stat/

2011 Summer Project Week re-parameterize fiber

2011-06-20T02:16:34Z

Wendyuu:

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:File:Tracts Pval.png|Interesting picture to be added...
</gallery>

'''Full Title of Project'''

==Key Investigators==
* UNC-Chapel Hill: Yundi Shi, Benjamin Yvernault, Martin Styner
* University of Utah: Anuja Sharma

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

<h3>Objective</h3>



</div>

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

<h3>Approach, Plan</h3>



</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==



==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
http://www.nitrc.org/projects/dti_tract_stat/

2011 Summer Project Week re-parameterize fiber

2011-06-20T02:16:01Z

Wendyuu:

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:Pval.png|Interesting picture to be added...
</gallery>

'''Full Title of Project'''

==Key Investigators==
* UNC-Chapel Hill: Yundi Shi, Benjamin Yvernault, Martin Styner
* University of Utah: Anuja Sharma

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

<h3>Objective</h3>



</div>

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

<h3>Approach, Plan</h3>



</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==



==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
http://www.nitrc.org/projects/dti_tract_stat/

File:Tracts Pval.png

2011-06-20T02:14:41Z

Wendyuu:

2011 Summer Project Week re-parameterize fiber

2011-06-20T02:14:14Z

Wendyuu: /* Delivery Mechanism */

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:notfound.png|Interesting picture to be added...
</gallery>

'''Full Title of Project'''

==Key Investigators==
* UNC-Chapel Hill: Yundi Shi, Benjamin Yvernault, Martin Styner
* University of Utah: Anuja Sharma

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

<h3>Objective</h3>



</div>

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

<h3>Approach, Plan</h3>



</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==



==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
http://www.nitrc.org/projects/dti_tract_stat/

2011 Summer Project Week

2011-06-20T02:10:03Z

Wendyuu:

Back to [[Events]]

[[image:PW-MIT2011.png|right|200px]]

*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT

==Preliminary Agenda==
==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 20
!style="width:18%" |Tuesday, June 21
!style="width:18%" |Wednesday, June 22
!style="width:18%" |Thursday, June 23
!style="width:18%" |Friday, June 24
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-11am:''' [[2011 Project Week Breakout Session: Slicer4|Slicer 4 Core Modules Usability Review]]''' [[MIT_Project_Week_Rooms#Star|Star Room]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> [[2011 Summer Project Week Breakout Session Slicer4 Annotation|Slicer4 Annotations]] (Nicole Aucoin)<br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-5:00pm: NA-MIC Kit Update''' Slicer4 Developers Guided Tour (Pieper) ([[media:2011 Summer-Slicer4.ppt|Draft Slides]]), Slicer4 Extension Writing Tutorial (Finet, Fillion-Robin)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:MultiVolumeContainer#Summer_2011_Project_Week_Breakout_Session Slicer4 MultiVolume Containers] (Nicole Aucoin)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[Summer_2011_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' [[2011 Summer Project Week Breakout Session VTKCharts|VTK Charts]] (Marcus Hanwell)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2011|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2011_Summer_Project_Week_Breakout_Session_EMRegistration|Inter-subject Registration for EM segmenter]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''1-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

* Please make a link for your project to a new page based on the [[2011_Summer_Project_Week_Template| 2011 Summer Project Page Template]]

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

#[[2011_Summer_Project_Week_Segmentation_TBI|Segmentation of Longitudinal TBI data]] (Bo Wang, Jack Van Horn, Andrei Irimia, Marcel Prastawa, Guido Gerig)
#[[2011_Summer_Project_Week_Slicer4_Tractography_Interaction_and_Display|Tractography Bundle/Cluster Interaction and Display in Slicer4]] (Lauren O'Donnell, Isaiah, Demian)
#[[2011_Summer_Project_Week_White_Matter_Laterality|White Matter Laterality in Python/Slicer4]] (Lauren O'Donnell)
#[[Multimodality Image Registration for TBI]] (Yifei Lou, Danielle Pace, Jack Van Horn?, Marcel Prastawa?)
#[[2011_Summer_Project_Week_Intraoperative_Brain_Shift_Monitor|Intraoperative Brain Shift Monitor]] (Jason White, Alex Golby, Steve Pieper)
#[[2011_Summer_Project_Week_GBM_Masks|Obtaining and Evaluation of Glioblastoma Multiforme (GBM) Segmentation Masks]] (Jan Egger,Tina Kapur, Andriy Fedorov, Rivka Colen, Ron Kikinis, Alex Golby, Christopher Nimsky)
#[[2011_Summer_Project_Week_NerveSeg|Segmentation of Nerve and Nerve Ganglia in the Spine]] (Adrian Dalca, Giovanna Danagoulian, Ron Kikinis, Ehud Schmidt, Polina Golland)
#[[2011_Summer_Project_Week_Spine_Segmentation_And_Osteoporosis_Screening_CT|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)

'''Radiation Therapy'''
#[[2011_Summer Project Week_Non-rigid_inter-patient_registration_of_bone_masks_derived_from_CT_for_Head_and_Neck_Cancer_Radiation_Therapy|Non-rigid, inter-patient registration of bone masks derived from CT for Head and Neck Cancer Radiation Therapy]] (Ivan Kolesov, Yi Gao, Gregory Sharp, and Allen Tannenbaum)
#[[2011_Summer_Project_Week_Contouring_Gyne_Structures|Contouring of Anatomy Structures like Tumor, Bladder, Rectum and Sigmoid for Gynecological Brachytherapy]] (Tina Kapur, Akila Viswanathan, Jan Egger)
#[[2011_Summer_Project_Week_Slicer_DICOM_RT_Brachytherapy|Visualization of DICOM RT Planning Contours and Dose Distributions for Prostate and Gynecologic Brachytherapy in Slicer]] (Firdaus Janoos, Jan Egger, Greg Sharp, Andriy Fedorov, Tina Kapur)
#[[2011_Summer_Project__Week_DVH|Dose volume histograms in Slicer]] (Greg Sharp, Nadya Shusharina, Steve Pieper, Csaba Pinter, Tina Kapur)
#[[2011_Summer_Project__Week_DICOM_RT|Synthetic images, vector fields, RT structures and RT doses in Slicer and ITK]]. (Nadya Shusharina, Greg Sharp, Luis Ibanez, Steve Pieper)

'''Huntington's Disease'''
#[[2011_Summer_Project_Week_normal_consistency_particles|Normal consistency in particle correspondence computation using great circles in principal spheres - Huntington's Disease]], (Beatriz Paniagua, Martin Styner, Sungkyu Jung, Mark Scully)
#[[2011_Summer_Project__Week_Shape_Analysis_UNC |SPHARM & particles shape analysis - Huntington's Disease]] (Lucile Bompard, Clement Vachet, Beatriz Paniagua, Martin Styner
#[[2011_Summer_Project_Week_long_shape_regression|Longitudinal Shape Regression - Huntington's Disease]] (James Fishbaugh, Guido Gerig)
#[[2011_Summer_Project_Week_DTIPrep|DTIPrep - "Study-specific Protocol" based automatic DWI/DTI quality control and preparation]] - Huntington's Disease (Mashid Farzinfar, Clement Vachet, Joy Matsui, Martin Styner)
#[[2011_Summer_Project_Week_DTI_PairWise_Registration|DTI pair-wise registration module]] - Huntington's Disease (Clement Vachet, Joy Matsui, Mark Scully, Martin Styner)
#[[2011_Summer_Project_Week_DTI analysis_for_Huntington's_disease | DTI analysis for Huntington's disease]] (Gopal Veni, Ross Whitaker)

'''Atrial Fibrillation'''
#[[2011_Summer_Project_Week_RSS_for_AFib_Ablation|Robust Statistical Segmentation (RSS) for the Atrial Fibrillation Ablation Therapy]] (Yi Gao, Kedar Patwardhan, Wassim Haddad, and Allen Tannenbaum, Rob MacLeod, Josh Blauer, and Josh Cates)
#[[2011_Summer_Project_Week_Watersheds|Interactive Watersheds Segmentation Module for Slicer for Atrial Fibrillation and HN Cancer]] (Josh Cates, Ross Whitaker, Steve Pieper, Jim Miller, Nadya)

'''Vessels'''
#[[2011_Summer_Project_Week_SlicerVmtk4|The Vascular Modeling Toolkit in 3D Slicer 4]] (Daniel Haehn, Luca Antiga, Steve Pieper, Kilian Pohl, Ron Kikinis)
#[[2011_Summer_Project__Week_Stenosis_Detector|Stenosis Detector in 3D Slicer 4]] (Suares Tamekue, Daniel Haehn, Luca Antiga)

'''Device Integration with Slicer and General Image Guided Therapy'''
#[[2011_Summer_Project__Week_Wireless_Joystick|Wireless joystick controlling medical devices and software (e.g. Slicer4) in the operating room]] (Szymon Kostrzewski)
#[[2011_Summer_Project__Week_Live_Tracked_Ultrasound|Live Tracked Ultrasound with Slicer4 (Tamas Heffter)]]
#[http://wiki.na-mic.org/Wiki/index.php/Survey_stealthlink_openigtlink Surveying research teams interested in Open IGT Link support of Stealth Station (Nobuhiko Hata, Ron Kikinis)]
#[[2011_Summer_Project_Week_Needle_Detection_to_Control_Scanner_for_Prostate_Biopsy | Needle Detection to Control Scanner for Prostate Biopsy ]] (Atsushi Yamada, Loïc Cadour, Junichi Tokuda and Nobuhiko Hata)
#[[2011_Summer_Project_Week_4DUltrasound_HybridProbe_OsteoPlan|4D Ultrasound / Hybrid Probe / OsteoPlan]] (Laurent Chauvin, Noby Hata)
#[[2011_Summer_Project_Week_AMIGO|AMIGO]] (Mallika Winsor, Vivian He, Dan Kacher, Tina Kapur)

'''General Segmentation'''
#[[2011_Summer_Project_Week_Integrate_BRAINSCut_into_Slicer3]](Regina Kim, ... )
#[[2011_Summer_Project_Week_EMSegmentation_in_3D_Slicer4|EM Segmentation in 3D Slicer 4]] (Daniel Haehn, Dominique Belhachemi, Kilian Pohl)
#[[2011_Summer_Project_Week_Customizing_EMSegmenter_pipelines_for_brain_lesions | Customizing EMSegmenter pipelines for brain lesions]] (Dominique Belhachemi, Alexander Zaitsev, Kilian Pohl)
#[[2011_Summer_Project_Week_Plastimatch_for_EMSegmenter | Integrating Plastimatch into the EMSegmenter]] (Dominique Belhachemi, Kilian Pohl, Greg Sharp, Daniel Haehn)
#[[2011_Summer_Project_Week_Slicer_Extension_for_GLISTR | Slicer extension for GLiome Image SegmenTation and Registration (GLISTR)]] (Andreas Schuh, Daniel Haehn, Kilian Pohl)
#[[2011_Summer_Project_Week_DTI_Volumetric_Segmentation_for_Group_studies | DTI Volumetric Segmentation for Group studies]] (Gopal Veni, Ross Whitaker)
#[[2011_Summer_Project_Week_Segementation_Reconstruction_Pericardial_Sac]] (Mohasen)

'''General Registration'''
#[[2011_Summer_Project_Week__BRAINSFit_new_features_integration|Integrate new features into BRAINSFit]] (Andrey Fedorov, Hans Johnson, Mark Scully)
#[[2011_Summer_Project_Week__LANDWARP_integration|Integration of LANDWARP into interactive registration module]] (Andrey Fedorov, Greg Sharp, Nadya Shusharina)
#[[2011_Summer_Project_Week_Registration_of_mouse_brains|Registration of mouse brains]] (Francois Budin)
#[[NonRigidRegistrationThatAccommodatesResection|Demons Based Non-Rigid Registration that Accommodates Resection in 3D Slicer]] (Petter Risholm, Sandy Wells)

'''General Atlas'''
#[[2011_Summer_Project_Week_DWI_Atlas | Slicer module for building an average population DWI Atlas]] (Ryan Eckbo, Sylvain Bouix)
#[[2011_Summer_Project_Week_Image_Manifold_Learning_with_Spectral_Embedding_and_Laplacian_Eigenmaps|Image Manifold Learning with Spectral Embedding and Laplacian Eigenmaps]] (Ramesh Sridharan, Polina Golland)

'''General Diffusion Tractography'''
#[[2011_Summer_Project_Week_WMGeometry_Slicer4 | White matter geometry measures in Slicer 4]] (Peter Savadjiev)
#[[2011_Summer_Project_Week_re-parameterize_fiber|Re-parameterize fiber tracts for fiber statistics analysis]] (Yundi Shi, Benjamin Yvernault, Anuja Sharma, Martin Styner)
#[[2011_Summer_Project_Week_ODF_though_Fiber_Counting | ODF computation through fiber counting]] (Yinpeng Li, Ipek Oguz, Martin Styner)
#[[2011_Summer_Project_Week_Nifti_Support_for_Diffusion_Tensor_Images|Nifti Support for Diffusion Tensor Images]] (Demian)
#[[2011_Summer_Project_Week_Finishing_details_on_the_workflows_DICOM_full_brain_tractography_peritumoral|Finishing details on the workflows: DICOM->Full brain tractography / peritumoral]] (Demian)
#[[Summer_project_week_2011_Finsler_Streamlines|Adding streamlined tractography to the Finsler front propagation tractography toolkit]] (Antonio Tristán-Vega)

'''Infrastructure'''
#[[2011_Summer_Project_Week_Annotation_Module|Annotation Module in Slicer4]] (Nicole Aucoin, Daniel Haehn)
#[[2011_Summer_Project_Week_RECIST|RECIST Slicer4 module]] (Nicole Aucoin)
#[[2011_Summer_Project_Week_Dicom2Nrrd|DicomToNrrdConverter refactoring]] ( Xiaodong Tao, Mark Scully)
#[[Summer_project_week_2011_Workflows_SOA|Workflows and Service Oriented Architecture Modules for Slicer4 as Extensions]] (Alexander Zaitsev, Wendy Plesniak, Ron Kikinis)
#[[2011_Summer_Project__Week_DICOM_Networking|DICOM Networking interface for Slicer4]] (Steve Pieper, Nicole Aucoin, Noby Hata)
#[[2011_Summer_Project_Week_Automated_GUI_Testing| Automated GUI Testing (Sonia Pujol, Steve Pieper, Dave Partyka, Jean-Christophe Fillion-Robin, Xiaodong Tao)]]
#[[2011_Summer_Project_Week_FetchMI:_Slicer_integration_with_XNAT |FetchMI: Slicer integration with XNAT 1.5]] (Misha Milchenko, Wendy Plesniak)
#[[2011_Summer_Project_Week_Internationalization_of_Slicer|Internationalization of Slicer]] (Luping Fang, Steve Pieper, Daniel Haehn, Suares Tamekue, Jean-Christophe Fillion-Robin, Julien Finet, Yiming Ge, Ping Cao)

==Background==

We are pleased to announce the 13th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 28th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

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

== Logistics ==
*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please register [http://guest.cvent.com/d/sdqy0l/4W here]. Payment must be made by credit card.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' Boston Marriott Cambridge, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. Group rate is $199/night plus tax. Book [http://www.marriott.com/hotels/travel/boscb?groupCode=jrbjrba&app=resvlink&fromDate=6/19/11&toDate=6/24/11 here] or call 1-617-494-6600 and mention that you are booking in the MIT Room Block. '''All reservations must be made by May 29, 2011 to receive the discounted rate.'''

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 28, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 12, all participants to add a one line title of their project to #Projects
#By 3pm ET on Thursday June 9, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 16: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Registrants==

Do not add your name to this list- it is maintained by the organizers based on your paid registration (see Logistics for link)
# Peter Anderson , retired
# Nicole Aucoin , Brigham and Women's Hospital
# Dominique Belhachemi , University of Pennsylvania
# Anthony Blumfiled , Radnostics
# Lucile Bompard , UNC NIRAL
# Sylvain Bouix , Brigham and Women's Hospital
# Francois Budin , UNC NIRAL
# Steve Callahan , University of Utah
# Joshua Cates , University of Utah
# Micah Chambers , Laboratory of NeuroImaging
# Laurent Chauvin , Brigham and Women's Hospital
# Rivka Colen, Brigham and Women's Hospital
# Nikos Chrisochoides, ODU
#Adrian Dalca, MIT
# Manasi Datar , University of Utah
# Colin Davey ,
# Ryan Eckbo , Brigham and Women's Hospital
# Jan Egger , University Hospital of Marburg
# Luping Fang , Zhejiang University of Technology, China
# mahshid farzinfar , UNC
# Andriy Fedorov , Brigham and Women's Hospital
# Jean-Christophe Fillion-Robin , Kitware, Inc.
# Julien Finet , Kitware, Inc.
# James Fishbaugh , University of Utah
# Yi Gao , Georgia Tech
# Greg Gardner , University of Utah
# Ronen Globinsky , Yale University
# Maged Goubran , Robarts Research Institute
# Daniel Haehn , University of Pennsylvania
# Mike Halle , Brigham and Women's Hospital
# Marcus Hanwell , Kitware, Inc.
# Noby Hata , Brigham and Women's Hospital
# Tamas Heffter , Queen's University
# Nicholas Herlambang , AZE, Ltd.
# Vivian Hu, Brigham and Women's Hospital
# Luis Ibanez , Kitware, Inc.
# Andrei Irimia , University of California, Los Angeles
#Firdaus Janoos, Brigham and Women's Hospital
# Hans Johnson , University of Iowa
# Ilknur Kabul , Kitware, Inc.
# Tina Kapur , Brigham and Women's Hospital
# Peter Karasev , Georgia Institute of Technology
# Ron Kikinis , Brigham and Women's Hospital; Harvard Medical School
# Regina Kim , University of Iowa
# Ivan Kolesov , Ga Tech
# Szymon Kostrzewski , Ecole Polytechnique Federale de Lausanne EPFL
# Dillon Lee , University of Utah
# Yinpeng Li , UNC-NIRAL
# Yifei Lou , Georgia Institute of Technology
# mohsen mahvash , Harvard Medical School (BWH and VA)
# Katie Mastrogiacomo , Brigham and Women's Hospital
# Joy Matsui , University of Iowa
# Dominik Meier , BWH
# Mikhail Milchenko , Washington University in St. Louis
# James Miller , GE Research
# Zach Mullen , Kitware, Inc.
# Isaiah Norton , Brigham and Women's Hospital
# Lauren O'Donnell , Brigham and Women's Hospital
# Danielle Pace , Kitware, Inc.
# Beatriz Paniagua , University of North Carolina at Chapel Hill
# Xenophon Papademetris , Yale University
# Kedar Patwardhan , GE Global Research
# Steve Pieper , Isomics, Inc.
# Csaba Pinter , Queen's University
# Wendy Plesniak , Brigham and Women's Hospital
# Kilian Pohl , UPenn
# Marcel Prastawa , University of Utah
# Sonia Pujol , Brigham and Women's Hospital
# Martin Rajchl , Robarts Research Institute
# Petter Risholm , Brigham and Women's Hospital
# Peter Savadjiev , Brigham and Women's Hospital
# Andreas Schuh , University of Pennsylvania
# Mark Scully , University of Iowa
# Gregory Sharp , MGH
# Yundi Shi , UNC-Chapel Hill
# Nadya Shusharina , MGH
#Ramesh Sridharan, MIT
# Hao Su , WPI
# Suarez Tamekue , Brigham and Women's Hospital
# Xiaodong Tao , GE Research
#Junichi Tokuda, Brigham and Women's Hospital
#Matthew Toews, Brigham and Women's Hospital
# Clement Vachet , UNC Chapel Hill
# Antonio Vega , Brigham and Women's Hospital
# Gopal Veni , University of Utah
# Bo Wang , University of Utah
# Demian Wasserman , Brigham and Women's Hospital
# Sandy Wells , Brigham and Women's Hospital
# Jason White , Brigham and Women's Hospital
# Mallika Winsor , Brigham and Women's Hospital
# Atsushi Yamada , Brigham and Women's Hospital
# Alexander Yarmarkovich , Isomics
# Alexander Zaitsev , Brigham and Women's Hospital

2011 Summer Project Week re-parameterize fiber

2011-06-07T14:16:54Z

Wendyuu: /* Key Investigators */

2011 Summer Project Week re-parameterize fiber

2011-06-07T14:11:40Z

Wendyuu: Created page with '__NOTOC__ <gallery> Image:PW-MIT2011.png|Projects List Image:notfound.png|Interesting picture to be added... </gallery> '''Full Title of P…'

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:notfound.png|Interesting picture to be added...
</gallery>

'''Full Title of Project'''

==Key Investigators==
* Institution1: Person1, Person2
* Institution2: Person3

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

<h3>Objective</h3>



</div>

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

<h3>Approach, Plan</h3>



</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==



==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
#Slicer Module
##Built-in:
##Extension -- commandline:
##Extension -- loadable:

2011 Summer Project Week

2011-06-07T14:11:03Z

Wendyuu: /* Projects */

Back to [[Events]]

[[image:PW-MIT2011.png|right|200px]]

*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT

==Preliminary Agenda==
==Agenda==

{|border="1"
|-style="background: #b0d5e6; color: #02186f; font-size: 130%"
!Time
!width="250px"|Monday, June 20
!width="250px"|Tuesday, June 21
!width="250px"|Wednesday, June 22
!width="250px"|Thursday, June 23
!width="250px"|Friday, June 24
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-11am:''' [[2011 Project Week Breakout Session: Slicer4|Slicer 4 Core Modules Usability Review]]''' [[MIT_Project_Week_Rooms#Star|Star Room]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> [[2011 Summer Project Week Breakout Session Slicer4 Annotation|Slicer4 Annotations]] (Nicole Aucoin)<br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-5:00pm: NA-MIC Kit Update''' (Aylward, Miller, Pieper)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:MultiVolumeContainer#Summer_2011_Project_Week_Breakout_Session Slicer4 MultiVolume Containers] (Nicole Aucoin)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[Summer_2011_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' [[2011 Summer Project Week Breakout Session VTKCharts|VTK Charts]] (Marcus Hanwell)
<br>[[MIT_Project_Week_Rooms#32-D407|32-D407]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2011|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2011_Summer_Project_Week_Breakout_Session_EMRegistration|Inter-subject Registration for EM segmenter]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''1-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

* Please make a link for your project to a new page based on the [[2011_Summer_Project_Week_Template| 2011 Summer Project Page Template]]

#valuate the applicability of DICOM RT I/O facility in Slicer (via Plastimatch Extension) for Brachytherapy Planning (Tina Kapur, Greg Sharp, Robert Cormack?)
#Visualization of b-spline and vector fields (Steve, Danielle, Dominik)
#Annotation Module in Slicer4 (Nicole Aucoin, Daniel Haehn)
#Slicer4 Multivolume Containers (Ron Kikinis, Nicole Aucoin, Steve Pieper, ... )
#RECIST Slicer4 module (Nicole Aucoin)
#DicomToNrrdConverter refactoring ( Xiaodong Tao, Mark Scully)
# [[2011_Summer_Project_Week_normal_consistency_particles|Normal consistency in particle correspondence computation using great circles in principal spheres - Huntington's Disease]], (Beatriz Paniagua, Martin Styner, Sungkyu Jung, Marc Scully)
# Group-wise Automatic Mesh-Based analysis of CortIcal Thickness (GAMBIT) - TBI (Clement Vachet, Martin Styner, Randi Gollub?)
#[[2011_Summer_Project__Week_Shape_Analysis_UNC |SPHARM & particles shape analysis - Huntington's Disease]] - Lucile Bompard, Clement Vachet, Beatriz Paniagua, Martin Styner
# Non-rigid, inter-patient registration of bone masks derived from CT for Head and Neck Cancer Radiation Therapy (Ivan Kolesov, Yi Gao, Gregory Sharp, and Allen Tannenbaum)
# Robust Statistical Segmentation (RSS) for the Atrial Fibrillation Ablation Therapy (Yi Gao, Kedar Patwardhan, Wassim Haddad, and Allen Tannenbaum, Rob MacLeod, Josh Blauer, and Josh Cates)
#Mass Spectrometry for Brain Tumor Therapy (Behnood Gholami, Nathalie Agar)
#Multimodality Image Registration for TBI? (Yifei Lou, Danielle Pace, Jack Van Horn?, Marcel Prastawa?)
# Segmentation of Longitudinal TBI data (Bo Wang, Jack Van Horn, Andrei Irimia, Marcel Prastawa, Guido Gerig)
# Longitudinal Shape Regression - Huntington's Disease (James Fishbaugh, Guido Gerig)
# [[2011_Summer_Project__Week_DVH|Dose volume histograms in Slicer]] (Greg Sharp, Nadya Shusharina, Steve Pieper, Csaba Pinter, Tina Kapur)
# [[2011_Summer_Project__Week_DICOM_RT|Synthetic images, vector fields, RT structures and RT doses in Slicer and ITK]]. (Nadya Shusharina, Greg Sharp, Luis Ibanez, Steve Pieper)
# Interactive Watersheds Segmentation Module for Slicer for Atrial Fibrillation and HN Cancer (Josh Cates, Ross Whitaker, Steve Pieper, Jim Miller, Nadya)
# Segmentation of Nerve and Nerve Ganglia in the Spine (Adrian Dalca, Giovanna Danagoulian, Ron Kikinis, Ehud Schmidt, Polina Golland)
# Image Manifold Learning with Spectral Embedding and Laplacian Eigenmaps (Ramesh Sridharan, Polina Golland)
# Shapeworks Shape Analysis for Atrial Fibrilliation and HD (Manasi Datar, Beatriz UNC, Marc Scully)
#Explore the applicability of RSS and Shapeworks for Ventricular Segmentation(Chiara Carminati, ?, ?)
# Integrate BRAINSCut into Slicer3(Regina Kim, ... )
# The Vascular Modeling Toolkit in 3D Slicer 4 (Daniel Haehn, Luca Antiga, Steve Pieper)
# Integration of LANDWARP into interactive registration module for MR-guided prostate biopsy (Andrey Fedorov, Greg Sharp, Nadya Shusharina)
# [[2011_Summer_Project_Week_Registration_of_mouse_brains|Registration of mouse brains]] (Francois Budin)
# ShapeWorks Applications (Manasi Datar, Beatriz Paniagua, Martin Styner, Ross Whitaker, ?)
# Wireless joystick controlling Slicer4 (Szymon Kostrzewski)
# Live Tracked Ultrasound in 3D Slicer 4 (Tamas Heffter)
# [http://wiki.na-mic.org/Wiki/index.php/Survey_stealthlink_openigtlink Surveying research teams interested in Open IGT Link support of Stealth Station (Nobuhiko Hata, Ron Kikinis)]
# DTIPrep - "Study-specific Protocol" based automatic DWI/DTI quality control and preparation - Huntington's Disease (Mashid Farzinfar, Clement Vachet, Joy Matsui, Martin Styner)
# DTIProcessing - Huntington's Disease (Clement Vachet, Joy Matsui, Martin Styner)
# Volumetric DTI into Slicer for HD for Tract based roi segmentation (Steve Callahan, Marc Scully, Jim Miller)
#Nifti Support for Diffusion Tensor Images (Demian)
# Finishing details on the workflows: DICOM->Full brain tractography / peritumoral (Demian)
# Refactoring of the tractography display widget (Isaiah)
# Laterality (Lauren)
# Selection for models and bundles post-clustering (Lauren)
#ROI-based / picking selection of fiber bundles (Maybe one of Sylvain's interns)
#Adding streamlined tractography to the Finsler front propagation tractography toolkit (Antonio)
#Add ODF estimation / visualization (Antonio)
# Workflows and Service Oriented Architecture Modules for Slicer4 as Extensions (Alexander Zaitsev, Wendy Plesniak, Ron Kikinis)
# [[2011_Summer_Project__Week_DICOM_Networking|DICOM Networking interface for Slicer4]] (Steve Pieper, Nicole Aucoin, Noby Hata)
# Stenosis Detector in 3D Slicer 4 (Suares Tamekue, Daniel Haehn, Luca Antiga)
# [[2011_Summer_Project_Week_Spine_Segmentation_And_Osteoporosis_Screening_CT|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)
# Slicer module for building an average population HARDI Atlas (Ryan Eckbo)
# 4D Ultrasound (Laurent Chauvin, Noby Hata, Atsushi Yamada)
# EM Segmentation in 3D Slicer 4 (Daniel Haehn, Dominique Belhachemi, Kilian Pohl)
# [[NonRigidRegistrationThatAccommodatesResection|Demons Based Non-Rigid Registration that Accommodates Resection in 3D Slicer]] (Petter Risholm, Sandy Wells)
# [[2011_Summer_Project_Week_re-parameterize_fiber|Re-parameterize fiber tracts for fiber statistics analysis]]

==Background==

We are pleased to announce the 13th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 28th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

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

== Logistics ==
*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please register [http://guest.cvent.com/d/sdqy0l/4W here]. Payment must be made by credit card.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' Boston Marriott Cambridge, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. Group rate is $199/night plus tax. Book [http://www.marriott.com/hotels/travel/boscb?groupCode=jrbjrba&app=resvlink&fromDate=6/19/11&toDate=6/24/11 here] or call 1-617-494-6600 and mention that you are booking in the MIT Room Block. '''All reservations must be made by May 29, 2011 to receive the discounted rate.'''

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 28, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 12, all participants to add a one line title of their project to #Projects
#By 3pm ET on Thursday June 9, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 16: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Registrants==

Do not add your name to this list- it is maintaining by the organizers based on your paid registration (see Logistics for link)
# Bompard, Lucile- UNC NIRAL
# Belhachemi, Dominique- University of Pennsylvania
# Budin, Francois- UNC NIRAL
# Callahan, Steve- University of Utah
# Cates, Joshua- University of Utah
# Datar, Manasi- University of Utah
# Davey, Colin-
# Fishbaugh, James- University of Utah
# Gardner, Greg- University of Utah
# Globinsky, Ronen- Yale University
# Goubran, Maged- Robarts Research Institute
# Haehn, Daniel- University of Pennsylvania
#Halle, Mike - BWH/HMS
# Heffter, Tamas- Queen's University
# Irimia, Andrei- University of California, Los Angeles
# Johnson, Hans- University of Iowa
# Kapur, Tina - Brigham and Women's Hospital; Harvard Medical School
# Kikinis, Ron- Brigham and Women's Hospital; Harvard Medical School
# Kim, Regina- University of Iowa
# Kostrzewski, Szymon- Ecole Polytechnique Federale de Lausanne EPFL
# Lee, Dillon- University of Utah
# Li, Yinpeng- UNC-NIRAL
# Lou, Yifei- Georgia Institute of Technology
#Mastrogiacomo, Katie- Brigham and Women's Hospital
# Matsui, Joy- University of Iowa
# Meier, Dominik- BWH
# Miller, James- GE Research
# Paniagua, Beatriz- University of North Carolina at Chapel Hill
# Papademetris, Xenophon- Yale University
# Patwardhan, Kedar- GE Global Research
# Pinter, Csaba- Queen's University
# Pohl, Kilian- UPenn
# Prastawa, Marcel- University of Utah
# Rajchl, Martin- Robarts Research Institute
# Schuh, Andreas- University of Pennsylvania
# Scully, Mark- University of Iowa
# Vachet, Clement- UNC Chapel Hill
# Wang, Bo- University of Utah
#Wells, Sandy- BWH/HMS
# Yamada, Atsushi- Brigham and Women's Hospital

2011 Summer Project Week

2011-06-07T14:06:43Z

Wendyuu: /* Projects */

Back to [[Events]]

[[image:PW-MIT2011.png|right|200px]]

*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT

==Preliminary Agenda==
==Agenda==

{|border="1"
|-style="background: #b0d5e6; color: #02186f; font-size: 130%"
!Time
!width="250px"|Monday, June 20
!width="250px"|Tuesday, June 21
!width="250px"|Wednesday, June 22
!width="250px"|Thursday, June 23
!width="250px"|Friday, June 24
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-11am:''' [[2011 Project Week Breakout Session: Slicer4|Slicer 4 Core Modules Usability Review]]''' [[MIT_Project_Week_Rooms#Star|Star Room]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> [[2011 Summer Project Week Breakout Session Slicer4 Annotation|Slicer4 Annotations]] (Nicole Aucoin)<br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-5:00pm: NA-MIC Kit Update''' (Aylward, Miller, Pieper)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:MultiVolumeContainer#Summer_2011_Project_Week_Breakout_Session Slicer4 MultiVolume Containers] (Nicole Aucoin)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[Summer_2011_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' [[2011 Summer Project Week Breakout Session VTKCharts|VTK Charts]] (Marcus Hanwell)
<br>[[MIT_Project_Week_Rooms#32-D407|32-D407]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2011|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2011_Summer_Project_Week_Breakout_Session_EMRegistration|Inter-subject Registration for EM segmenter]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''1-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

* Please make a link for your project to a new page based on the [[2011_Summer_Project_Week_Template| 2011 Summer Project Page Template]]

#valuate the applicability of DICOM RT I/O facility in Slicer (via Plastimatch Extension) for Brachytherapy Planning (Tina Kapur, Greg Sharp, Robert Cormack?)
#Visualization of b-spline and vector fields (Steve, Danielle, Dominik)
#Annotation Module in Slicer4 (Nicole Aucoin, Daniel Haehn)
#Slicer4 Multivolume Containers (Ron Kikinis, Nicole Aucoin, Steve Pieper, ... )
#RECIST Slicer4 module (Nicole Aucoin)
#DicomToNrrdConverter refactoring ( Xiaodong Tao, Mark Scully)
# [[2011_Summer_Project_Week_normal_consistency_particles|Normal consistency in particle correspondence computation using great circles in principal spheres - Huntington's Disease]], (Beatriz Paniagua, Martin Styner, Sungkyu Jung, Marc Scully)
# Group-wise Automatic Mesh-Based analysis of CortIcal Thickness (GAMBIT) - TBI (Clement Vachet, Martin Styner, Randi Gollub?)
#[[2011_Summer_Project__Week_Shape_Analysis_UNC |SPHARM & particles shape analysis - Huntington's Disease]] - Lucile Bompard, Clement Vachet, Beatriz Paniagua, Martin Styner
# Non-rigid, inter-patient registration of bone masks derived from CT for Head and Neck Cancer Radiation Therapy (Ivan Kolesov, Yi Gao, Gregory Sharp, and Allen Tannenbaum)
# Robust Statistical Segmentation (RSS) for the Atrial Fibrillation Ablation Therapy (Yi Gao, Kedar Patwardhan, Wassim Haddad, and Allen Tannenbaum, Rob MacLeod, Josh Blauer, and Josh Cates)
#Mass Spectrometry for Brain Tumor Therapy (Behnood Gholami, Nathalie Agar)
#Multimodality Image Registration for TBI? (Yifei Lou, Danielle Pace, Jack Van Horn?, Marcel Prastawa?)
# Segmentation of Longitudinal TBI data (Bo Wang, Jack Van Horn, Andrei Irimia, Marcel Prastawa, Guido Gerig)
# Longitudinal Shape Regression - Huntington's Disease (James Fishbaugh, Guido Gerig)
# [[2011_Summer_Project__Week_DVH|Dose volume histograms in Slicer]] (Greg Sharp, Nadya Shusharina, Steve Pieper, Csaba Pinter, Tina Kapur)
# [[2011_Summer_Project__Week_DICOM_RT|Synthetic images, vector fields, RT structures and RT doses in Slicer and ITK]]. (Nadya Shusharina, Greg Sharp, Luis Ibanez, Steve Pieper)
# Interactive Watersheds Segmentation Module for Slicer for Atrial Fibrillation and HN Cancer (Josh Cates, Ross Whitaker, Steve Pieper, Jim Miller, Nadya)
# Segmentation of Nerve and Nerve Ganglia in the Spine (Adrian Dalca, Giovanna Danagoulian, Ron Kikinis, Ehud Schmidt, Polina Golland)
# Image Manifold Learning with Spectral Embedding and Laplacian Eigenmaps (Ramesh Sridharan, Polina Golland)
# Shapeworks Shape Analysis for Atrial Fibrilliation and HD (Manasi Datar, Beatriz UNC, Marc Scully)
#Explore the applicability of RSS and Shapeworks for Ventricular Segmentation(Chiara Carminati, ?, ?)
# Integrate BRAINSCut into Slicer3(Regina Kim, ... )
# The Vascular Modeling Toolkit in 3D Slicer 4 (Daniel Haehn, Luca Antiga, Steve Pieper)
# Integration of LANDWARP into interactive registration module for MR-guided prostate biopsy (Andrey Fedorov, Greg Sharp, Nadya Shusharina)
# [[2011_Summer_Project_Week_Registration_of_mouse_brains|Registration of mouse brains]] (Francois Budin)
# ShapeWorks Applications (Manasi Datar, Beatriz Paniagua, Martin Styner, Ross Whitaker, ?)
# Wireless joystick controlling Slicer4 (Szymon Kostrzewski)
# Live Tracked Ultrasound in 3D Slicer 4 (Tamas Heffter)
# [http://wiki.na-mic.org/Wiki/index.php/Survey_stealthlink_openigtlink Surveying research teams interested in Open IGT Link support of Stealth Station (Nobuhiko Hata, Ron Kikinis)]
# DTIPrep - "Study-specific Protocol" based automatic DWI/DTI quality control and preparation - Huntington's Disease (Mashid Farzinfar, Clement Vachet, Joy Matsui, Martin Styner)
# DTIProcessing - Huntington's Disease (Clement Vachet, Joy Matsui, Martin Styner)
# Volumetric DTI into Slicer for HD for Tract based roi segmentation (Steve Callahan, Marc Scully, Jim Miller)
#Nifti Support for Diffusion Tensor Images (Demian)
# Finishing details on the workflows: DICOM->Full brain tractography / peritumoral (Demian)
# Refactoring of the tractography display widget (Isaiah)
# Laterality (Lauren)
# Selection for models and bundles post-clustering (Lauren)
#ROI-based / picking selection of fiber bundles (Maybe one of Sylvain's interns)
#Adding streamlined tractography to the Finsler front propagation tractography toolkit (Antonio)
#Add ODF estimation / visualization (Antonio)
# Workflows and Service Oriented Architecture Modules for Slicer4 as Extensions (Alexander Zaitsev, Wendy Plesniak, Ron Kikinis)
# [[2011_Summer_Project__Week_DICOM_Networking|DICOM Networking interface for Slicer4]] (Steve Pieper, Nicole Aucoin, Noby Hata)
# Stenosis Detector in 3D Slicer 4 (Suares Tamekue, Daniel Haehn, Luca Antiga)
# [[2011_Summer_Project_Week_Spine_Segmentation_And_Osteoporosis_Screening_CT|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)
# Slicer module for building an average population HARDI Atlas (Ryan Eckbo)
# 4D Ultrasound (Laurent Chauvin, Noby Hata, Atsushi Yamada)
# EM Segmentation in 3D Slicer 4 (Daniel Haehn, Dominique Belhachemi, Kilian Pohl)
# [[NonRigidRegistrationThatAccommodatesResection|Demons Based Non-Rigid Registration that Accommodates Resection in 3D Slicer]] (Petter Risholm, Sandy Wells)
# Re-parameterize fiber tracts for fiber statistics analysis

==Background==

We are pleased to announce the 13th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 28th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

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

== Logistics ==
*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please register [http://guest.cvent.com/d/sdqy0l/4W here]. Payment must be made by credit card.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' Boston Marriott Cambridge, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. Group rate is $199/night plus tax. Book [http://www.marriott.com/hotels/travel/boscb?groupCode=jrbjrba&app=resvlink&fromDate=6/19/11&toDate=6/24/11 here] or call 1-617-494-6600 and mention that you are booking in the MIT Room Block. '''All reservations must be made by May 29, 2011 to receive the discounted rate.'''

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 28, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 12, all participants to add a one line title of their project to #Projects
#By 3pm ET on Thursday June 9, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 16: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Registrants==

Do not add your name to this list- it is maintaining by the organizers based on your paid registration (see Logistics for link)
# Bompard, Lucile- UNC NIRAL
# Belhachemi, Dominique- University of Pennsylvania
# Budin, Francois- UNC NIRAL
# Callahan, Steve- University of Utah
# Cates, Joshua- University of Utah
# Datar, Manasi- University of Utah
# Davey, Colin-
# Fishbaugh, James- University of Utah
# Gardner, Greg- University of Utah
# Globinsky, Ronen- Yale University
# Goubran, Maged- Robarts Research Institute
# Haehn, Daniel- University of Pennsylvania
#Halle, Mike - BWH/HMS
# Heffter, Tamas- Queen's University
# Irimia, Andrei- University of California, Los Angeles
# Johnson, Hans- University of Iowa
# Kapur, Tina - Brigham and Women's Hospital; Harvard Medical School
# Kikinis, Ron- Brigham and Women's Hospital; Harvard Medical School
# Kim, Regina- University of Iowa
# Kostrzewski, Szymon- Ecole Polytechnique Federale de Lausanne EPFL
# Lee, Dillon- University of Utah
# Li, Yinpeng- UNC-NIRAL
# Lou, Yifei- Georgia Institute of Technology
#Mastrogiacomo, Katie- Brigham and Women's Hospital
# Matsui, Joy- University of Iowa
# Meier, Dominik- BWH
# Miller, James- GE Research
# Paniagua, Beatriz- University of North Carolina at Chapel Hill
# Papademetris, Xenophon- Yale University
# Patwardhan, Kedar- GE Global Research
# Pinter, Csaba- Queen's University
# Pohl, Kilian- UPenn
# Prastawa, Marcel- University of Utah
# Rajchl, Martin- Robarts Research Institute
# Schuh, Andreas- University of Pennsylvania
# Scully, Mark- University of Iowa
# Vachet, Clement- UNC Chapel Hill
# Wang, Bo- University of Utah
#Wells, Sandy- BWH/HMS
# Yamada, Atsushi- Brigham and Women's Hospital

2010 Summer Project Week

2010-06-25T14:57:15Z

Wendyuu: /* Analysis */

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

[[Image:PW-MIT2010.png|500px|right]]

__TOC__
<br>
[http://www.smugmug.com/gallery/12687574_DsJjF '''Photos ''']
<br>
==Agenda==

{|border="1"
|-style="background: #b0d5e6; color: #02186f; font-size: 130%"
!Time
!width="250px"|Monday, June 21
!width="250px"|Tuesday, June 22
!width="250px"|Wednesday, June 23
!width="250px"|Thursday, June 24
!width="250px"|Friday, June 25
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am:''' [[Media:NAMIC Kit-2010-6-22.ppt|NA-MIC Kit Update]] (Jim Miller)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''9:20am:''' [[Media:2010_Project_Week_Slicer.ppt|3D Slicer Update]] (Steve Pieper)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''10am:''' Superbuild Demo (Dave Partyka)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''10:15am:''' Break
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''10:30-11am:''' [[Media:2010_Project_Week_OpenIGTLink.ppt|OpenIGTLink Update]] (Junichi Tokuda)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''11am-12pm:''' [[2010_Summer_Project_Week_Slicer_Hands-on_Workshop|Slicer Hands-on Workshop]] (Randy Gollub, Sonia Pujol)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''9am-5pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-5:30pm: Tutorial:''' [[2010 Summer Project Week Breakout: Getting Started with Qt|Getting Started with Qt]] (Adam Weinrich, Nokia)
<br>[[MIT_Project_Week_Rooms#32-155|32-155 (Stata Lecture Hall)]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> QT/Slicer (Steve, JC, J2)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm: <font color="#4020ff">Breakout Session:'''</font>
<br> [[2010 Summer Project Week Breakout Session: Data Management |Data Management]] (Stephen Aylward)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [[Microscopy_Image_Analysis|Microscopy Image Analysis]] (Sean Megason)
<br>[[MIT_Project_Week_Rooms#Kiva|Kiva Room]]
<br>----------------------------------------<br>
'''3-5pm: <font color="#4020ff">Breakout Session:'''</font><br>
[[2010 Summer Project Week Breakout Session:QA Training|QA Training]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:VTK Widget|VTK Widgets]] (Nicole, Kilian, JC)
<br>[[MIT_Project_Week_Rooms#32-261|32-261 Room]]
<br>----------------------------------------<br>
<br>'''5pm: <font color="#4020ff">Reception'''</font><br>
<br>[[MIT_Project_Week_Rooms#R&D Pub|R&D Pub]]
|'''1-2pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:GWE|GWE]] (Marco Ruiz)
<br>----------------------------------------<br>
'''2-3pm:''' Simple Git (Steve Pieper) [[media:Simple Git-pieper-2010-06-24.ppt|(Slides)]]
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br>
[[2010 Summer Project Week Breakout Session: Volume Rendering|Volume Rendering Demos and Discussion]] (Yin Wu, Steve Pieper)
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

Please note:
*We need to empty room by 1:30pm on Friday. You are welcome to use wireless in Stata.
*Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
*Next Project Week [[AHM_2011| January 3-7, 2011, Salt Lake City, Utah]]

==Projects==

=== Segmentation ===
#[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
#[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
#[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)
#[[2010_Summer_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Karol Chudy, Allen Tannenbaum, GT; Ron Kikinis, BWH)
#[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping integration with Slicer]] (Nicole Aucoin, Min Chen)
#[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)
#[[2010_Summer_Project_Week_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans ]](Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)
#[[2010_Summer_Project_Week_Left ventricular scar segmentation| LV scar segmentation display and fusion]] (Dana C. Peters, Felix Liu, BIDMC, Boston)
#[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Johannes Schick, Steve Pieper, Ron Kikinis)

=== Registration ===
#[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
#[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)
#[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)
#[[2010_Summer_Project_Week_Best_Regularization_Term_for_Demons_Registration_Algorithm|Best Regularization Term for Demons Registration Algorithm]] (Rui Li, Greg Sharp)
#[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Nadya Shusharina, Greg Sharp)
#[[2010_Summer_Project_Week_MR_to_Ultrasound_Registration_Methodology|MR to Ultrasound Registration Methodology]] (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward, Andriy Fedorov)
#[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Sylvain Bouix, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)

=== Shape Analysis ===
#[[2010_Summer_Project_Week_Shape_Test_Bench|Shape Test Bench]] (Marc Niethammer, Sylvain Bouix)
#[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)
# [[2010_Summer_Project_Week_Shape_Analysis_UNC|Shape Analysis projects, integration with Slicer3]] (Beatriz Paniagua, Martin Styner)
# [[Particle Based Shape Regression]] (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)
#[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)

=== Diffusion ===
#[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
#[[2010_Summer_Project_Two_Tensor|Implementing Two-tensor tractography in Slicer (Python) ]](Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)
#[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)
#[[2010_Summer_Project_Week_Diffusion|Fluid Mechanics Based Tractography ]](Nathan Hageman)
#[[2010_Summer_Project_QSpace_Reconstruction_for_Diffusion_Spectrum_Imaging_Data|QSpace Imaging Reconstruction for Diffusion Spectrum Imaging Data]] (Sudhir Pathak)

=== IGT ===
#[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Dose_Calculation|MR to CT Registration for Prostate Brachytherapy Dose Calculation]] (Andriy Fedorov, Dominik Meier, Hans Johnson)
#[[2010_Summer_Project_Week_Intraoperative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound|Intraoprative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound]] (Jason White, Steve Pieper, Junichi Tokuda?, Pratik Patel?)
#[[2010_Summer_Project_Week_Prostate_Intervention|Prostate Intervention(Junichi Tokuda, Tamas Ungi, Haiying Liu, Sam Song)]]
#[[2010_Summer_Project_Week_Liver_Ablation|Liver Ablation (Haiying Liu, Noby Hata)]]
# [[2010_Summer_Project_Week_BrainLab_Aurora_Hybrid_Navigation|BrainLab-Aurora Hybrid Navigation]] (Isaiah Norton, Dan Marcus, Noby Hata)
# [[2010_Summer_Project_Week_PerkStationModule|PerkStation Module]] (Tamas Ungi, Xiaodong Tao)
#[[2010_Summer_Project_Week_Co-registration_of_PET_and_DWI_Images_for_the_targeting_of_Glioma_Biopsies|Co-registration of PET and DWI Images for the targeting of Glioma Biopsies]] (Gareth Smith, Dominik Meir, Vince Magnotta)
#[[2010_Summer_Project_Week_Implementing_Open_IGT_Link_to_Virtual_Place_for_research_support|Implementing Open IGT Link to Virtual Place for research support]] (Nicholas Herlambang, Masakatsu Hoashi, Junichi Tokuda, Noby Hata)
#[[2010_Summer_Project_Week_Tracking_Neuroendoscope_Using_EM_Tracker_and_OpenIGTLink|Tracking Neuroendoscope Using EM Tracker and OpenIGTLink]] (Laurent Chauvin, Junichi Tokuda, Noby Hata)
#[[2010_Summer_Project_Week_Implementing_OpenCV_to_Slicer3_for_Neuroendoscopic_Surgery|Implementing OpenCV to Slicer3 for Neuroendoscopic Surgery]] (Atsushi Yamada, Junichi Tokuda, Noby Hata)

=== Radiotherapy ===
#[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp, Tamas Ungi)
#[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)
#[[2010_Summer_Project_Week_Seg_Adapt_HNT|Segmentation for Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Greg Sharp, and Allen Tannenbaum )

=== Analysis ===
#[[2010_NAMIC_Project_week:IA-FEMesh| IA-FEMesh Slicer3 Finite Meshing Module]] (N Grosland, V Magnotta, C Lisle, S Pieper)
#[[2010_Summer_Project_Week_Cortical_Thickness_Analysis|Cortical thickness analysis]] (Clement Vachet, Heather Cody Hazlett, Martin Styner)
#[[2010_Summer_Project_Week_Mouse_Brain_Cortical_Thickness_Analysis|Mouse brain cortical thickness analysis]] (Joohwi Lee, Ipek Oguz, Martin Styner)
#[[2010_Summer_Project_Week_Primate image analysis using the standard Slicer pipeline|Primate image analysis using the standard Slicer pipeline]] (Yundi Shi, Martin Styner, Clement Vache, Mar Sanchez, Andriy Fedorov)
#[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
#[[2010_Summer_Project_Week_FractureClassification_Brainstorming|Femoral Fracture Classification Brainstorming Session]] (Karl Fritscher, Vince Magnotta, Peter Karasev, Curt Lisle, Ron Kikinis)
#[[2010_Summer_Project_Week_Computer_Aided_Photodynamic_Therapy| Computer_Aided_Photodynamic_Therapy]] (E Pietka, D Spinczyk, P Szabelak)
#[[2010_Summer_Project_Week_Quantification_Of_Lesion_Diffusion_Disruption| Quantification of Lesion Diffusion Disruption]](M Scully, H J Bockholt)
#[[2010_Summer_Project_Week_Lupus_Lesion_Segmentation_and_Review_Statistics|Lupus Lesion Segmentation and Review Statistics]](M Scully, H J Bockholt)

===[[Microscopy Image Analysis]] ===
# [[ 2010 Project Week DICOM supplement 145 | DICOM supplement 145 ]] : Microscopy Image in the Dicom Standard (Mathieu Malaterre, Alex. Gouaillard)
# [[ 2010 Summer Project Week Microscopy extensions for ITK | Microscopy Extensions for ITK ]]: convolution, deconvolution, wavelets and more ( Gaetan Lemhann, Alex. Gouaillard )
# [[Import/Export Farsight-GoFigure results]] (Arnaud Gelas, Lydie Souhait, Kedar Grama, Raghav Padmanabhan, Sean Megason, Badri Roysam)
# [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)
# [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Kishore Mosaliganti, Arnaud Gelas, Sean Megason, Raghu Machiraju)
# [[ITK Analysis of Large Histology Datasets]] (Liya Ding, Kun Huang, Sean Megason, Raghu Machiraju)
# [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Arnaud Gelas, Stever Pieper)
# [[Seedings results comparison]] (Antonin Perrot-Audet, Raghav Padmanabhan, Kishore Mosaliganti, Badri Roysam, Sean Megason)
# [[ITK GPAC level set|ITK Multiphase and GPAC level sets]] (K. Palaniappan, Ilker Ersoy, Filiz Bunyak, Kishore Mosaliganti, Sean Megason)
# [[MedianTexture|Median binary pattern texture measures for cell nuclei segmentation]] (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)
# [[StandardsInterfaces|Standards and Interfaces for Microscopy Image Analysis in ITK]] (whoever has an opinion, Sean Megason)

=== NA-MIC Kit Internals ===
#[[2010 NAMIC Project week: Module Inventory|Module Inventory]] (Steve, Jim)
#[[2010 NAMIC Project week: Viewer Manager Factory|Viewer Manager Factory]] (Alex Yarmarkovich, Kilian, Steve, Nicole)
#[[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andriy Fedorov, Yanling Liu, Alex Yarmarkovich, Jim Barabas)
#[[2010 NAMIC Project week:Inventory of Volume Rendering Functionality|Inventory of Volume Rendering Functionality]] (Jim Barabas, Noby Hata)
#[[2010_NAMIC_Project_week:Slicer4Icons|Consistent visual language for Slicer4: icon rework marathon]] (Wendy Plesniak)
#[[2010_NAMIC_Project_week:LongitudinalPETSUV_Wizard | Slicer Wizard for PET/CT workflow]] (Wendy Plesniak, Ron Kikinis, Alexander Zaitsev)
#[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)
#[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)
#[[2010_Summer_Project_Week_Superbuild |Superbuild ]](David Partyka, Steve Pieper, Katie Hayes)
#[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)
#[[2010 NAMIC Project week: Real-Time Volume Rendering for Virtual Colonoscopy|Real-Time Volume Rendering for Virtual Colonoscopy]] (Hiro Yoshida, Yin Wu, Steve Pieper, Ron Kikinis)

=== Workflows and Integration ===
# [[Summer_project_week_2010_Workflows_SOA|Workflows and Service Oriented Architecture Solutions for Slicer3 Modules]] (Alexander Zaitsev, Wendy Plesniak, Charles Guttmann, Ron Kikinis)

==Background==

We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

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

== Logistics ==
*'''Dates:''' June 21-25, 2010
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here] to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&app=resvlink&fromDate=6/20/10&toDate=6/25/10 Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process.

''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''
''' $189/night/room (plus tax).'''
''' This rate is good only through June 1.'''

Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290.

*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on June 10, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Attendee List==

<big>'''NOTE:'''</big> <font color="maroon">THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD '''NOT''' EDIT THIS, BUT [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 REGISTER BY CLICKING HERE.]</font>

# Yousef Al-Kofahi , CompuCyte Corporation
# Peter Anderson , retired
# Nicole Aucoin , BWH
# Michel Audette , Kitware
# Stephen Aylward , Kitware, Inc
# Jim Barabas, MIT
#Barrett, Ryan, BWH
# Alexis Boucharin , UNC Neuro Image Research and Analysis Laboratories
# Sylvain Bouix , BWH
# Michael Bowers , Johns Hopkins University
# Francois Budin , UNC
# Everette Burdette , Acoustic MedSystems, Inc.
# Laurent CHAUVIN , Brigham and Women's Hospital
# Min Chen , Johns Hopkins University
# Jason Crane , UCSF
#Nikos Chrisochoides, College of William and Mary
# Manasi Datar , SCI Institute
# Liya Ding , The Ohio State University
# Ryan Eckbo , BWH
# Ilker Ersoy , University of Missouri Columbia
# Andriy Fedorov , Surgical Planning Lab
# Jean-Christophe Fillion-Robin , Kitware Inc.
# Julien Finet , Kitware Inc
# James Fishbaugh , SCI Institute
# Karl Fritscher , UMIT
# Yi Gao , Gerogia Tech
# Arnaud GELAS , Harvard Medical School
# Randy Gollub , MGH
# Chris Gorgolewski , SPL
# alexandre gouaillard , CoSMo Software
# Sylvain Gouttard , SCI Institute
# Kedar Grama , Rensselaer Polytechnic Institute
# Daniel Haehn , University of Pennsylvania
# Adel Hafiane , ENSI-Bourges
# Nathan Hageman ,
# Dieter Hahn , University Erlangen
# Michael Halle , BWH/SPL
# Corentin Hamel , UNC Chapel Hill
# Nobuhiko Hata , Brigham and Women's Hospital
# Kathryn Hayes , Brigham and Women's Hospital
# Nicholas Herlambang , AZE, Ltd.
#Masakatsu Hoashi, AZE Ltd.
# Leslie Holton , Medtronic Navigation
# Luis Ibanez , KITWARE Inc.
# Jayender Jagadeesan , SPL
# Hans Johnson , University of Iowa
# Tina Kapur , Brigham and Women's Hospital
#Peter Karasev, Georgia Tech
# Ron Kikinis , Brigham and Women's Hospital
# Minjeong Kim , UNC-Chapel Hill
# Ivan Kolesov , Georgia Institute of Technology
# Garrett Larson , UNC-CH
# Joohwi Lee , UNC Chapel Hill
# Rui Li , MGH
# Stefan Lienhard , LMI
# Curtis Lisle , KnowledgeVis, LLC
# Haiying Liu , Brigham and Women's Hospital
# Felix Liu , Beth Israel Deaconess Medical Center
# Yanling Liu , SAIC-Frederick, Inc.
# Bradley Lowekamp , Lockheed Martin
# raghu machiraju , The Ohio State University
# Vincent Magnotta , The University of Iowa
# mathieu malaterre , CoSMo Software
#Charles Maneval, BWH
# Daniel Marcus , Washington University
# William Marks , Focused Ultrasound Lab, BWH, HMS
# Katie Mastrogiacomo , Brigham and Women's Hospital
# Joy Matsui , University
# Sean Megason , Harvard Medical School
# Dominik Meier , BWH, Boston MA
# bjoern menze , CSAIL MIT
# Mikhail Milchenko , WUSTL
# James Miller , GE Research
# Kishore Mosaliganti , Harvard Medical School
# Marc Niethammer , UNC Chapel Hill
# Isaiah Norton , BWH Neurosurgery
# Beck Olson , UCSF
# John Onofrey , Yale University
# Raghav Padmanabhan , RPI
# Kannappan Palaniappan , university of Missouri
# Beatriz Paniagua , University of North Caolina at Chapel Hill
# Xenophon Papademetris , Yale University
# Eun-Joo Park , Brigham & Women's Hospital
# David Partyka , Kitware Inc
# Pratik Patel ,
# Sudhir Pathak , Univeristy Of Pittsburgh
# Thierry PECOT , Ohio State University
# Marta Peroni , Politecnico di Milano
# Antonin Perrot-Audet , Harvard Medical School
# Steve Pieper , Isomics, Inc.
# Wendy Plesniak , BWH
# Kilian Pohl , IBM
# Sonia Pujol , Brigham and Women's Hospital
# Nicolas Rannou , Harvard Medical School
# Tammy Riklin Raviv , MIT, CSAIL
# Marco Ruiz , UCSD
# Johannes Schick , SPL
# William Schroeder , Kitware
# Mark Scully , The Mind Research Network
#Gunasekaran Seetharaman, US Air Force Research Lab
# Greg Sharp , MGH
# Yundi Shi , UNC Chapel Hill
# Nadya Shusharina , MGH
# Shantanu Singh , The Ohio State University
# Gareth Smith , Wolfson Medical Imaging Centre (WMIC)
# Lydie Souhait , Harvard Medical School
# Dominik Spinczyk , Silesian University of Technology
# Padmapriya Srinivasan ,
# Xiaodong Tao , GE Research
# Matthew Toews , Brigham and Women's Hospital, Harvard Medical School
# Junichi Tokuda , Brigham and Women's Hospital
# Tamas Ungi , Queen's University
# Clement Vachet , UNC Chapel Hill
# Veda Vadyar , Brigham and Women's Hospital
# Gopalkrishna Veni , SCI Institute
# Stuart Wallace , Massachusetts General Hospital
# Demian Wassermann , SPL/LMI/PNL
#Yihan Wei, BWH
# Adam Weinrich , Nokia
# Sandy Wells , BWH
# Phillip White , BWH/HMS
# Guorong Wu , University of North Carolina at Chapel Hill
# Yin Wu , Mass General Hospital
# Atsushi Yamada , Nagoya Institute of Technology
# Alexander Yarmarkovich , ISOMICS
# Alexander Zaitsev , Brigham and Womens Hospital

2010 Summer Project Week Primate image analysis using the standard Slicer pipeline

2010-06-25T14:32:03Z

Wendyuu:

__NOTOC__
<gallery>
Image:Slide1.png
Image:snapshot0001.png
</gallery>

==Key Investigators==
* UNC: Yundi(Wendy) Shi, Clement Vachet, Martin Styner
* Emory: Mar Sanchez
* BWH: Andriy Fedorov

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

<h3>Objective</h3>
To build an open-source software (mainly involving Slicer3) based pipeline for primate imaging, including skull stripping of T1,T2 and DTI images, tissue segmentation, cortical thickness analysis, atlas building and fiber tracing and tract-based analysis. This is part of a longitudinal study of rhesus macaque monkeys

</div>

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

<h3>Approach, Plan</h3>

* Skull stripping and Tissue segmentation
ABC (developed by Marcel Prastawa, SCI, Utah) is currently used for skull stripping and tissue segmentation of the 3 months, 6 months and 12 months T1 and T2 images.
Challenge include: Application of ABC or neoseg for the same task on 2 weeks old monkey images, due to the different anatomical structures during early ages and small brain size of the monkeys

* Cortical thickness analysis
Will work with Clement Vachet and adapt the tools for human data to primate data

* Affine alignment
RVIEW is currently used for affine alignment of the monkey images. Working on testing the data with the Slicer tools and replace rview tools with them. We need to work with ?? for the special challenge in registration of the monkey brains.

* Atlas building
AtlasWerks is the tool for atlas building with fWarp (developed by Sarang Joshi, SCI, UTAH). We would like to start using open source tools like the deamons registration in Slicer for the same task.

</div>

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

<h3>Progress</h3>
* Attended the DTI breakout session, and identified the problem/challenge of the commonly used tools in the pipeline used by people in the community and the tools we usually use (DicomtoNrrdConvert...)

* Work with Hans, and tested BrainsFit for the "affine alignment" task in tissue segmentation, which includes rigid registration of T1 and T2 images, as well as the alignment of subject with template using affine registration. Parameters were selected for monkey data with good results.

* Testing Demons for warping the subjects to atlas, instead of fWarp.

* Meeting with Steve for using the color module for visualization of fiber bundles with scalars with custom min and max and workaround to visualize fibers as tubes with scalar values written in the vtk lookup table.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered as open-source software and open dataset

==References==
*M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. In Proc SPIE Vol 6512, Medical Imaging, 2007, pp. 65122 L1-8.

</div>

File:Snapshot0001.png

2010-06-25T14:31:13Z

Wendyuu:

2010 Summer Project Week Primate image analysis using the standard Slicer pipeline

2010-06-25T14:15:11Z

Wendyuu: /* Key Investigators */

__NOTOC__
<gallery>
Image:Slide1.png
</gallery>

==Key Investigators==
* UNC: Yundi(Wendy) Shi, Clement Vachet, Martin Styner
* Emory: Mar Sanchez
* BWH: Andriy Fedorov

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

<h3>Objective</h3>
To build an open-source software (mainly involving Slicer3) based pipeline for primate imaging, including skull stripping of T1,T2 and DTI images, tissue segmentation, cortical thickness analysis, atlas building and fiber tracing and tract-based analysis. This is part of a longitudinal study of rhesus macaque monkeys

</div>

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

<h3>Approach, Plan</h3>

* Skull stripping and Tissue segmentation
ABC (developed by Marcel Prastawa, SCI, Utah) is currently used for skull stripping and tissue segmentation of the 3 months, 6 months and 12 months T1 and T2 images.
Challenge include: Application of ABC or neoseg for the same task on 2 weeks old monkey images, due to the different anatomical structures during early ages and small brain size of the monkeys

* Cortical thickness analysis
Will work with Clement Vachet and adapt the tools for human data to primate data

* Affine alignment
RVIEW is currently used for affine alignment of the monkey images. Working on testing the data with the Slicer tools and replace rview tools with them. We need to work with ?? for the special challenge in registration of the monkey brains.

* Atlas building
AtlasWerks is the tool for atlas building with fWarp (developed by Sarang Joshi, SCI, UTAH). We would like to start using open source tools like the deamons registration in Slicer for the same task.

</div>

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

<h3>Progress</h3>
* Attended the DTI breakout session, and identified the problem/challenge of the commonly used tools in the pipeline used by people in the community and the tools we usually use (DicomtoNrrdConvert...)

* Work with Hans, and tested BrainsFit for the "affine alignment" task in tissue segmentation, which includes rigid registration of T1 and T2 images, as well as the alignment of subject with template using affine registration. Parameters were selected for monkey data with good results.

* Testing Demons for warping the subjects to atlas, instead of fWarp.

* Meeting with Steve for using the color module for visualization of fiber bundles with scalars with custom min and max and workaround to visualize fibers as tubes with scalar values written in the vtk lookup table.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered as open-source software and open dataset

==References==
*M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. In Proc SPIE Vol 6512, Medical Imaging, 2007, pp. 65122 L1-8.

</div>

2010 Summer Project Week Primate image analysis using the standard Slicer pipeline

2010-06-25T13:36:46Z

Wendyuu:

__NOTOC__
<gallery>
Image:Slide1.png
</gallery>

==Key Investigators==
* UNC: Yundi(Wendy) Shi, Clement Vachet, Martin Styner
* Emory: Mar Sanchez
* BWH: Andriy Fedorov

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

<h3>Objective</h3>
To build an open-source software (mainly involving Slicer3) based pipeline for primate imaging, including skull stripping of T1,T2 and DTI images, tissue segmentation, cortical thickness analysis, atlas building and fiber tracing and tract-based analysis. This is part of a longitudinal study of rhesus macaque monkeys

</div>

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

<h3>Approach, Plan</h3>

* Skull stripping and Tissue segmentation
ABC (developed by Marcel Prastawa, SCI, Utah) is currently used for skull stripping and tissue segmentation of the 3 months, 6 months and 12 months T1 and T2 images.
Challenge include: Application of ABC or neoseg for the same task on 2 weeks old monkey images, due to the different anatomical structures during early ages and small brain size of the monkeys

* Cortical thickness analysis
Will work with Clement Vachet and adapt the tools for human data to primate data

* Affine alignment
RVIEW is currently used for affine alignment of the monkey images. Working on testing the data with the Slicer tools and replace rview tools with them. We need to work with ?? for the special challenge in registration of the monkey brains.

* Atlas building
AtlasWerks is the tool for atlas building with fWarp (developed by Sarang Joshi, SCI, UTAH). We would like to start using open source tools like the deamons registration in Slicer for the same task.

</div>

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

<h3>Progress</h3>
* Attended the DTI breakout session, and identified the problem/challenge of the commonly used tools in the pipeline used by people in the community and the tools we usually use (DicomtoNrrdConvert...)

* Testing BrainsFit for the "affine alignment" task in tissue segmentation, which includes rigid registration of T1 and T2 images, as well as the alignment of subject with template.

* Testing Demons for warping the subjects to atlas, instead of fWarp.

* Meeting with Steve for using the color module for visualization of fiber bundles with scalars with custom min and max and workaround to visualize fibers as tubes with scalar values written in the vtk lookup table.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered as open-source software and open dataset

==References==
*M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. In Proc SPIE Vol 6512, Medical Imaging, 2007, pp. 65122 L1-8.

</div>

2010 Summer Project Week Primate image analysis using the standard Slicer pipeline

2010-06-25T13:36:25Z

Wendyuu:

__NOTOC__
<gallery>
Image:Slide1.png|[[thumb|500px|P values visualized on the fiber tracts as tubes]]
</gallery>

==Key Investigators==
* UNC: Yundi(Wendy) Shi, Clement Vachet, Martin Styner
* Emory: Mar Sanchez
* BWH: Andriy Fedorov

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

<h3>Objective</h3>
To build an open-source software (mainly involving Slicer3) based pipeline for primate imaging, including skull stripping of T1,T2 and DTI images, tissue segmentation, cortical thickness analysis, atlas building and fiber tracing and tract-based analysis. This is part of a longitudinal study of rhesus macaque monkeys

</div>

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

<h3>Approach, Plan</h3>

* Skull stripping and Tissue segmentation
ABC (developed by Marcel Prastawa, SCI, Utah) is currently used for skull stripping and tissue segmentation of the 3 months, 6 months and 12 months T1 and T2 images.
Challenge include: Application of ABC or neoseg for the same task on 2 weeks old monkey images, due to the different anatomical structures during early ages and small brain size of the monkeys

* Cortical thickness analysis
Will work with Clement Vachet and adapt the tools for human data to primate data

* Affine alignment
RVIEW is currently used for affine alignment of the monkey images. Working on testing the data with the Slicer tools and replace rview tools with them. We need to work with ?? for the special challenge in registration of the monkey brains.

* Atlas building
AtlasWerks is the tool for atlas building with fWarp (developed by Sarang Joshi, SCI, UTAH). We would like to start using open source tools like the deamons registration in Slicer for the same task.

</div>

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

<h3>Progress</h3>
* Attended the DTI breakout session, and identified the problem/challenge of the commonly used tools in the pipeline used by people in the community and the tools we usually use (DicomtoNrrdConvert...)

* Testing BrainsFit for the "affine alignment" task in tissue segmentation, which includes rigid registration of T1 and T2 images, as well as the alignment of subject with template.

* Testing Demons for warping the subjects to atlas, instead of fWarp.

* Meeting with Steve for using the color module for visualization of fiber bundles with scalars with custom min and max and workaround to visualize fibers as tubes with scalar values written in the vtk lookup table.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered as open-source software and open dataset

==References==
*M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. In Proc SPIE Vol 6512, Medical Imaging, 2007, pp. 65122 L1-8.

</div>

2010 Summer Project Week Primate image analysis using the standard Slicer pipeline

2010-06-25T13:35:51Z

Wendyuu:

__NOTOC__
<gallery>
[[Image:Slide1.png|thumb|500px|P values visualized on the fiber tracts as tubes]]
</gallery>

==Key Investigators==
* UNC: Yundi(Wendy) Shi, Clement Vachet, Martin Styner
* Emory: Mar Sanchez
* BWH: Andriy Fedorov

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

<h3>Objective</h3>
To build an open-source software (mainly involving Slicer3) based pipeline for primate imaging, including skull stripping of T1,T2 and DTI images, tissue segmentation, cortical thickness analysis, atlas building and fiber tracing and tract-based analysis. This is part of a longitudinal study of rhesus macaque monkeys

</div>

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

<h3>Approach, Plan</h3>

* Skull stripping and Tissue segmentation
ABC (developed by Marcel Prastawa, SCI, Utah) is currently used for skull stripping and tissue segmentation of the 3 months, 6 months and 12 months T1 and T2 images.
Challenge include: Application of ABC or neoseg for the same task on 2 weeks old monkey images, due to the different anatomical structures during early ages and small brain size of the monkeys

* Cortical thickness analysis
Will work with Clement Vachet and adapt the tools for human data to primate data

* Affine alignment
RVIEW is currently used for affine alignment of the monkey images. Working on testing the data with the Slicer tools and replace rview tools with them. We need to work with ?? for the special challenge in registration of the monkey brains.

* Atlas building
AtlasWerks is the tool for atlas building with fWarp (developed by Sarang Joshi, SCI, UTAH). We would like to start using open source tools like the deamons registration in Slicer for the same task.

</div>

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

<h3>Progress</h3>
* Attended the DTI breakout session, and identified the problem/challenge of the commonly used tools in the pipeline used by people in the community and the tools we usually use (DicomtoNrrdConvert...)

* Testing BrainsFit for the "affine alignment" task in tissue segmentation, which includes rigid registration of T1 and T2 images, as well as the alignment of subject with template.

* Testing Demons for warping the subjects to atlas, instead of fWarp.

* Meeting with Steve for using the color module for visualization of fiber bundles with scalars with custom min and max and workaround to visualize fibers as tubes with scalar values written in the vtk lookup table.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered as open-source software and open dataset

==References==
*M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. In Proc SPIE Vol 6512, Medical Imaging, 2007, pp. 65122 L1-8.

</div>

2010 Summer Project Week Primate image analysis using the standard Slicer pipeline

2010-06-25T13:35:15Z

Wendyuu:

__NOTOC__
<gallery>
Image:Slide1.png|thumb|500px|P values visualized on the fiber tracts as tubes
</gallery>

==Key Investigators==
* UNC: Yundi(Wendy) Shi, Clement Vachet, Martin Styner
* Emory: Mar Sanchez
* BWH: Andriy Fedorov

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

<h3>Objective</h3>
To build an open-source software (mainly involving Slicer3) based pipeline for primate imaging, including skull stripping of T1,T2 and DTI images, tissue segmentation, cortical thickness analysis, atlas building and fiber tracing and tract-based analysis. This is part of a longitudinal study of rhesus macaque monkeys

</div>

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

<h3>Approach, Plan</h3>

* Skull stripping and Tissue segmentation
ABC (developed by Marcel Prastawa, SCI, Utah) is currently used for skull stripping and tissue segmentation of the 3 months, 6 months and 12 months T1 and T2 images.
Challenge include: Application of ABC or neoseg for the same task on 2 weeks old monkey images, due to the different anatomical structures during early ages and small brain size of the monkeys

* Cortical thickness analysis
Will work with Clement Vachet and adapt the tools for human data to primate data

* Affine alignment
RVIEW is currently used for affine alignment of the monkey images. Working on testing the data with the Slicer tools and replace rview tools with them. We need to work with ?? for the special challenge in registration of the monkey brains.

* Atlas building
AtlasWerks is the tool for atlas building with fWarp (developed by Sarang Joshi, SCI, UTAH). We would like to start using open source tools like the deamons registration in Slicer for the same task.

</div>

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

<h3>Progress</h3>
* Attended the DTI breakout session, and identified the problem/challenge of the commonly used tools in the pipeline used by people in the community and the tools we usually use (DicomtoNrrdConvert...)

* Testing BrainsFit for the "affine alignment" task in tissue segmentation, which includes rigid registration of T1 and T2 images, as well as the alignment of subject with template.

* Testing Demons for warping the subjects to atlas, instead of fWarp.

* Meeting with Steve for using the color module for visualization of fiber bundles with scalars with custom min and max and workaround to visualize fibers as tubes with scalar values written in the vtk lookup table.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered as open-source software and open dataset

==References==
*M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. In Proc SPIE Vol 6512, Medical Imaging, 2007, pp. 65122 L1-8.

</div>

2010 Summer Project Week Primate image analysis using the standard Slicer pipeline

2010-06-25T13:33:34Z

Wendyuu:

__NOTOC__
<gallery>
Image:Slide1.png
</gallery>

==Key Investigators==
* UNC: Yundi(Wendy) Shi, Clement Vachet, Martin Styner
* Emory: Mar Sanchez
* BWH: Andriy Fedorov

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

<h3>Objective</h3>
To build an open-source software (mainly involving Slicer3) based pipeline for primate imaging, including skull stripping of T1,T2 and DTI images, tissue segmentation, cortical thickness analysis, atlas building and fiber tracing and tract-based analysis. This is part of a longitudinal study of rhesus macaque monkeys

</div>

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

<h3>Approach, Plan</h3>

* Skull stripping and Tissue segmentation
ABC (developed by Marcel Prastawa, SCI, Utah) is currently used for skull stripping and tissue segmentation of the 3 months, 6 months and 12 months T1 and T2 images.
Challenge include: Application of ABC or neoseg for the same task on 2 weeks old monkey images, due to the different anatomical structures during early ages and small brain size of the monkeys

* Cortical thickness analysis
Will work with Clement Vachet and adapt the tools for human data to primate data

* Affine alignment
RVIEW is currently used for affine alignment of the monkey images. Working on testing the data with the Slicer tools and replace rview tools with them. We need to work with ?? for the special challenge in registration of the monkey brains.

* Atlas building
AtlasWerks is the tool for atlas building with fWarp (developed by Sarang Joshi, SCI, UTAH). We would like to start using open source tools like the deamons registration in Slicer for the same task.

</div>

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

<h3>Progress</h3>
* Attended the DTI breakout session, and identified the problem/challenge of the commonly used tools in the pipeline used by people in the community and the tools we usually use (DicomtoNrrdConvert...)

* Testing BrainsFit for the "affine alignment" task in tissue segmentation, which includes rigid registration of T1 and T2 images, as well as the alignment of subject with template.

* Testing Demons for warping the subjects to atlas, instead of fWarp.

* Meeting with Steve for using the color module for visualization of fiber bundles with scalars with custom min and max and workaround to visualize fibers as tubes with scalar values written in the vtk lookup table.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered as open-source software and open dataset

==References==
*M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. In Proc SPIE Vol 6512, Medical Imaging, 2007, pp. 65122 L1-8.

</div>

File:Slide1.png

2010-06-25T13:32:46Z

Wendyuu:

2010 Summer Project Week Primate image analysis using the standard Slicer pipeline

2010-06-25T13:30:45Z

Wendyuu:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* UNC: Yundi(Wendy) Shi, Clement Vachet, Martin Styner
* Emory: Mar Sanchez
* BWH: Andriy Fedorov

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

<h3>Objective</h3>
To build an open-source software (mainly involving Slicer3) based pipeline for primate imaging, including skull stripping of T1,T2 and DTI images, tissue segmentation, cortical thickness analysis, atlas building and fiber tracing and tract-based analysis. This is part of a longitudinal study of rhesus macaque monkeys

</div>

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

<h3>Approach, Plan</h3>

* Skull stripping and Tissue segmentation
ABC (developed by Marcel Prastawa, SCI, Utah) is currently used for skull stripping and tissue segmentation of the 3 months, 6 months and 12 months T1 and T2 images.
Challenge include: Application of ABC or neoseg for the same task on 2 weeks old monkey images, due to the different anatomical structures during early ages and small brain size of the monkeys

* Cortical thickness analysis
Will work with Clement Vachet and adapt the tools for human data to primate data

* Affine alignment
RVIEW is currently used for affine alignment of the monkey images. Working on testing the data with the Slicer tools and replace rview tools with them. We need to work with ?? for the special challenge in registration of the monkey brains.

* Atlas building
AtlasWerks is the tool for atlas building with fWarp (developed by Sarang Joshi, SCI, UTAH). We would like to start using open source tools like the deamons registration in Slicer for the same task.

</div>

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

<h3>Progress</h3>
* Attended the DTI breakout session, and identified the problem/challenge of the commonly used tools in the pipeline used by people in the community and the tools we usually use (DicomtoNrrdConvert...)

* Testing BrainsFit for the "affine alignment" task in tissue segmentation, which includes rigid registration of T1 and T2 images, as well as the alignment of subject with template.

* Testing Demons for warping the subjects to atlas, instead of fWarp.

* Meeting with Steve for using the color module for visualization of fiber bundles with scalars with custom min and max and workaround to visualize fibers as tubes with scalar values written in the vtk lookup table.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered as open-source software and open dataset

==References==
*M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. In Proc SPIE Vol 6512, Medical Imaging, 2007, pp. 65122 L1-8.

</div>

2010 Summer Project Week Primate image analysis using the standard Slicer pipeline

2010-06-24T18:22:52Z

Wendyuu: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* UNC: Yundi(Wendy) Shi, Clement Vachet, Martin Styner
* Emory: Mar Sanchez
* BWH: Andriy Fedorov

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

<h3>Objective</h3>
To build an open-source software (mainly involving Slicer3) based pipeline for primate imaging, including skull stripping of T1,T2 and DTI images, tissue segmentation, cortical thickness analysis, atlas building and fiber tracing and tract-based analysis. This is part of a longitudinal study of rhesus macaque monkeys

</div>

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

<h3>Approach, Plan</h3>

* Skull stripping and Tissue segmentation
ABC (developed by Marcel Prastawa, SCI, Utah) is currently used for skull stripping and tissue segmentation of the 3 months, 6 months and 12 months T1 and T2 images.
Challenge include: Application of ABC or neoseg for the same task on 2 weeks old monkey images, due to the different anatomical structures during early ages and small brain size of the monkeys

* Cortical thickness analysis
Will work with Clement Vachet and adapt the tools for human data to primate data

* Affine alignment
RVIEW is currently used for affine alignment of the monkey images. Working on testing the data with the Slicer tools and replace rview tools with them. We need to work with ?? for the special challenge in registration of the monkey brains.

* Atlas building
AtlasWerks is the tool for atlas building with fWarp (developed by Sarang Joshi, SCI, UTAH). We would like to start using open source tools like the deamons registration in Slicer for the same task.

</div>

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

<h3>Progress</h3>
* Testing BrainsFit for the "affine alignment" task in tissue segmentation, which includes rigid registration of T1 and T2 images, as well as the alignment of subject with template.

* Testing Demons for warping the subjects to atlas, instead of fWarp.

* Meeting with Steve for using the color module for visualization of fiber bundles with scalars with custom min and max and workaround to visualize fibers as tubes with scalar values written in the vtk lookup table.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered as open-source software and open dataset

==References==
*M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. In Proc SPIE Vol 6512, Medical Imaging, 2007, pp. 65122 L1-8.

</div>

2010 Summer Project Week Primate image analysis using the standard Slicer pipeline

2010-06-24T18:09:18Z

Wendyuu: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* UNC: Yundi(Wendy) Shi, Clement Vachet, Martin Styner
* Emory: Mar Sanchez
* BWH: Andriy Fedorov

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

<h3>Objective</h3>
To build an open-source software (mainly involving Slicer3) based pipeline for primate imaging, including skull stripping of T1,T2 and DTI images, tissue segmentation, cortical thickness analysis, atlas building and fiber tracing and tract-based analysis. This is part of a longitudinal study of rhesus macaque monkeys

</div>

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

<h3>Approach, Plan</h3>

* Skull stripping and Tissue segmentation
ABC (developed by Marcel Prastawa, SCI, Utah) is currently used for skull stripping and tissue segmentation of the 3 months, 6 months and 12 months T1 and T2 images.
Challenge include: Application of ABC or neoseg for the same task on 2 weeks old monkey images, due to the different anatomical structures during early ages and small brain size of the monkeys

* Cortical thickness analysis
Will work with Clement Vachet and adapt the tools for human data to primate data

* Affine alignment
RVIEW is currently used for affine alignment of the monkey images. Working on testing the data with the Slicer tools and replace rview tools with them. We need to work with ?? for the special challenge in registration of the monkey brains.

* Atlas building
AtlasWerks is the tool for atlas building with fWarp (developed by Sarang Joshi, SCI, UTAH). We would like to start using open source tools like the deamons registration in Slicer for the same task.

</div>

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

<h3>Progress</h3>
* Testing BrainsFit for the "affine alignment" task in tissue segmentation, which includes rigid registration of T1 and T2 images, as well as the alignment of subject with template.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered as open-source software and open dataset

==References==
*M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. In Proc SPIE Vol 6512, Medical Imaging, 2007, pp. 65122 L1-8.

</div>

2010 Summer Project Week Primate image analysis using the standard Slicer pipeline

2010-06-22T13:05:21Z

Wendyuu: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* UNC: Yundi(Wendy) Shi, Clement Vachet, Martin Styner
* Emory: Mar Sanchez
* BWH: Andriy Fedorov

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

<h3>Objective</h3>
To build an open-source software (mainly involving Slicer3) based pipeline for primate imaging, including skull stripping of T1,T2 and DTI images, tissue segmentation, cortical thickness analysis, atlas building and fiber tracing and tract-based analysis. This is part of a longitudinal study of rhesus macaque monkeys

</div>

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

<h3>Approach, Plan</h3>

* Skull stripping and Tissue segmentation
ABC (developed by Marcel Prastawa, SCI, Utah) is currently used for skull stripping and tissue segmentation of the 3 months, 6 months and 12 months T1 and T2 images.
Challenge include: Application of ABC or neoseg for the same task on 2 weeks old monkey images, due to the different anatomical structures during early ages and small brain size of the monkeys

* Cortical thickness analysis
Will work with Clement Vachet and adapt the tools for human data to primate data

* Affine alignment
RVIEW is currently used for affine alignment of the monkey images. Working on testing the data with the Slicer tools and replace rview tools with them. We need to work with ?? for the special challenge in registration of the monkey brains.

* Atlas building
AtlasWerks is the tool for atlas building with fWarp (developed by Sarang Joshi, SCI, UTAH). We would like to start using open source tools like the deamons registration in Slicer for the same task.

</div>

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

<h3>Progress</h3>
* Building BRAINS3 tools (including BrainsFit, BrainsDemonsWarp) and test them on the data

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered as open-source software and open dataset

==References==
*M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. In Proc SPIE Vol 6512, Medical Imaging, 2007, pp. 65122 L1-8.

</div>

2010 Summer Project Week Primate image analysis using the standard Slicer pipeline

2010-06-21T17:29:43Z

Wendyuu: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* UNC: Yundi(Wendy) Shi, Clement Vachet, Martin Styner
* Emory: Mar Sanchez
* BWH: Andriy Fedorov

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

<h3>Objective</h3>
To build an open-source software (mainly involving Slicer3) based pipeline for primate imaging, including skull stripping of T1,T2 and DTI images, tissue segmentation, cortical thickness analysis, atlas building and fiber tracing and tract-based analysis. This is part of a longitudinal study of rhesus macaque monkeys

</div>

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

<h3>Approach, Plan</h3>

* Skull stripping and Tissue segmentation
ABC (developed by Marcel Prastawa, SCI, Utah) is currently used for skull stripping and tissue segmentation of the 3 months, 6 months and 12 months T1 and T2 images.
Challenge include: Application of ABC or neoseg for the same task on 2 weeks old monkey images, due to the different anatomical structures during early ages and small brain size of the monkeys

* Cortical thickness analysis
Will work with Clement Vachet and adapt the tools for human data to primate data

* Affine alignment
RVIEW is currently used for affine alignment of the monkey images. Working on testing the data with the Slicer tools and replace rview tools with them. We need to work with ?? for the special challenge in registration of the monkey brains.

* Atlas building
AtlasWerks is the tool for atlas building with fWarp (developed by Sarang Joshi, SCI, UTAH). We would like to start using open source tools like the deamons registration in Slicer for the same task.

</div>

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

<h3>Progress</h3>

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered as open-source software and open dataset

==References==
*M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. In Proc SPIE Vol 6512, Medical Imaging, 2007, pp. 65122 L1-8.

</div>

2010 Summer Project Week Primate image analysis using the standard Slicer pipeline

2010-06-21T00:38:10Z

Wendyuu: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* UNC: Yundi Shi, Clement Vachet, Martin Styner
* Emory: Mar Sanchez
* BWH: Andriy Fedorov

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

<h3>Objective</h3>
To build an open-source software (mainly involving Slicer3) based pipeline for primate imaging, including skull stripping of T1,T2 and DTI images, tissue segmentation, cortical thickness analysis, atlas building and fiber tracing and tract-based analysis. This is part of a longitudinal study of rhesus macaque monkeys

</div>

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

<h3>Approach, Plan</h3>

* Skull stripping and Tissue segmentation
ABC (developed by Marcel Prastawa, SCI, Utah) is currently used for skull stripping and tissue segmentation of the 3 months, 6 months and 12 months T1 and T2 images.
Challenge include: Application of ABC or neoseg for the same task on 2 weeks old monkey images, due to the different anatomical structures during early ages and small brain size of the monkeys

* Cortical thickness analysis
Will work with Clement Vachet and adapt the tools for human data to primate data

* Affine alignment
RVIEW is currently used for affine alignment of the monkey images. Working on testing the data with the Slicer tools and replace rview tools with them. We need to work with ?? for the special challenge in registration of the monkey brains.

* Atlas building
AtlasWerks is the tool for atlas building with fWarp (developed by Sarang Joshi, SCI, UTAH). We would like to start using open source tools like the deamons registration in Slicer for the same task.

</div>

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

<h3>Progress</h3>

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered as open-source software and open dataset

==References==
*M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. In Proc SPIE Vol 6512, Medical Imaging, 2007, pp. 65122 L1-8.

</div>

2010 Summer Project Week Primate image analysis using the standard Slicer pipeline

2010-06-17T15:54:49Z

Wendyuu: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* UNC: Yundi Shi, Clement Vachet, Martin Styner
* Emory: Mar Sanchez

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

<h3>Objective</h3>
To build an open-source software (mainly involving Slicer3) based pipeline for primate imaging, including skull stripping of T1,T2 and DTI images, tissue segmentation, cortical thickness analysis, atlas building and fiber tracing and tract-based analysis. This is part of a longitudinal study of rhesus macaque monkeys

</div>

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

<h3>Approach, Plan</h3>

* Skull stripping and Tissue segmentation
ABC (developed by Marcel Prastawa, SCI, Utah) is currently used for skull stripping and tissue segmentation of the 3 months, 6 months and 12 months T1 and T2 images.
Challenge include: Application of ABC or neoseg for the same task on 2 weeks old monkey images, due to the different anatomical structures during early ages and small brain size of the monkeys

* Cortical thickness analysis
Will work with Clement Vachet and adapt the tools for human data to primate data

* Affine alignment
RVIEW is currently used for affine alignment of the monkey images. Affine registration in Slicer was tested but not producing very satisfying results. We need to work with ?? for the special challenge in registration of the monkey brains.

* Atlas building
Atlaswerks is the tool for atlas building with fWarp (developed by Sarang Joshi, SCI, UTAH). We would like to start using open source tools like the deamons registration in Slicer for the same task.

</div>

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

<h3>Progress</h3>

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered as open-source software and open dataset

==References==
*M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. In Proc SPIE Vol 6512, Medical Imaging, 2007, pp. 65122 L1-8.

</div>

2010 Summer Project Week Primate image analysis using the standard Slicer pipeline

2010-06-16T20:57:58Z

Wendyuu: /* Delivery Mechanism */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* UNC: Yundi Shi, Martin Styner
* Emory: Mar Sanchez

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

<h3>Objective</h3>
To build an open-source software (mainly involving Slicer3) based pipeline for primate imaging, including skull stripping of T1,T2 and DTI images, tissue segmentation, cortical thickness analysis, atlas building and fiber tracing and tract-based analysis. This is part of a longitudinal study of rhesus macaque monkeys

</div>

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

<h3>Approach, Plan</h3>

* Skull stripping and Tissue segmentation
ABC (developed by Marcel Prastawa, SCI, Utah) is currently used for skull stripping and tissue segmentation of the 3 months, 6 months and 12 months T1 and T2 images.
Challenge include: Application of ABC or neoseg for the same task on 2 weeks old monkey images, due to the different anatomical structures during early ages and small brain size of the monkeys

* Affine alignment
RVIEW is currently used for affine alignment of the monkey images. Affine registration in Slicer was tested but not producing very satisfying results. We need to work with ?? for the special challenge in registration of the monkey brains.

* Atlas building
Atlaswerks is the tool for atlas building with fWarp (developed by Sarang Joshi, SCI, UTAH). We would like to start using open source tools like the deamons registration in Slicer for the same task.

</div>

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

<h3>Progress</h3>

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered as open-source software and open dataset

==References==
*M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. In Proc SPIE Vol 6512, Medical Imaging, 2007, pp. 65122 L1-8.

</div>

2010 Summer Project Week Primate image analysis using the standard Slicer pipeline

2010-06-16T20:57:25Z

Wendyuu: /* References */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* UNC: Yundi Shi, Martin Styner
* Emory: Mar Sanchez

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

<h3>Objective</h3>
To build an open-source software (mainly involving Slicer3) based pipeline for primate imaging, including skull stripping of T1,T2 and DTI images, tissue segmentation, cortical thickness analysis, atlas building and fiber tracing and tract-based analysis. This is part of a longitudinal study of rhesus macaque monkeys

</div>

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

<h3>Approach, Plan</h3>

* Skull stripping and Tissue segmentation
ABC (developed by Marcel Prastawa, SCI, Utah) is currently used for skull stripping and tissue segmentation of the 3 months, 6 months and 12 months T1 and T2 images.
Challenge include: Application of ABC or neoseg for the same task on 2 weeks old monkey images, due to the different anatomical structures during early ages and small brain size of the monkeys

* Affine alignment
RVIEW is currently used for affine alignment of the monkey images. Affine registration in Slicer was tested but not producing very satisfying results. We need to work with ?? for the special challenge in registration of the monkey brains.

* Atlas building
Atlaswerks is the tool for atlas building with fWarp (developed by Sarang Joshi, SCI, UTAH). We would like to start using open source tools like the deamons registration in Slicer for the same task.

</div>

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

<h3>Progress</h3>

</div>
</div>

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

==Delivery Mechanism==

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

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable '''YES'''
#Other (Please specify)

==References==
*M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. In Proc SPIE Vol 6512, Medical Imaging, 2007, pp. 65122 L1-8.

</div>

2010 Summer Project Week Primate image analysis using the standard Slicer pipeline

2010-06-16T20:56:29Z

Wendyuu: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* UNC: Yundi Shi, Martin Styner
* Emory: Mar Sanchez

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

<h3>Objective</h3>
To build an open-source software (mainly involving Slicer3) based pipeline for primate imaging, including skull stripping of T1,T2 and DTI images, tissue segmentation, cortical thickness analysis, atlas building and fiber tracing and tract-based analysis. This is part of a longitudinal study of rhesus macaque monkeys

</div>

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

<h3>Approach, Plan</h3>

* Skull stripping and Tissue segmentation
ABC (developed by Marcel Prastawa, SCI, Utah) is currently used for skull stripping and tissue segmentation of the 3 months, 6 months and 12 months T1 and T2 images.
Challenge include: Application of ABC or neoseg for the same task on 2 weeks old monkey images, due to the different anatomical structures during early ages and small brain size of the monkeys

* Affine alignment
RVIEW is currently used for affine alignment of the monkey images. Affine registration in Slicer was tested but not producing very satisfying results. We need to work with ?? for the special challenge in registration of the monkey brains.

* Atlas building
Atlaswerks is the tool for atlas building with fWarp (developed by Sarang Joshi, SCI, UTAH). We would like to start using open source tools like the deamons registration in Slicer for the same task.

</div>

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

<h3>Progress</h3>

</div>
</div>

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

==Delivery Mechanism==

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

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable '''YES'''
#Other (Please specify)

==References==
*Grosland Nicole M; Shivanna Kiran H; Magnotta Vincent A; Kallemeyn Nicole A; DeVries Nicole A; Tadepalli Srinivas C; Lisle Curtis R; IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development. Computer methods and programs in biomedicine 2009;94(1):96-107.
*Shivanna KH, Grosland NM, Russell ME, Pedersen DR, Diarthrodial Joint Contact Models: A finite element analysis of the human hip, Engineering with Computers (accepted).

</div>

2010 Summer Project Week Primate image analysis using the standard Slicer pipeline

2010-06-16T20:55:29Z

Wendyuu: Created page with '__NOTOC__ <gallery> Image:PW-MIT2010.png|Projects List </gallery> ==Key Investigators== * University of Iowa: Nicole Grosland, Vince Magno…'

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* University of Iowa: Nicole Grosland, Vince Magnotta, Kiran Shivanna
* Isomics: Steve Pieper, Curtis Lisle

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

<h3>Objective</h3>
We are integrating finite element mesh creation tools developed at the University of Iowa into 3D Slicer. The result will be that 3D Slicer models can be further processed into meshes for analysis using external finite element programs, such as ABAQUS.

Standalone mesh creation tools exist in the standalone application IA-FEMesh found [http://www.ccad.uiowa.edu/mimx/IA-FEMesh by clicking here.]

</div>

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

<h3>Approach, Plan</h3>

The first integration of the IA-FEMesh module was released at the NA-MIC All Hands Meeting in January 2009. The module's first release functions in 3D Slicer for creating meshes interactively, but didn't support import or save with MRML scenes. Since this time, we have developed a direct import of MRML Models and Volumes into the IA-FEMesh workflow and improved integration with Slicer internals.

During the project week, we plan to resolve image orientation issues in the algorithm which extracts mesh material properties automatically from the source volume. The volume IJK2RAS matrix will be used to orient the image in the material properties algorithm. We also expect to improve MRML integration and code cleanliness during the week.

</div>

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

<h3>Progress</h3>
IA-FEMesh now creates and registers four specialized MRML node classes. We completed MRML volume import to IA-FEMesh and are storing the IJ2RAS matrix. We are ready to adapt the material properties algorithm to work with the imported Slicer3 volume.

An updated [http://wiki.na-mic.org/Wiki/index.php/Slicer3:IAFEMesh_TutorialContestSummer2010 tutorial for the module] including screencasts of module operations was recently completed. The tutorial complements the existing module [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide] to provide multiple documentation methods for using IA-FEMesh to new problems in finite element mesh development.

</div>
</div>

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

==Delivery Mechanism==

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

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable '''YES'''
#Other (Please specify)

==References==
*Grosland Nicole M; Shivanna Kiran H; Magnotta Vincent A; Kallemeyn Nicole A; DeVries Nicole A; Tadepalli Srinivas C; Lisle Curtis R; IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development. Computer methods and programs in biomedicine 2009;94(1):96-107.
*Shivanna KH, Grosland NM, Russell ME, Pedersen DR, Diarthrodial Joint Contact Models: A finite element analysis of the human hip, Engineering with Computers (accepted).

</div>

2010 Summer Project Week

2010-06-16T20:51:17Z

Wendyuu: /* Analysis */

__NOTOC__

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

[[Image:PW-MIT2010.png|300px]]

==Background==

We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

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

== Logistics ==
*'''Dates:''' June 21-25, 2010
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here] to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&app=resvlink&fromDate=6/20/10&toDate=6/25/10 Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process.

''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''
''' $189/night/room (plus tax).'''
''' This rate is good only through June 1.'''

Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290.

*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

==Agenda==

{|border="1"
|-style="background: #b0d5e6; color: #02186f; font-size: 130%"
!Time
!width="200px"|Monday, June 21
!width="200px"|Tuesday, June 22
!width="200px"|Wednesday, June 23
!width="200px"|Thursday, June 24
!width="200px"|Friday, June 25
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|8:30
|rowspan="5"|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|9:00-9:45
|NA-MIC Kit Update (Jim Miller)
|rowspan="4"|'''Breakout Session:''' [[2010 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
|rowspan="4"|'''Breakout Session:''' [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
|rowspan="4"|[[#Projects|Project Progress Updates]]
|-
|9:45-10:30
|bgcolor="#c1c2ec"|3D Slicer Update (Steve Pieper)
|-
|10:30-11:00
|OpenIGTLink Update (Junichi Tokuda)
|-
|11:00-12:00
|bgcolor="#c1c2ec"|Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
|-
|12:00-1:00
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes
|-
|12:45-1:00
|
|
|bgcolor="#ccffcc"|[[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
|
|
|-
|1:00-1:30
|rowspan="5"|<font color="#0000cc">Ron Kikinis: Welcome<br> </font> (5 minutes)<br>_____________________<br> [[#Projects|Project Introductions]] (all Project Leads)
|rowspan="4"|'''Breakout Session:''' QT/Slicer (Steve, JC, J2)
|rowspan="4"|'''Breakout Session:''' [[Microscopy_Image_Analysis|Microscopy Image Analysis]] (Sean Megason)
|rowspan="2"|'''Breakout Session:''' [[2010 Summer Project Week Breakout Session:GWE|GWE]] (Marco Ruiz)
|bgcolor="#f0e68b"|Adjourn by 1:30pm
|-
|1:30-2:00
|rowspan="9"|
|-
|2:00-2:30
|bgcolor="#ccffcc"|Build Instructions: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)
|-
|2:30-3:00
|rowspan="6"|
|-
|3:00-3:30
|rowspan="2" style="background: #ccffcc;"|[[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
|rowspan="5"|'''Breakout Session:''' [[2010 Summer Project Week Breakout Session:QA Training|QA Training]] (Luis Ibanez)<br>_____________________<br>'''Breakout Session:''' [[2010 Summer Project Week Breakout Session:VTK Widget|VTK Widget]] (Nicole, Kilian, JC)
|-
|3:30-4:00
|rowspan="4" style="background: #ccffcc;"|Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt|Getting Started with Qt]] (Adam Weinrich, Nokia)
|-
|4:00-4:30
|rowspan="3"|'''Breakout Session:''' [[2010 Summer Project Week Breakout Session: Data Management|Data Management]] (Dan Marcus, Stephen Aylward)
|-
|4:30-5:00
|-
|5:00-5:30
|-
|5:30
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|}

Note:
***We need to empty room by 1:30pm on Friday. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2011|in Utah]]

==Projects==

=== Segmentation ===
#[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
#[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
#[[2010_Summer_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Karol Chudy, Allen Tannenbaum, GT; Ron Kikinis, BWH)
#[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)
#[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)
#[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping integration with Slicer]] (Nicole Aucoin, Min Chen)
#[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)
#[[2010_Summer_Project_Week_Left ventricular scar segmentation| LV scar segmentation display and fusion]] (Dana C. Peters, Felix Liu, BIDMC, Boston)
#[[2010_Summer_Project_Week_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans ]](Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)

=== Registration ===
#[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
#[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Nadya Shusharina, Greg Sharp)
#[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)
#[[2010_Summer_Project_Week_Best_Regularization_Term_for_Demons_Registration_Algorithm|Best Regularization Term for Demons Registration Algorithm]] (Rui Li, Greg Sharp)
#[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)
#[[2010_Summer_Project_Week_MR_to_Ultrasound_Registration_Methodology|MR to Ultrasound Registration Methodology]] (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward)
#[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Sylvain Bouix, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)

=== IGT ===
#[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Dose_Calculation|MR to CT Registration for Prostate Brachytherapy Dose Calculation]] (Andriy Fedorov, Dominik Meier, Hans Johnson)
#[[2010_Summer_Project_Week_Intraoperative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound|Intraoprative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound]] (Jason White, Steve Pieper, Junichi Tokuda?, Pratik Patel?)
#Prostate Intervention(Junichi, Sam Song, Tamas Ungi)
# Liver Ablation (Haiying Liu)
# [[2010_Summer_Project_Week_BrainLab_Aurora_Hybrid_Navigation|BrainLab-Aurora Hybrid Navigation]] (Isaiah Norton, Dan Marcus, Noby Hata)
#[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)
# [[2010_Summer_Project_Week_PerkStationModule|PerkStation Module]] (Tamas Ungi, Xiaodong Tao)
#[[2010_Summer_Project_Week_Co-registration_of_PET_and_DWI_Images_for_the_targeting_of_Glioma_Biopsies|Co-registration of PET and DWI Images for the targeting of Glioma Biopsies]] (Gareth Smith, Dominik Meir, Vince Magnotta)
#[[2010_Summer_Project_Week_Implementing_Open_IGT_Link_to_Virtual_Place_for_research_support|Implementing Open IGT Link to Virtual Place for research support]] (Nicholas Herlambang, Noby Hata)

=== Radiotherapy ===
#[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp, Tamas Ungi)
#[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)
#[[2010_Summer_Project_Week_Seg_Adapt_HNT|Segmentation for Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Greg Sharp, and Allen Tannenbaum )

=== Analysis ===
#[[2010_Summer_Project_Week_FractureClassification_Brainstorming|Femoral Fracture Classification Brainstorming Session]] (Karl Fritscher, Vince Magnota, Peter Karasev, Curt Lisle, Ron Kikinis)
#[[2010_Summer_Project_Week_Cortical_Thickness_Analysis|Cortical thickness analysis]] (Clement Vachet, Heather Cody Hazlett, Martin Styner)
#[[2010_Summer_Project_Week_Primate image analysis using the standard Slicer pipeline|Primate image analysis using the standard Slicer pipeline]] (Yundi Shi, Martin Styner)
#[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
#[[2010_Summer_Project_Week_Computer_Aided_Photodynamic_Therapy| Computer_Aided_Photodynamic_Therapy]] (E Pietka, D Spinczyk, P Szabelak)
#[[2010_NAMIC_Project_week:IA-FEMesh| IA-FEMesh Slicer3 Finite Meshing Module]] (N Grosland, V Magnotta, C Lisle, S Pieper)

===[[Microscopy Image Analysis]] ===
# [[ 2010 Project Week DICOM supplement 145 | DICOM supplement 145 ]] : Microscopy Image in the Dicom Standard (Mathieu Malaterre, Alex. Gouaillard)
# [[ 2010 Summer Project Week Microscopy extensions for ITK | Microscopy Extensions for ITK ]]: convolution, deconvolution, wavelets and more ( Gaetan Lemhann, Alex. Gouaillard )
# [[ 2010 Summer Project Week Flow Cytometry | Flow Cytometry ]] (Bertrand Moreau, Rossella Melchiotti, Alex. Gouaillard)
# [[Import/Export Farsight-GoFigure results]] (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)
# [[Farsight nuclear segmentation as GoFigure plugin]] (Arnaud Gelas, Sean Megason, Badri Roysam)
# [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju)
# [[ITK Analysis of Large Histology Datasets]] (Liya Ding, Kun Huang, Sean Megason, Raghu Machiraju)
# [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Stever Pieper)
# [[Seedings results comparison]] (Antonin Perrot-Audet, Kishore Mosaliganti, Badri Roysam, Sean Megason)
# [[ITK GPAC level set|ITK Multiphase and GPAC level sets]] (K. Palaniappan, Ilker Ersoy, Filiz Bunyak, Kishore Mosaliganti, Sean Megason)
# [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)
# [[MedianTexture|Median binary pattern texture measures for cell nuclei segmentation]] (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)
# [[StandardsInterfaces|Standards and Interfaces for Microscopy Image Analysis in ITK]] (whoever has an opinion, Sean Megason)

=== Shape Analysis ===
#[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)
# [[2010_Summer_Project_Week_Shape_Analysis_UNC|Shape Analysis projects, integration with Slicer3]] (Beatriz Paniagua, Martin Styner)
# [[Particle Based Shape Regression]] (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)
#[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)
#[[2010_Summer_Project_Week_Shape_Test_Bench|Shape Test Bench]] (Marc Niethammer, Sylvain Bouix)

=== Diffusion ===
#[[2010_Summer_Project_Week_Diffusion|Fluid Mechanics Based Tractography ]](Nathan Hageman)
#[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)
#[[2010_Summer_Project_Two_Tensor|Implementing Two-tensor tractography in Slicer (Python) ]](Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)
#[[Application of the DTI pipeline to the teenage substance abuse study]] (Gopalkrishna Veni, Sarang Joshi, Ross Whitaker)
#[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
#[[2010_Summer_Project_QSpace_Reconstruction_for_Diffusion_Spectrum_Imaging_Data|QSpace Imaging Reconstruction for Diffusion Spectrum Imaging Data]] (Sudhir Pathak)

=== NA-MIC Kit Internals ===
#[[2010 NAMIC Project week: Module Inventory|Module Inventory]] (Steve, Jim)
#[[2010 NAMIC Project week: Viewer Manager Factory|Viewer Manager Factory]] (Alex Yarmarkovich, Kilian, Steve, Nicole)
#[[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andrey Fedorov, Yanling Liu, Alex Yarmarkovich)
#[[2010_NAMIC_Project_week:Slicer4Icons|Consistent visual language for Slicer4: icon rework marathon]] (Wendy Plesniak)
#[[2010_NAMIC_Project_week:LongitudinalPETSUV_Wizard | Slicer Wizard for PET/CT workflow]] (Wendy Plesniak, Ron Kikinis)
#[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)
#[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)
#[[2010_Summer_Project_Week_Superbuild |Superbuild ]](David Partyka, Steve Pieper, Katie Hayes)
#[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on June 10, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Attendee List==

<big>'''NOTE:'''</big> <font color="maroon">THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD '''NOT''' EDIT THIS, BUT [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 REGISTER BY CLICKING HERE.]</font>

# Anderson Peter , GE Navigation (Retired)
# Aucoin Nicole , BWH
# Audette Michel , Kitware
# Aylward Stephen , Kitware, Inc
# Boucharin Alexis , UNC Neuro Image Research and Analysis Laboratories
# Bouix Sylvain , BWH
# Bowers Michael , Johns Hopkins University
# Budin Francois , UNC
# Burdette Everette , Acoustic MedSystems, Inc.
# CHAUVIN Laurent , Brigham and Women's Hospital
# Chen Min , Johns Hopkins University
# Crane Jason , UCSF
# Datar Manasi , SCI Institute
# Ding Liya , The Ohio State University
# Eckbo Ryan , BWH
# Ersoy Ilker , University of Missouri Columbia
# Fedorov Andriy , Surgical Planning Lab
# Fillion-Robin Jean-Christophe , Kitware Inc.
# Finet Julien , Kitware Inc
# Fishbaugh James , SCI Institute
# Fritscher Karl , UMIT
# Gao Yi , Gerogia Tech
# GELAS Arnaud , Harvard Medical School
# Gorgolewski Chris , SPL
# gouaillard alexandre , CoSMo Software
# Gouttard Sylvain , SCI Institute
# Grama Kedar , Rensselaer Polytechnic Institute
# Haehn Daniel , University of Pennsylvania
# Hafiane Adel , ENSI-Bourges
# Hageman Nathan , UCLA
# Hahn Dieter , University Erlangen
# Halle Michael , BWH/SPL
# Hamel Corentin , UNC Chapel Hill
# Hata Nobuhiko , Brigham and Women's Hospital
# Hayes Kathryn , Brigham and Women's Hospital
# Herlambang Nicholas , AZE, Ltd.
# Holton Leslie , Medtronic Navigation
# Ibanez Luis , KITWARE Inc.
# Jagadeesan Jayender , SPL
# Johnson Hans , University of Iowa
# Kapur Tina , Brigham and Women's Hospital
# Kikinis Ron , Brigham and Women's Hospital
# Kim Minjeong , UNC-Chapel Hill
# Kolesov Ivan , Georgia Institute of Technology
# Larson Garrett , UNC-CH
# Lee Joohwi , UNC Chapel Hill
# Li Rui , MGH
# Lienhard Stefan , LMI
# Lisle Curtis , KnowledgeVis, LLC
# Liu Felix , Beth Israel Deaconess Medical Center
# Liu Yanling , SAIC-Frederick, Inc.
# Liu Haiying , Brigham and Women's Hospital
# Lowekamp Bradley , Lockheed Martin
# machiraju raghu , The Ohio State University
# Magnotta Vincent , The University of Iowa
# malaterre mathieu , CoSMo Software
# Marcus Daniel , Washington University
# Marks William , Focused Ultrasound Lab, BWH, HMS
# Mastrogiacomo Katie , Brigham and Women's Hospital
# Matsui Joy , University of Iowa
# Megason Sean , Harvard Medical School
# Meier Dominik , BWH, Boston MA
# menze bjoern , CSAIL MIT
# menze bjoern , CSAIL MIT
# Milchenko Mikhail , WUSTL
# Miller James , GE Research
# Mosaliganti Kishore , Harvard Medical School
# Niethammer Marc , UNC Chapel Hill
# Norton Isaiah , BWH Neurosurgery
# Olson Beck , UCSF
# Onofrey John , Yale University
# Padmanabhan Raghav , RPI
# Palaniappan Kannappan , university of Missouri
# Paniagua Beatriz , University of North Caolina at Chapel Hill
# Papademetris Xenophon , Yale University
# Partyka David , Kitware Inc
# Patel Pratik , Brainlab Inc
# Pathak Sudhir , Univeristy Of Pittsburgh
# PECOT Thierry , Ohio State University
# Peroni Marta , Politecnico di Milano, MIT, MGH
# Perrot-Audet Antonin , Harvard Medical School
# Pieper Steve , Isomics, Inc.
# Plesniak Wendy , BWH
# Pohl Kilian , IBM
# Pujol Sonia , Brigham and Women's Hospital
# Rannou Nicolas , Harvard Medical School
# Riklin Raviv Tammy , MIT, CSAIL
# Ruiz Marco , UCSD
# Schroeder William , Kitware
# Scully Mark , The Mind Research Network
# Sharp Greg , MGH
# Shi Yundi , UNC Chapel Hill
# Shusharina Nadya , MGH
# Singh Shantanu , The Ohio State University
# Smith Gareth , Wolfson Medical Imaging Centre (WMIC)
# Souhait Lydie , Harvard Medical School
# Spinczyk Dominik , Silesian University of Technology
# Srinivasan Padmapriya , BWH
# Tao Xiaodong , GE Research
# Tokuda Junichi , Brigham and Women's Hospital
# Ungi Tamas , Queen's University
# Vachet Clement , UNC Chapel Hill
# Veni Gopalkrishna , SCI Institute
# Wassermann Demian , SPL/LMI/PNL
# Weinrich Adam , Nokia
# Wells Sandy , BWH
# White Phillip , BWH/HMS
# Wu Guorong , University of North Carolina at Chapel Hill
# Yamada Atsushi , Nagoya Institute of Technology
# Yarmarkovich Alexander , ISOMICS
# Zaitsev Alexander , Brigham and Womens Hospital

2010 Summer Project Week Cortical Thickness Analysis

2010-06-16T20:50:23Z

Wendyuu: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:Arctic_Logo.png‎|[http://www.nitrc.org/projects/arctic ARCTIC: Automatic Regional Cortical ThICkness]
Image:BrainDevelopment.jpg|[http://www.nitrc.org/projects/gambit GAMBIT: Group-wise Automatic Mesh-Based analysis of cortIcal Thickness ]
Image:MeshBasedCortThick_CorticalThickness.jpg|Cortical thickness on white matter surface
Image:MeshBasedCortThick_SulcalDepth.jpg‎|Sucal depth on genus-zero cortical surface
Image:MeshBasedCortThick_Particles.jpg‎|Particles on inflated genus-zero cortical surface
</gallery>

==Key Investigators==
* UNC: Yundi Shi, Martin Styner
* Emory: Mar Sanchez

<h3>Objective</h3>

To build an open-source software (mainly involving Slicer3) based pipeline for primate imaging, including skull stripping of T1,T2 and DTI images, tissue segmentation, cortical thickness analysis, atlas building and fiber tracing and tract-based analysis. This is part of a longitudinal study of rhesus macaque monkeys

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<h3>Approach, Plan</h3>
** Skull stripping and Tissue segmentation
ABC (developed by Marcel Prastawa, SCI, Utah) is currently used for skull stripping and tissue segmentation of the 3 months, 6 months and 12 months T1 and T2 images.
Challenge include: Application of ABC or neoseg for the same task on 2 weeks old monkey images, due to the different anatomical structures during early ages and small brain size of the monkeys

** Affine alignment
RVIEW is currently used for affine alignment of the monkey images. Affine registration in Slicer was tested but not producing very satisfying results. We need to work with ?? for the special challenge in registration of the monkey brains.

** Atlas building
Atlaswerks is the tool for atlas building with fWarp (developed by Sarang Joshi, SCI, UTAH). We would like to start using open source tools like the deamons registration in Slicer for the same task.

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<h3>Progress</h3>

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==Delivery Mechanism==

This work will be delivered as an open-source software with open dataset.

==References==
** M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. In Proc SPIE Vol 6512, Medical Imaging, 2007, pp. 65122 L1-8..

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