'''Link to [[ProjectWeek200706:ContrastingTractographyMeasures|DTI Validation Project Management Page]]'''

== Tractography Validation Beadeker ==

**9:00am: Guido Gerig, Overview of Project goals and progress to date including Santa Fe meeting [http://www.na-mic.org/Wiki/index.php/Projects/Diffusion/Contrasting_Tractography_Measures | Link to tractography algorithms]
**9:15am: Randy Gollub, Morphometry BIRN DTI acquisition and analysis update [[Media:NA-MIC.2008.AHM.mBIRN.ppt |Morphometry BIRN DTI calibration]]
**9:25am: Randy Gollub, MIND Reliability dataset goals [[Media:NA-MIC.2008.AHM.MINDintro.ppt‎ |Impact of using MIND data for this project]]

== Algorithm specific presentations ==

**9:35 Sonia Pujol (BWH) Streamline Tractography in Slicer 2.7 using ROI and Whole Brain Seeding
**9:45 Sylvain Gouttard (Utah) FiberViewer
**9:55 Casey Goodlett (Utah) DTI Atlas
**10:05 John Melonakos (Georgia Tech) Geodesic Tractography Segmentation ([[media:AHM2008TractographyConferenceGeorgiaTech.ppt|slides]])
**10:15 Tri Ngo (MIT/BWH) Stochastic Tractography ([[media:STpresentationpack.zip|slides]])
**10:25 Vince Magnotta (UIowa) GTract
'''10:35am: Coffee break'''
**11:00 Tom Fletcher (Utah) Volumetric Connectivity ([[media:VolumetricPathwayResults_NAMIC_AHM2008.ppt|slides]])
**11:10 Sonia Pujol (BWH) Cross algorithm summary statistics

== Discussion, future planning ==

**11:25 CF Westin to kick-off discussion of Tractography results with summarizing ideas. [[2008_Winter_Project_Week_Tractography_Meeting_Notes|Meeting Notes]]
'''12:00pm: Lunch'''
**1:00- 1:20pm Presentation of current status of Slicer 3 DTI infrastructure (Alex Yarmarkovich)[http://www.na-mic.org/Wiki/index.php/Slicer3:DTMRI Slicer3 DTI status]
**1:20-1:30pm Dan Marcus to gather requirements to post this dataset for consideration of whether this is an XNATophilic project
**1:30- 3:00pm Continue discussion of Tractography results with focus on:
***Data formats and coordinate system requirements/guidelines/recommendations
***Quality control methods and implementation
***ROIs: what works, what doesn't, what to do?
***Registration &/or resampling to support visit 1- visit 2 analysis and group analysis
***Freesurfer to B0 transform for white matter mask
***Quantification of registration error and its propagation forward and impact on final results
***Plans for data sharing curation and timeline (integration with XNAT project, should we make plans for a NAMIC sponsored MICCAI event: Tractography Grand Challenge e.g. the one done last year for segmentation? See http://mbi.dkfz-heidelberg.de/grand-challenge2007/)
***Outcome metrics and how to best frame scientific questions for this project, steps towards manuscript preparation, milestones for spring 2008 and for Programming Week in June
'''3pm: coffee break'''
*3-4PM Batchmake break-out session
**4:00pm Guido to lead discussion of "NAMIC software infrastructure for DWI analysis" to clarify what the community expects from a powerful NAMIC DWI Analysis toolkit and identify areas of high priority development, keeping in mind the work already done by Alex (see 1 PM talk).
***Identify and agree upon essential processing steps (pipeline) necessary for clinical DTI studies
***Identify Core-1 modules and methods that are a) recently integrated, b) ready to be integrated, c) in development
***Integrate with other on-going efforts

== Meeting Notes ==
Notes of Tractography Meeting Jan 9, 2008: [[2008_Winter_Project_Week_Tractography_Meeting_Notes| Meeting Notes]]

Back to [[AHM_2008]], [[Events]]

File:STpresentationpack.zip

2008-02-11T15:06:36Z

Tringo: Stochastic Tractography presentation at AHM2008 in salt lake. File size is large due to moves.

Stochastic Tractography presentation at AHM2008 in salt lake. File size is large due to moves.

Projects:DTIStochasticTractography

2007-04-24T17:52:29Z

Tringo:

= Project Description: Stochastic Tractography =

Collaborators: Tri Ngo (MIT), Marek Kubicki (BWH), Carl-Fredrik Westin (BWH) & Polina Golland (MIT)

Stochastic Tractography is a Bayesian approach to estimating nerve fiber tracts from DWMRI (Diffusion Weighted Magnetic Imaging) images. The Bayesian framework provides a measure of confidence regarding the estimated tracts. This measure of confidence allows the algorithm to generate tracts which pass through regions with uncertain fiber directions, revealing more details about structural connectivity than non-Bayesian tractography algorithms. We will further develop the theory and application of stochastic tractography by applying it in a clinical study of nerve fiber tract abnormalities in schizophrenia.

Magnetic Resonance Imaging (MRI) is a valuable imaging modality for studying the brain in-vivo. We can use use MRI to differentiate between tissue types, which is valuable for anatomical studies. However, anatomical MRI provides a homogeneous image of white matter making it difficult to characterize white matter fiber tracts which pass through this region. Diffusion Weighted Magnetic Resonance Imaging (DWMRI) provides information about the diffusion of water molecules in the brain. DWMRI images can be used to construct a DTI data set which provides a complete description of water diffusion.

Researchers have hypothesized that white matter abnormalities may underlie some neurological conditions. For instance, the neurological disease schizophrenia by is characterized by its behavioral symptoms, which include auditory hallucinations, disordered thinking and delusion[6]. Studies have suggested that these behavioral symptoms have some connection with the neuroanatomical abnormalities observed in schizophrenia patients. Using DTI, Researchers can noninvasively investigate the relationship between brain white matter abnormalities and schizophrenia by using DTI.

We can visualize DTI data sets using a number of methods. DTI provides information about the diffusion of water at each voxel, or volume element in the form of diffusion tensors. A popular technique to visualize these diffusion tensors is to draw fiber tracts which utilize the diffusion information across many voxels. This technique is known as DTI Tractography.

One possible method to perform tractography is to draw tracts which are oriented along the direction of maximal water diffusion of the voxels they pass through[1]. However, this method does not provide information about the uncertainty of the generated tracks due to noise or insufficient spatial resolution. Probabilistic white matter tractography addresses this problem by performing tractography under a probabilistic framework and provides a metric for assessing the uncertainty of generated fiber tracts. Several mathematical formulations of probabilistic tractography have existed for some time with the earliest being Behren's [3].

Ultimately the success of the algorithm will depend on its use in the research community. To this end, we have created a complete user interface to support the algorithm. This interface will be integrated into the popular 3D Slicer medical image visualization program. Additionally, the algorithm will be implemented within the ITK medical image analysis toolkit. ITK provides a standardized programming interface for a large collection of medical image processing algorithms which enable application developers to quickly incorporate the algorithms into new applications.

Finally, we will apply this system towards the analysis of clinical schizophrenia DWMRI data. Originally, the data was investigated using only on a local voxel-wise basis. Our probabilistic tractography system will integrate information across multiple voxels and provide a more holistic view of fiber tract abnormalities. This clinical application will help us uncover properties of stochastic tractography which will suggest further developments in the algorithm.

<br clear="all" />
[[Image:Slicer3CML.png|thumb|left|400px|Slicer 3 interface]]
<br clear="all" />
[[Image:ConnectivityMap.png|thumb|left|400px|Connectivity Probability Map of fibers originativing from the right internal capsule and progressing towards the frontal cortex.]]
[[Image:FAdistribution.png|thumb|left|400px|Distribution of Tract-Average FA values]]
[[Image:TractLengthDistribution.png|thumb|left|400px|Distribution of Tract Lengths]]
<br clear="all" />

= Publications =
[1] Ola Friman, Gunnar Farneback, and Carl-Fredrik Westin. A Bayesian approach for stochastic white matter tractography. TMI, 2006. In Press.

[2]Raymond Salvador, Alonso Pena, David K. Menon, T. Adrian, T. Adrian Carpenter, John D. Pickard, and Ed T. Bullmore. Formal characterization and extension of the linearized diffusion tensor model. Human Brain Mapping , 24:144-155, 2005.

[3]T.E.J Behrens, M.W. Woolrich, M. Jenkinson, H. Johansen-Berg, R. G. Nunes, S. Clare, P.M. Matthews, J.M Brady, and S.M. Smith. Characterization and propagation of uncertainty in diffusion-weighted mr imaging. Magnetic Resonance in Medicine, 50:1077-1088, 2003.

[4]Brigham and Women's Hospital. 3d slicer medical visualization and processing environment for research. http://www.slicer.org/.

[5]Insight Software Consortium. National library of medicine insight segmentation and registration toolkit(itk). http://www.itk.org/.

[6]M. Kubicki, C.-F. Westin, R. McCarley, and M. E. Shenton. The application of dti to investigate white matter abnormalities in schizophrenia. Ann NY Acad Sci, 1064:134-148, 2005.

= Software =

The software employed in this process includes:

* New multithreaded ITK Filter (itkStochasticTractographyFilter)

Algorithm:MIT

2007-04-24T17:33:50Z

Tringo: /* DTI Analysis and Visualization */

= Shape- and Atlas-Based Segmentation =

The goal of this project is to augment the segmentation process with prior information on the shape of the anatomical structures (shape atlas) learned from previously segmented scans (using, for example, Principal Component Analysis). We are working on methods that integrate the shape atlases with segmentation algorithms.

=== Tissue Classification ===

This type of algorithms assigns a tissue type to each voxel in the volume. Incorporating prior shape information biases the label assignment towards contiguous regions that are consistent with the shape model. [[Algorithm:MIT:Shape_Based_Segmentation_And_Registration|More...]]

<font color="red">'''New: '''</font> K.M. Pohl, J. Fisher, S. Bouix, M. Shenton, R. W. McCarley, W.E.L. Grimson, R. Kikinis, and W.M. Wells. Using the Logarithm of Odds to Define a Vector Space on Probabilistic Atlases. Accapted to the Special Issue of Best Selected Papers from MICCAI 06 in Medical Image Analysis [[Algorithm:MIT:Shape_Based_Segmentation_And_Registration#Publications|More...]]

<font color="red">'''New: '''</font> K.M. Pohl, R. Kikinis, and W.M. Wells. Active Mean Fields: Solving the Mean Field Approximation in the Level Set Framework. Accapted to IPMI 2007. [[Algorithm:MIT:Shape_Based_Segmentation_And_Registration#Publications|More...]]

[[Algorithm:MIT:Shape_Based_Segmentation_And_Registration|'''Description''']] - [[Algorithm:MIT:Shape_Based_Segmentation_And_Registration#Publications|'''Publications''']] - [[Algorithm:MIT:Shape_Based_Segmentation_And_Registration#Software|'''Software''']] -
[[AHM_2006:ProjectsJointRegistrationSegmentation|''' AHM 2006''']] -
[[AHM_2007:Slicer3_Developer_Feedback#EM|''' AHM 2007''']]

=== Boundary Localization ===

This class of algorithms explicitly manipulates the representation of the object boundary to fit the strong gradients in the image, indicative of the object outline. Bias in the boundary evolution towards the likely shapes improves the robustness of the segmentation results when the intensity information alone is insufficient for boundary detection. [[Algorithm:MIT:Shape_Based_Level_Set_Segmentation|More...]]

[[Algorithm:MIT:Shape_Based_Level_Set_Segmentation|'''Description''']] - [[Algorithm:MIT:Shape_Based_Level_Set_Segmentation#Publications|'''Publications''']] - [[Algorithm:MIT:Shape_Based_Level_Set_Segmentation#Software|'''Software''']]

=== Registration Regularization ===

We are interested in the effects of registration regularization on segmentation accuracy in joint registration-segmentation.
[[Algorithm:MIT:RegistrationRegularization|More...]]

<font color="red">'''New:'''</font> Submission for MICCAI 2007

= DTI Analysis and Visualization =

Our work in DTI analysis focuses on identifying new ways to provide an interpretation of the white matter connectivity and to utilize the information contained in the DTI images to create more comperehsive models of the brain architecture.

=== DTI Fiber Clustering/Atlas Creation/Analysis ===

The goal of this project is to provide structural description of the white matter architecture as a partition into coherent fiber bundles and clusters, and to use these bundles for quantitative measurement. [[Algorithm:MIT:DTI_Clustering|More...]]

<font color="red">'''New:'''</font>
Monica E. Lemmond, Lauren J. O'Donnell, Stephen Whalen, Alexandra J. Golby.
Characterizing Diffusion Along White Matter Tracts Affected by Primary Brain Tumors.
Accepted to HBM 2007.
[[Algorithm:MIT:DTI_Clustering#Publications|More...]]

[[Algorithm:MIT:DTI_Clustering|'''Description''']] -
[[Algorithm:MIT:DTI_Clustering#Publications|'''Publications''']] -
[[Algorithm:MIT:DTI_Clustering#Software|'''Software''']] -
[[AHM_2006:ProjectsWhiteMatterClustering|'''AHM 2006''']] - [[NA-MIC/Projects/Diffusion_Image_Analysis/Slicer_Fiber_Anatomical_Labeling|'''PW 2006''']]

=== Fiber Tract Modeling, Clustering and Quantitative Analysis ===

The goal of this work is to model the shape of the fiber bundles and use this model discription in clustering and statistical analysis of fiber tracts. [[Algorithm:MIT:DTI_Modeling|More...]]

<font color="red">'''New:'''</font>
M. Maddah, W. M. Wells, S. K. Warfield, C.-F. Westin, and W. E. L. Grimson, Probabilistic Clustering and Quantitative Analysis of White Matter Fiber Tracts,IPMI 2007, Netherlands.

<font color="red">'''New:'''</font>
M. Maddah, S. K. Warfield, W. E. L. Grimson, W. M. Wells, A Unified Framework for Clustering and Quantitative Analysis of White Matter Fiber Tracts, Accepted for publication in Medical Image Analysis.

<font color="red">'''New:'''</font>
M. Maddah, W. M. Wells, S. K. Warfield, C-F. Westin, and W. E. L. Grimson, A Spatial Model of White Matter Fiber Tracts to be presented at ISMRM 2007, Berlin.

[[Algorithm:MIT:DTI_Modeling|'''Description''']] - [[Algorithm:MIT:DTI_Modeling#Publications|'''Publications''']] - [[Algorithm:MIT:DTI_Modeling#Software|'''Software''']]

=== DTI-based Segmentation ===

Unlike conventional MRI, DTI provides adequate contrast to segment the thalamic nuclei, which are gray matter structures. [[Algorithm:MIT:DTI_Segmentation|More...]]

<font color="red">'''New:'''</font> Ulas Ziyan, David Tuch, Carl-Fredrik Westin. Segmentation of Thalamic Nuclei from DTI using Spectral Clustering. Accepted to MICCAI 2006. [[Algorithm:MIT:DTI_Segmentation#Publications|More...]]

[[Algorithm:MIT:DTI_Segmentation|'''Description''']] - [[Algorithm:MIT:DTI_Segmentation#Publications|'''Publications''']] - [[Algorithm:MIT:DTI_Segmentation#Software|'''Software''']]

=== Fiber-Tract-Bundle-based Non-Linear Registration ===

The goal of this work is to utilize the anatomical information from segmented fiber bundles and use this information for registering fiber tracts and the underlying DTI images. [[Algorithm:MIT:DTI_FiberRegistration|More...]]

[[Algorithm:MIT:DTI_FiberRegistration|'''Description''']] - [[Algorithm:MIT:DTI_FiberRegistration#Publications|'''Publications''']] - [[Algorithm:MIT:DTI_FiberRegistration#Software|'''Software''']]

=== Stochastic Tractograhy ===

This work calculates posterior distributions of white matter fiber tract parameters given diffusion observations in a DWI volume. [[Algorithm:MIT:DTI_StochasticTractography|More...]]

[[Algorithm:MIT:DTI_StochasticTractography|'''Description''']] - [[Algorithm:MIT:DTI_StochasticTractography#Publications|'''Publications''']] - [[Algorithm:MIT:DTI_StochasticTractography#Software|'''Software''']]

= fMRI Detection and Analysis =

We are exploring algorithms for improved fMRI detection and interpretation by incorporting spatial priors and anatomical information to guide the detection. [[Algorithm:MIT:fMRI_Detection|More...]]

<font color="red">'''New:'''</font> Wanmei Ou, Sandy Wells, Polina Golland. Bridging Spatial Regularization And Anatomical Priors in fMRI Detection. In preparation for submission to IEEE TMI. [[Algorithm:MIT:fMRI_Detection#Publications|More...]]

[[Algorithm:MIT:fMRI_Detection|'''Description''']] - [[Algorithm:MIT:fMRI_Detection#Publications|'''Publications''']] - [[Algorithm:MIT:fMRI_Detection#Software|'''Software''']] - [[NA-MIC/Projects/fMRI_Analysis/Spatial_Regularization_for_fMRI_Detection|'''PW 2006''']]

= Population Analysis of Anatomical Variability=

Our goal is to develop mathematical approaches to modeling anatomical variability within and across populations using tools like local shape descriptors of specific regions of interest and global constellation descriptors of multiple ROI's. [[Algorithm:MIT:Shape_Analisys|More...]]

<font color="red">'''New:'''</font> Mert R Sabuncu and Polina Golland. Structural Constellations for Population Analysis of Anatomical Variability.

[[Algorithm:MIT:Shape_Analisys|'''Description''']] - [[Algorithm:MIT:Shape_Analisys#Publications|'''Publications''']] - [[Algorithm:MIT:Shape_Analisys#Software|'''Software''']] - [[AHM_2006:ProjectsShapeAnalysis|'''AHM 2006''']]

= Groupwise Registration =

We are exploring algorithms for groupwise registration of medical data. [[Algorithm:MIT:Groupwise_Registration|More...]]

<font color="red">'''New:'''</font> Serdar K Balci, Polina Golland, Sandy Wells, Lilla Zollei, Mert R Sabuncu and Kinh Tieu. Groupwise registration of medical data.

[[Algorithm:MIT:Groupwise_Registration#Introduction|'''Description''']] - [[Algorithm:MIT:Groupwise_Registration#Software|'''Software''']]

= Collaborations with other groups in NAMIC =

* Algorithms:
** Segmentation: joint development of the algorithms and GUI for shape-based hierarchical segmentation with BWH (Kilian Pohl, Steve Pieper).
** Shape Analysis: joint pipeline I/O formulation and development with Kitware (Brad Davis) and UNC (Martin Styner).
** fMRI Detection: joint integration of fMRI detectors into Slicer with BWH (Steve Pieper).

* Clinical:
** Continuing collaboration with [[DBP:Harvard|Harvard]] on shape-based segmentation and DTI analysis.
** New collaboration, enabled and facilitated by NAMIC, with [[DBP:Dartmouth|Dartmouth]] on DTI and fMRI analysis.

NAC-NAMIC-Jan2007-meeting

2007-01-31T20:10:00Z

Tringo: /* Joint Meeting NAC and NAMIC: Stochastic tractogrpahy */

=Joint Meeting NAC and NAMIC: Stochastic tractogrpahy =
* What is the objective
**To report progress on stochastic tractography
**To define define application projects in schizophrenia

[[Media:StochasticTractography2.ppt|Stochastic tractography background slides]]

[[Media:ST_pres.ppt|ITK-Slicer3 implementation]]

=Participants=
#Carl-Fredrik Westin
#Martha Shenton
#Polina Golland
#Tri Ngo
#Steve Pieper

please add your name

File:2007 Project Half Week StochasticTractography.ppt

2007-01-10T18:08:47Z

Tringo:

2007 Project Half Week

2007-01-10T18:08:11Z

Tringo: /* Diffusion Image Analysis */

Back to [[AHM_2007|AHM_2007]]

== Results ==
Results of this event will be summarized here after it is completed.

==Please note==
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.

== Projects ==
This is the list of projects discussed in the preparation tcons on [[Engineering:TCON_12_07_2006|December 7]] and [[Engineering:TCON_12_14_2006|December 14, 2006]]. Each project lead (first name in the list) needs to complete a [[Media:2007_Project_Half_Week_Template.ppt|new 4-block PPT]], and upload and link it to this page.

===Structural Analysis===
# [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Delphine Nain - GT, Yi Gao - GT, Jim Miller - GE, Luis Ibanez - Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT Summer 2006]],[[Media:2007_Project_Half_Week_SphericalWaveletInITK.ppt| 4-block PPT Jan 2007]]
# [[Algorithm:GATech:Multiscale_Shape_Analysis|UNC shape analysis with Spherical Wavelet Features]] (Delphine Nain, Yi Gao (GaTech), Martin Styner (UNC)): [[Media:2007_Project_Half_Week_ShapeAnalysis_WithSphericalWavelets.ppt| 4-block PPT Jan 2007]]
#EMSegmenter Software Development (Kilian, Brad) [[Media:2007_Project_Half_Week_EMSegment.ppt | 4-block PPT Jan 2007]] ‎
# Data assimilation for NAMIC (Stephen) [[Media:2007_Project_Half_Week_MIDAS.ppt | 4 block PPT Jan 2007]]
#[[Non_Rigid_Registration|Parallelization of ITK for deformable registration]] (Stephen, Jim, Ross) [[Media:2007_Project_Half_Week_ITKRegistrationParallelization.ppt| 4-block PPT Jan 2007]]
## Driving problem: Non-rigid registration of anatomical MRI (Kilian, Stephen)
# Integrating KWMeshVisu into Slicer (Ipek, Martin, Sebastien), [[Media:2006_AHM_Programming_Half_week_MeshVisu.ppt|4-block PPT Jan 2006]], [[Media:2007_AHM_Programming_Half_week_MeshVisu.ppt |4-block PPT Jan 2007 ]]
#Group-wise Registration of Medical Images(Serdar, Polina, Mert, Sandy ), [[Media:2007_Project_Half_Week_GroupWiseRegistration.ppt| 4-block PPT Jan 2007]]
#Genus Zero Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_GenusZeroImageFilter.ppt| 4-block PPT Jan 2007]]
#Thickness Slicer3 Module (Marc, Sylvain, Steve), [[Media:2007_Project_Half_Week_ThicknessImageFilter.ppt| 4-block PPT Jan 2007]]
#Shape Analysis of Caudate paper (Jim, Martin, Marc, Sylvain, Martha), [[Media:2007_Project_Half_Week_Caudate_Paper.ppt| 4-block PPT Jan 2007]]

===Diffusion Image Analysis===
#Finsler Tractography (John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerTractography.ppt| 4-block PPT Jan 2007]]
#Finsler Levelsets (Vandana Mohan - GT, John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerLevelsets.ppt| 4-block PPT Jan 2007]]
#Tensor estimation and Monte-Carlo simulation (Casey Goodlett - UNC, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_TensorEstimation.ppt | 4-block PPT Jan 2007]]
#Rician Noise Remvoal in Diffusion Tensor MRI (McKay Davis - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_RicianNoiseDTI.ppt | 4-block PPT Jan 2007]]
#ITK implementation of POIStat, and Integration into Slicer3 (Dennis, Steve), [[Media:2007_Project_Half_Week_PoistatsSlicerItkIntegration.ppt| 4-block PPT Jan 2007]]
#Image Format issues in application of POIStats to Dartmouth data (Dennis, Steve, Luis, John West, Andy Saykin), [[Media:2007_Project_Half_Week_PoistatsImageFormatDartmouth.ppt| 4-block PPT Jan 2007]]
#ITK Stochastic Tractography Filter (Tri Ngo - MIT, C-F Westin - LMI, Polina Golland - MIT), [[Media:2007_Project_Half_Week_StochasticTractography.ppt| 4-block PPT Jan 2007]]

===NA-MIC Kit===
#'''[[Slicer3:Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata) [[Media:2007 Programming Half Week SlicerArch.ppt | 4-block ppt]]
#'''[[Slicer3:Data_Model|Slicer3: Data Model / libMRML]]''' ('''Alex''', Steve) [[media:2007_Programming_Half_Week_MRML.ppt | 4-block ppt]]
#'''[[Slicer3:Execution_Model|Slicer3: Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)
#'''[[Slicer3:Interface_Design|Slicer3: Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan) [[Media:2007_Project_Half_Week_SlicerUI.ppt| 4-block PPT Jan 2007]]
#'''[[Slicer3:Transition_of_Slicer2.x_Modules|Slicer3: Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)
##[[Slicer3:DTMRI|DTMRI]] '''Raul''', [http://lmi.bwh.harvard.edu LMI] [[Media:2007_Project_Half_Week_DTI.ppt| 4-block PPT Jan 2007]]
##[[Slicer3:DTMRI|Tractography]] '''Lauren''' [[Media:2007_Project_Half_Week_Tractography.ppt| 4-block PPT Jan 2007]]
##[[Slicer3:Editor|Editor]] '''Steve''' [[Media:2007_Programming_Half_Week_Editor.ppt | 4-block ppt]]
##[[Slicer3:ColorsFiducialsFreesurferModelmaker|Slicer3: Colors, Fiducials, FreeSurfer, ModelMaker]] '''Nicole''' [[Media:2007_Project_Half_Week_Slicer3Colors.ppt | 4 block:Colors]],[[Media:2007_Project_Half_Week_Slicer3Fiducials.ppt | 4 block:Fiducials]],[[Media:2007_Project_Half_Week_Slicer3FreeSurfer.ppt | 4 block:FreeSurfer]], [[Media:2007_Project_Half_Week_Slicer3ModelMaker.ppt | 4 block:ModelMaker]]
##[[Slicer3:_Image_Guided_Therapy_%28IGT%29|Slicer3: IGT, Trackers]] '''Haiying'''
#'''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie) [[media:2007 AHM Programming Half Week PackagingAndDeployment.ppt | 4-block PPT]]
#Slicer3 launch and deployment issues (Steve, Jim, Bill, Will, Sebastien, Andy) [[media:2007 AHM Programming Half Week Slicer3 Launch.ppt | 4-block PPT]]
#'''[[Slicer3:Pipeline_Integration|Slicer3: Pipeline Integration]]''' ('''Jags''') [[media:2007_Project_Half_Week_Loni_Pipeline.ppt| 4-block PPT]]
#'''[[Slicer3:Grid_Interface|Slicer3: Grid Integration]]''' ('''Neil''', Bill, Jim) [[media:2007_Project_Half_Week_GridExecution.ppt| 4-block PPT Jan 2007]]
#'''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''') [[Media:2007_Programming_Half_Week_Performance_Analysis.ppt| 4-block PPT Jan 2007]]
#Malab-Slicer3 pipeline enhancement (Katharina, Sylvain, Steve, Marc, Mahnaz), [[Media:2007_Project_Half_Week_SlicerMatlabPipeline.ppt| 4-block PPT Jan 2007]]
#Model Hierarchies (Alex, Lauren, Kilian, Brad, Ron) -- generalize concepts from DTI and EM group nodes to support atlas hierachies like in slicer2, [[Media:2007_Programming_Half_Week_HierModel.ppt| 4-block PPT Jan 2007]]

===External Collaborations===
#Converting ITK Pipeline for Archip's, HPC based, deformable registration to Slicer3 Module (Daniel Goldberg, Jim Miller, Bill Lorensen) [[Media:2007_Project_Half_Week_ConvertingITKPipelineDeformableRegistrationtoSlicer3.ppt|4 block PPT Jan 2007]]
#[[IGT|IGT Workflow for Slicer3: Interventional Imaging]] (Simon DiMaio, Haiying Liu, Noby Hata, Stephen Aylward) [[Media:2007_Project_Half_Week_InterventionalImaging.ppt|4 block PPT Jan 2007]]
#Radiology Workstation Module for Slicer3 (Pat, Steve)
#vmtk module for Slicer (Luca Antiga, Jim Miller) [[Media:2007 Project Half Week vmtkSlicerModule.ppt | 4 block PPT Jan 2007]]
#Hexahedral Voxel Meshing into Slicer3 [[NA-MIC_Collaborations#PAR-05-063_Automated_FE_Mesh_Development | for collaboration grant]]
##Voxel meshing as an execuation module in Slicer3 [[Media:2007_AHM_Programming_Half Week_VoxelMeshing.ppt|Voxel Meshing 4 block PPT Jan 2007]] (Ritesh Bafna, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Mesh Quality Visualization Development [[Media:Mesh_Quality_Visualization.ppt|Mapped Quality 4 block PPT Jan 2007]] (Curt Lisle, Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper)
##Bounding Box Projection Meshing [[Media:2007_AHM_Programming_Half Week_VoxelMeshing.ppt|Voxel Meshing 4 block PPT Jan 2007]] (Kiran Shivanna, Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Steve Pieper, Curt Lisle)
##Tetrahedral Mesh Generation Tools in VTK [[Media:Tetmesh_VTK_Tools.ppt|VTK Tetrahedral Meshing 4 block PPT Jan 2007]] (Srinivas Tadepalli, Nicole Grosland, Vincent Magnotta, Will Schroeder, Bill Lorensen)
#Nonhuman Primate slicer Module (Alcohol Exposure) (Kilian Pohl, Chris Wyatt) [[Media:2007_Project_Half_Week_AlcoholExposureStructuralImaging.ppt | 4 block PPT Jan 2007]]

== Logistics ==

'''Dates:''' January 10 & 12, 2007 (There will be no project-week related events scheduled for Thursday, January 11th, the day of the AHM.)

'''Registration Fee:''' Registration fee is $215 for this event, and includes registration for the NA-MIC AHM. Separate registration, either for the AHM, or the project event are not available. To register and reserve hotel rooms, please [[AHM_2007#Registration_and_Hotel_Logistics|follow this link]].

== Background and Preparation ==

We continue to call this event "Project Week" or "Project Half Week", depending on how its duration, rather than by its original name of "Programming Week". Along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.

=== Goals ===

The main goal of this week is to move forward the deliverables of NA-MIC. All NA-MIC participants and their collaborators are welcome.

* Members of all cores are welcome. This event involves programming, algorithm design, and clinical application development/testing.
* The event is open to people outside NA-MIC, subject to availability.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.
* Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
* This is not an introduction to the components of the NA-MIC Kit.
* Submit any projects that you would like to work on during this week, and what type of help you might need for it.

=== Preparation for the workshop ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_12_07_2006|December 7: Kickoff TCON]]
# December 14: Create a Wiki page per project (the participants must do this, hopefully jointly)
# [[Engineering:TCON_12_14_2006|December 14: TCON#2 to discuss projects and verify teams]]
# December: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)
# [[Engineering:TCON_2007#2007-Jan-04|January 4, 2007: TCON#3 last preparation tcon]]
# By January 9th: Complete the top half of [[Media:2007_Project_Half_Week_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.
# 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...

== A History in Wiki Links ==

A history of all the programming/project events in NA-MIC is available by following [[Engineering:Programming_Events|this link]].