NAMIC Wiki - User contributions [en]

2010 Summer Project Week Diffusion

2010-06-23T18:14:04Z

Nhageman: /* Key Investigators */

__NOTOC__
{|
|[[Image:PW-MIT2010.png|thumb|320px|[[2010_Summer_Project_Week#Projects|Project Week Main Page]] ]]
|[[Image:Hageman_cspfig4NAMIC_07-06-22.png|thumb|320px|Corticospinal tracts segmented using our fluid mechanics based tractography method.]]
|[[Image:Hageman_FullBrainSlicerTractography.jpg|thumb|320px|Full brain tracts segmented using multiple fluid sources/sinks.]]
|[[Image:FMModuleScreenshot.png|thumb|320px|Screenshot of Slicer Module for Fluid Mechanics Tractography.]]
|}

===Key Investigators===
* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D
* Isomics: Steve Pieper and Alex Yarmarkovich

<div style="margin: 20px;">

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

<h1>Objective</h1>
Computational fluid dynamics is a rich field and its application to the analysis of diffusion tensor imaging (DTI) datasets has yielded possible applications to tractography, image registration, and white matter pathology. We are developing several useful and novel diffusion tensor imaging (DTI) analysis algorithms modeled on the principles of fluid mechanics for inclusion within the NA-MIC framework. The goal of this project is to develop these methods, make them compatible with the NA-MIC ITK-based software infrastructure (i.e. Slicer), and promote their dissemination to the scientific community.

See our [[hageman:NAMICFluidMechDTITractography|Project Page]] for more information.

</div>

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

<h1>Approach, Plan</h1>

We have developed and initially validated a DTI tractography method based on Navier-Stokes fluid mechanics. See the papers listed in the reference section for complete details on the method. Our approach for this project week will focus on the following:
* Building the our current CL Slicer module into Slicer 3. Our method is currently integrated as a CL Slicer module in a custom build of Slicer 3. The module has the following functionalities:
**computation of fluid velocity vector field volume
**reconstruction of tracts based on the above fluid velocity volume
** Optimizing initial coding of method in ITK (better use of multithreading)
* Working with the interested groups in analyzing control and white matter pathology data. Specifically, we have seen promising results when looking at the flow perturbation around white matter lesions seen in multiple sclerosis or stroke that may suggest a novel method for automatic lesion detection in DTI.
</div>

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

<h1>Progress</h1>
*Code for module is available for download and compilation via the NAMIC Sandbox (in directory "FluidMechanicsTractography").
*Code has successfully been built into an experimental branch of Slicer - Slicer3.6-hagemanFMTractography. Download and build using getbuildtest.tcl to get module.

</div>

<br style="clear: both;" />

</div>

===References===
* Hageman NS, Shattuck DW, Narr K, Toga AW (2006). A diffusion tensor imaging tractography method based on Navier-Stokes fluid mechanics. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2006), Arlington, VA, USA, 6-9 April 2006. p. 798-801
* Hageman NS, Toga AW, Narr K, Shattuck DW (2009). A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics. IEEE Trans. in Medicial Imaging, 28(3): 348-360.

File:FMTractography TutorialContestSummer2010.pdf

2010-06-22T20:28:16Z

Nhageman: uploaded a new version of "File:FMTractography TutorialContestSummer2010.pdf"

Hageman:NAMICFluidMechDTITractography

2010-06-22T18:11:39Z

Nhageman: /* Links */

__NOTOC__
<br>
= Fluid Mechanics Based DTI Tractography =

== Overview ==

Currently, our project is focused on developing a novel method for diffusion tensor imaging (DTI) tractography modeled on the dynamics of a viscous fluid described by the second order non-linear Navier-Stokes equations. Even though these equations are most commonly seen in the context of fluid mechanics, they have been shown to be successful in modeling a large number of diverse physical phenomena. Our second order nonlinear-based approach is an extension of previous linear PDE methods, but our model contains a viscous force not present in previous methods, represented as an additional convection term in the PDE. We model local viscosity of the fluid as a function of the local intervoxel and intravoxel anisotropy in the corresponding DTI image volume. The incorporation of this convection term in our flow field calculation allows us to closely couple the magnitude of the fluid velocity to the magnitude of the underlying anisotropy of the DTI tensor field, providing a dampening force in background areas, such as gray matter and CSF. This eliminates the need for the white matter mask used by other PDE-based methods to prevent the model from entering these areas. To compute an estimate of the most likely connection path between two regions in the brain, we simulate the flow of an artificial fluid between those two points through a volume whose dimensions, pressure, and local viscosity are derived from the underlying DTI data. We then numerically solve for the fluid velocity vector field. The estimated connection path is then computed by finding the optimal path through the fluid velocity that simultaneously maximizes both the fluid velocity and its gradient.

Computational fluid dynamics is a rich field and, in addition to this tractography method, we are investigating its application to the analysis of diffusion tensor imaging (DTI) datasets for registration and analysis of white matter pathology. We are currently developing several useful and novel diffusion tensor imaging (DTI) analysis algorithms modeled on the principles of fluid mechanics for inclusion within the NA-MIC framework. The goal of this project is to fully develop these methods, make them compatible with the NA-MIC ITK-based software infrastructure (i.e. Slicer), and promote their dissemination to the scientific community.

== Description ==

Our algorithm simulates the flow of an artificial fluid through a volume whose dimensions, viscosity, and pressure tensor field are derived from a DTI volume. Specific regions of interest are chosen as sources and/or sinks, and we simulate the flow of an artificial fluid governed by the Navier-Stokes equations. The most likely connection path is then estimated using a generalized gradient vector flow (GGVF) based approach to compute the trajectory through the fluid velocity vector field that simultaneously maximizes the magnitude of the fluid velocity and its gradient along the path. Our fluid model is valid only as a theoretical framework for generating a connectivity metric and does not try to model any aspect of the underlying diffusion process.

[[Image:NAMICFMech_VisFig.jpg|Viscosity Map]]

Viscosity maps derived from 2D slices of DTI data from human control subjects. Viscosity values were calculated from the corresponding diffusion tensor image and are color-coded according to the legend bar seen on the right side of the figure. A. Axial slice taken at the level of the internal capsule. The corpus callosum, marked with a star is a highly organized white matter tract and is therefore characterized by low viscosity. Conversely, the lateral ventricle, marked with a delta contains CSF and is highly viscous. B. A mid-sagittal slice. As in A, the corpus callosum is marked with a star and is characterized by low viscosity. In contrast, the lateral ventricular space, marked with a delta contains CSF and therefore has no architecture. Consequently, it is highly viscous.

[[Image:NAMICFMech_PressureFig.jpg|Pressure Map]]

Representations of the pressure tensor derived from 2D slices from human control subjects. At each voxel in the image, the pressure force is represented by a tensor glyph, an ellipsoid whose axis is obtained from a diagonalization of the corresponding pressure tensor. The color of the ellipsoid represents the dominant diffusion direction, according to the color coded axes in the figure with the superior-inferior z-axis (blue) coming out of the page, the anterior-posterior y-axis (green) vertical, and the left-right x-axis (red) horizontal. A. A 2D axial slice taken at the level of the internal capsule. The white box marks the enlarged area shown in B. B. Enlarged view from A. The posterior limb of the corpus callosum, marked with a star is a highly organized white matter tract, and the pressure force acts on the artificial fluid co-linear with the fiber tract. In contrast, the lateral ventricular space, marked with a delta contains little structure. Consequently, the pressure force is isotropic in that region.

[[Image:NAMICflowfieldlesion.JPG|400 px|Fluid Velocity Field Solution]]

We solve our modified Navier-Stokes fluid mechanics model with these variables to get a fluid velocity field which is then used as a metric of regional connectivity. Tracts are generated using a modified method based on a generalized gradient vector field approach.

[[Image:NAMICFMech_CspFig.jpg|Human Corticospinal Tracts]]

Segmentation results of the corticospinal tracts using our method in human control DTI images. ROIs were placed within the brainstem below the level of the crossing pontine fibers and within the corona radiata above the level of the corpus callosum. Cross-sections of the approximate location of these ROIs are shown Figure 8D, drawn in white, superimposed on the corresponding axial DEC slices. Figure 8A shows the estimated connection paths between these ROIs generated by our method. An axial slice of the tensor glyphs at the level of the mid-brain is shown for spatial reference. The tracts show a prominent lateral course at the level of the mid-pons (Figure 8A: white arrow). This corresponds to a strong lateral diffusion component at that point as seen in the directionally encoded color (DEC) image of the axial slice at the mid-pontine level (Figure 8B, 8C: white arrow). The tensor glyphs and DEC image are color-coded by the axes shown in the figure.

[[Image:Hageman_FullBrainSlicerTractography.jpg|Full brain tracts segmented using our fluid mechanics based tractography method.]]

== Key Investigators ==

* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D

== Publications ==

''In Print''
* [http://www.na-mic.org/Special:Publications?text=Projects:MultiscaleShapeSegmentation&submit=Search&keywords=checked NA-MIC Publications Database].
* Hageman NS, Toga AW, Narr K, Shattuck DW (2009). A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics. IEEE Trans. in Medicial Imaging, 28(3): 348-360.



''In Submission''
* Hamilton L, Nuechterlein K, Hageman NS, Woods R, Asarnow R, Alger J, Gaser C, Toga AW, Narr K (2008). Mean Diffusivity and Fractional Anisotropy as Indicators of Schizophrenia and Genetic Vulnerability, ''Neuroimage'', In Submission.

== Links ==

* Hageman NS, Shattuck DW, Narr K, Toga AW (2006). A diffusion tensor imaging tractography method based on Navier-Stokes fluid mechanics. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2006), Arlington, VA, USA, 6-9 April 2006. p. 798-801 ([[media:Hageman-Toga2006.pdf|PDF]])
* [http://www.loni.ucla.edu LONI Website]

Project Week Results: [[2008_Winter_Project_Week:Fluid_Mechanics_Tractography|2008 Winter]], [[2008_Summer_Project_Week|2008 Summer]], [[2009_Winter_Project_Week|2009 Winter]], [[2009_Summer_Project_Week|2009 Summer]], [[2010_Summer_Project_Week|2010 Summer]]

Hageman:NAMICFluidMechDTITractography

2010-06-22T17:52:26Z

Nhageman: /* Publications */

Hageman:NAMICFluidMechDTITractography

2010-06-22T17:51:22Z

Nhageman: /* Publications */

__NOTOC__
<br>
= Fluid Mechanics Based DTI Tractography =

== Overview ==

Currently, our project is focused on developing a novel method for diffusion tensor imaging (DTI) tractography modeled on the dynamics of a viscous fluid described by the second order non-linear Navier-Stokes equations. Even though these equations are most commonly seen in the context of fluid mechanics, they have been shown to be successful in modeling a large number of diverse physical phenomena. Our second order nonlinear-based approach is an extension of previous linear PDE methods, but our model contains a viscous force not present in previous methods, represented as an additional convection term in the PDE. We model local viscosity of the fluid as a function of the local intervoxel and intravoxel anisotropy in the corresponding DTI image volume. The incorporation of this convection term in our flow field calculation allows us to closely couple the magnitude of the fluid velocity to the magnitude of the underlying anisotropy of the DTI tensor field, providing a dampening force in background areas, such as gray matter and CSF. This eliminates the need for the white matter mask used by other PDE-based methods to prevent the model from entering these areas. To compute an estimate of the most likely connection path between two regions in the brain, we simulate the flow of an artificial fluid between those two points through a volume whose dimensions, pressure, and local viscosity are derived from the underlying DTI data. We then numerically solve for the fluid velocity vector field. The estimated connection path is then computed by finding the optimal path through the fluid velocity that simultaneously maximizes both the fluid velocity and its gradient.

Computational fluid dynamics is a rich field and, in addition to this tractography method, we are investigating its application to the analysis of diffusion tensor imaging (DTI) datasets for registration and analysis of white matter pathology. We are currently developing several useful and novel diffusion tensor imaging (DTI) analysis algorithms modeled on the principles of fluid mechanics for inclusion within the NA-MIC framework. The goal of this project is to fully develop these methods, make them compatible with the NA-MIC ITK-based software infrastructure (i.e. Slicer), and promote their dissemination to the scientific community.

== Description ==

Our algorithm simulates the flow of an artificial fluid through a volume whose dimensions, viscosity, and pressure tensor field are derived from a DTI volume. Specific regions of interest are chosen as sources and/or sinks, and we simulate the flow of an artificial fluid governed by the Navier-Stokes equations. The most likely connection path is then estimated using a generalized gradient vector flow (GGVF) based approach to compute the trajectory through the fluid velocity vector field that simultaneously maximizes the magnitude of the fluid velocity and its gradient along the path. Our fluid model is valid only as a theoretical framework for generating a connectivity metric and does not try to model any aspect of the underlying diffusion process.

[[Image:NAMICFMech_VisFig.jpg|Viscosity Map]]

Viscosity maps derived from 2D slices of DTI data from human control subjects. Viscosity values were calculated from the corresponding diffusion tensor image and are color-coded according to the legend bar seen on the right side of the figure. A. Axial slice taken at the level of the internal capsule. The corpus callosum, marked with a star is a highly organized white matter tract and is therefore characterized by low viscosity. Conversely, the lateral ventricle, marked with a delta contains CSF and is highly viscous. B. A mid-sagittal slice. As in A, the corpus callosum is marked with a star and is characterized by low viscosity. In contrast, the lateral ventricular space, marked with a delta contains CSF and therefore has no architecture. Consequently, it is highly viscous.

[[Image:NAMICFMech_PressureFig.jpg|Pressure Map]]

Representations of the pressure tensor derived from 2D slices from human control subjects. At each voxel in the image, the pressure force is represented by a tensor glyph, an ellipsoid whose axis is obtained from a diagonalization of the corresponding pressure tensor. The color of the ellipsoid represents the dominant diffusion direction, according to the color coded axes in the figure with the superior-inferior z-axis (blue) coming out of the page, the anterior-posterior y-axis (green) vertical, and the left-right x-axis (red) horizontal. A. A 2D axial slice taken at the level of the internal capsule. The white box marks the enlarged area shown in B. B. Enlarged view from A. The posterior limb of the corpus callosum, marked with a star is a highly organized white matter tract, and the pressure force acts on the artificial fluid co-linear with the fiber tract. In contrast, the lateral ventricular space, marked with a delta contains little structure. Consequently, the pressure force is isotropic in that region.

[[Image:NAMICflowfieldlesion.JPG|400 px|Fluid Velocity Field Solution]]

We solve our modified Navier-Stokes fluid mechanics model with these variables to get a fluid velocity field which is then used as a metric of regional connectivity. Tracts are generated using a modified method based on a generalized gradient vector field approach.

[[Image:NAMICFMech_CspFig.jpg|Human Corticospinal Tracts]]

Segmentation results of the corticospinal tracts using our method in human control DTI images. ROIs were placed within the brainstem below the level of the crossing pontine fibers and within the corona radiata above the level of the corpus callosum. Cross-sections of the approximate location of these ROIs are shown Figure 8D, drawn in white, superimposed on the corresponding axial DEC slices. Figure 8A shows the estimated connection paths between these ROIs generated by our method. An axial slice of the tensor glyphs at the level of the mid-brain is shown for spatial reference. The tracts show a prominent lateral course at the level of the mid-pons (Figure 8A: white arrow). This corresponds to a strong lateral diffusion component at that point as seen in the directionally encoded color (DEC) image of the axial slice at the mid-pontine level (Figure 8B, 8C: white arrow). The tensor glyphs and DEC image are color-coded by the axes shown in the figure.

[[Image:Hageman_FullBrainSlicerTractography.jpg|Full brain tracts segmented using our fluid mechanics based tractography method.]]

== Key Investigators ==

* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D

== Publications ==

''In Print''
* [http://www.na-mic.org/Special:Publications?text=Projects:MultiscaleShapeSegmentation&submit=Search&keywords=checked NA-MIC Publications Database].



''In Submission''
* Hamilton L, Nuechterlein K, Hageman NS, Woods R, Asarnow R, Alger J, Gaser C, Toga AW, Narr K (2008). Mean Diffusivity and Fractional Anisotropy as Indicators of Schizophrenia and Genetic Vulnerability, ''Neuroimage'', In Submission.

== Links ==

* Hageman NS, Shattuck DW, Narr K, Toga AW (2006). A diffusion tensor imaging tractography method based on Navier-Stokes fluid mechanics. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2006), Arlington, VA, USA, 6-9 April 2006. p. 798-801 ([[media:Hageman-Toga2006.pdf|PDF]])
* [http://www.loni.ucla.edu LONI Website]

Project Week Results: [[2008_Winter_Project_Week:Fluid_Mechanics_Tractography|2008 Winter]], [[2008_Summer_Project_Week|2008 Summer]], [[2009_Winter_Project_Week|2009 Winter]], [[2009_Summer_Project_Week|2009 Summer]]

2010 Summer Project Week Diffusion

2010-06-22T17:49:31Z

Nhageman: /* Key Investigators */

__NOTOC__
{|
|[[Image:PW-MIT2010.png|thumb|320px|[[2010_Summer_Project_Week#Projects|Project Week Main Page]] ]]
|[[Image:Hageman_cspfig4NAMIC_07-06-22.png|thumb|320px|Corticospinal tracts segmented using our fluid mechanics based tractography method.]]
|[[Image:Hageman_FullBrainSlicerTractography.jpg|thumb|320px|Full brain tracts segmented using multiple fluid sources/sinks.]]
|[[Image:FMModuleScreenshot.png|thumb|320px|Screenshot of Slicer Module for Fluid Mechanics Tractography.]]
|}

===Key Investigators===
* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D
* Isomics: Steve Pieper and Alex Yarmarkovich

<div style="margin: 20px;">

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

<h1>Objective</h1>
Computational fluid dynamics is a rich field and its application to the analysis of diffusion tensor imaging (DTI) datasets has yielded possible applications to tractography, image registration, and white matter pathology. We are developing several useful and novel diffusion tensor imaging (DTI) analysis algorithms modeled on the principles of fluid mechanics for inclusion within the NA-MIC framework. The goal of this project is to develop these methods, make them compatible with the NA-MIC ITK-based software infrastructure (i.e. Slicer), and promote their dissemination to the scientific community.

See our [[hageman:NAMICFluidMechDTITractography|Project Page]] for more information.

</div>

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

<h1>Approach, Plan</h1>

We have developed and initially validated a DTI tractography method based on Navier-Stokes fluid mechanics. See the papers listed in the reference section for complete details on the method. Our approach for this project week will focus on the following:
* Building the our current CL Slicer module into Slicer 3. Our method is currently integrated as a CL Slicer module in a custom build of Slicer 3. The module has the following functionalities:
**computation of fluid velocity vector field volume
**reconstruction of tracts based on the above fluid velocity volume
** Optimizing initial coding of method in ITK (better use of multithreading)
* Working with the interested groups in analyzing control and white matter pathology data. Specifically, we have seen promising results when looking at the flow perturbation around white matter lesions seen in multiple sclerosis or stroke that may suggest a novel method for automatic lesion detection in DTI.
</div>

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

<h1>Progress</h1>
*Code for module is available for download and compilation via the NAMIC Sandbox (in directory "FluidMechanicsTractography").

</div>

<br style="clear: both;" />

</div>

===References===
* Hageman NS, Shattuck DW, Narr K, Toga AW (2006). A diffusion tensor imaging tractography method based on Navier-Stokes fluid mechanics. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2006), Arlington, VA, USA, 6-9 April 2006. p. 798-801
* Hageman NS, Toga AW, Narr K, Shattuck DW (2009). A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics. IEEE Trans. in Medicial Imaging, 28(3): 348-360.

File:FMTractography TutorialContestSummer2010.pdf

2010-06-22T10:07:17Z

Nhageman: uploaded a new version of "File:FMTractography TutorialContestSummer2010.pdf"

2010 Summer Project Week Diffusion

2010-06-22T08:34:26Z

Nhageman: /* Key Investigators */

__NOTOC__
{|
|[[Image:PW-MIT2010.png|thumb|320px|[[2010_Summer_Project_Week#Projects|Project Week Main Page]] ]]
|[[Image:Hageman_cspfig4NAMIC_07-06-22.png|thumb|320px|Corticospinal tracts segmented using our fluid mechanics based tractography method.]]
|[[Image:Hageman_FullBrainSlicerTractography.jpg|thumb|320px|Full brain tracts segmented using multiple fluid sources/sinks.]]
|[[Image:FMModuleScreenshot.png|thumb|320px|Screenshot of Slicer Module for Fluid Mechanics Tractography.]]
|}

===Key Investigators===
* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D
* Isomics: Steve Pieper and Alex Yarmarkovich

<div style="margin: 20px;">

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

<h1>Objective</h1>
Computational fluid dynamics is a rich field and its application to the analysis of diffusion tensor imaging (DTI) datasets has yielded possible applications to tractography, image registration, and white matter pathology. We are developing several useful and novel diffusion tensor imaging (DTI) analysis algorithms modeled on the principles of fluid mechanics for inclusion within the NA-MIC framework. The goal of this project is to develop these methods, make them compatible with the NA-MIC ITK-based software infrastructure (i.e. Slicer), and promote their dissemination to the scientific community.

See our [[hageman:NAMICFluidMechDTITractography|Project Page]] for more information.

</div>

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

<h1>Approach, Plan</h1>

We have developed and initially validated a DTI tractography method based on Navier-Stokes fluid mechanics. See the papers listed in the reference section for complete details on the method. Our approach for this project week will focus on the following:
* Building the our current CL Slicer module into Slicer 3. Our method is currently integrated as a CL Slicer module in a custom build of Slicer 3. The module has the following functionalities:
**computation of fluid velocity vector field volume
**reconstruction of tracts based on the above fluid velocity volume
** Optimizing initial coding of method in ITK (better use of multithreading)
* Working with the interested groups in analyzing control and white matter pathology data. Specifically, we have seen promising results when looking at the flow perturbation around white matter lesions seen in multiple sclerosis or stroke that may suggest a novel method for automatic lesion detection in DTI.
</div>

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

<h1>Progress</h1>

</div>

<br style="clear: both;" />

</div>

===References===
* Hageman NS, Shattuck DW, Narr K, Toga AW (2006). A diffusion tensor imaging tractography method based on Navier-Stokes fluid mechanics. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2006), Arlington, VA, USA, 6-9 April 2006. p. 798-801
* Hageman NS, Toga AW, Narr K, Shattuck DW (2009). A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics. IEEE Trans. in Medicial Imaging, 28(3): 348-360.

File:FMTractographyData TutorialContestSummer2010.tar.gz

2010-06-15T13:15:53Z

Nhageman:

File:FMTractography TutorialContestSummer2010.pdf

2010-06-15T13:02:10Z

Nhageman:

Slicer3:FluidMechanicsTractography TutorialContestSummer2010

2010-06-15T13:01:07Z

Nhageman:

This is the page for the tutorial materials for the Fluid Mechanics Tractography Module in Slicer 3.6:

[http://wiki.na-mic.org/Wiki/index.php/File:FMTractography_TutorialContestSummer2010.pdf pdf]

[http://wiki.na-mic.org/Wiki/index.php/File:FMTractographyData_TutorialContestSummer2010.tar.gz Data]

[http://wiki.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest Back to tutorial contest]

Slicer3:FluidMechanicsTractography TutorialContestSummer2010

2010-06-15T10:51:18Z

Nhageman: Created page with 'This is the page for the tutorial materials for the Fluid Mechanics Tractography Module in Slicer 3.6: [http://wiki.na-mic.org/Wiki/index.php/File:FMTractography_TutorialContest…'

This is the page for the tutorial materials for the Fluid Mechanics Tractography Module in Slicer 3.6:

[http://wiki.na-mic.org/Wiki/index.php/File:FMTractography_TutorialContestSummer2010.pdf pdf]

[http://wiki.na-mic.org/Wiki/index.php/File:FMTractography_TutorialContestSummer2010.zip Data]

[http://wiki.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest Back to tutorial contest]

Summer 2010 Tutorial Contest

2010-06-15T10:50:03Z

Nhageman: /* List of submitted tutorials */

'''Organizational Telephone Call May 13th at 3pm Eastern Time (part of standard NA-MIC Engineering tcon)'''

=Background=

[http://www.slicer.org Slicer3] is used to perform meaningful research tasks. As part of the NA-MIC Training Core activities we are building a curated portfolio of tutorials for the basic functions and specialized functionality available in Slicer. Our current portfolio of tutorials as well as tutorials that were developed in past contests are posted on the [http://www.slicer.org/slicerWiki/index.php/Slicer3.4:Training#Software_tutorials| NA-MIC training compendium].

=Tutorial Contest Goal=
The primary purpose of this contest is to enrich the training materials that are available to end-users and developers using 3D Slicer and the NA-MIC kit. We believe contestants will be motivated to participate to enhance the dissemination of their own algorithms that they have incorporated into the Slicer3 platform and/or to enhance training of Slicer3 functionality for their own laboratory groups.

There will be three categories:
#'''END TO END SOLUTION TUTORIAL:''' In this category, the tutorial will teach a user how to solve a particular clinical problem using the NA-MIC Kit. Entries into this category will require at least:
#*materials about the scientific and application background and motivation,
#*step-by-step guides, and
#*sample data
#*Examples: [[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ ARCTIC (Automatic Regional Cortical Thickness) Tutorial]] , [[IGT:ToolKit/Neurosurgical-Planning|Neurosurgical Planning for Image Guided Therapy using Slicer3]]
#'''ALGORITHM TUTORIAL:''' In this category the tutorial will teach a user how to make an algorithm work on their data. Entries into this category will require at least:
#*materials about the scientific and application background of the algorithm(s) and their use in the Slicer environment
#*step-by-step guides, and
#*at least two different sample data sets from two different institutions
#*Examples: [[media:EMSegment_TrainingTutorial.pdf| Non-human Primates Segmentation Tutorial]], [[Media:AutomaticSegmentation_SoniaPujol_Munich2008.ppt|Automatic Segmentation Tutorial ]]
# '''METHODOLOGY TUTORIAL'''. Application-level tutorials for users and developers.
<br>

=Rules=
*Tutorial must be based on the '''Slicer3.6 release'''
*To enter the contest, you must provide '''a version of the tutorial that works on at least one platform'''.
*Tutorial and all of its components (data, powerpoints/pdfs, additional modules etc.) must be released under the [http://www.slicer.org/slicerWiki/index.php/Slicer:license Slicer license]
*Tutorial must include contact information of the primary author (e-mail and phone number)
*Tutorial must follow the guidelines specified above and use the [[Media:TutorialContest_Template.ppt‎| tutorial template]].
*If applicable, the tutorial must provide clear directions for downloading and installing additional modules
*Applicants must agree to work with the NA-MIC Training and Dissemination Cores to curate their submission.

=Submission Dead-line and Presentation=

* '''<span style="background-color: yellow"> Submission dead-line: Monday June 14, 2010'''</span>
* Presentation: all tutorials will be presented by the authors during the Summer 2010 Project Week, on '''Tuesday June 22 from 3:00 pm to 5:30 pm'''. Each tutorial presentation should be 10 minutes long.
* If you wish to participate in the contest, please follow the three steps below:
**1. Create a wiki page for your tutorial
**2. Upload your slides and tutorial dataset. Your tutorial and data must be named as 'TutorialName_TutorialContestSummer2010.pdf' and 'TutorialData_TutorialContestSummer2010.zip'
**3. Add a link to the uploaded tutorial and datasets on your tutorial page.
**4. Add a link to your tutorial page in the list below.

= List of submitted tutorials=

[[Slicer3:Fiducials_TutorialContestSummer2010 | Fiducials]]

[[Slicer3:RSS_TutorialContestSummer2010 | RSS (Robust Statistics Segmenter)]]

[[Slicer3:Automatic SPHARM Shape Analysis in 3D Slicer_TutorialContestSummer2010 | Automatic SPHARM Shape Analysis in 3D Slicer]]

[[Slicer3:LabelFusion_TutorialContestSummer2010| Atlas Label Fusion & Surface Registration]]

[[Slicer3:Stochastic_tractography| Stochastic Tractography]]

[[Slicer3:ProstateNav_TutorialContestSummer2010| Robot-assisted MRI-guided prostate biopsy]]

[[Slicer3:GAMBIT_TutorialContestSummer2010| GAMBIT: Group-wise Automatic Mesh-Based analysis of cortIcal Thickness]]

[[Slicer3:White Matter Lesion Segmentation_TutorialContestSummer2010| White Matter Lesion Segmentation]]

[[Slicer3:PerkStationModule_TutorialContestSummer2010| Image-overlay Guided Needle Insertion]]

[[Slicer3:FluidMechanicsTractography_TutorialContestSummer2010| Fluid Mechanics Tractography]]

2010 Summer Project Week Diffusion

2010-06-10T19:45:46Z

Nhageman:

__NOTOC__
{|
|[[Image:PW-MIT2010.png|thumb|320px|[[2010_Summer_Project_Week#Projects|Project Week Main Page]] ]]
|[[Image:Hageman_cspfig4NAMIC_07-06-22.png|thumb|320px|Corticospinal tracts segmented using our fluid mechanics based tractography method.]]
|[[Image:Hageman_FullBrainSlicerTractography.jpg|thumb|320px|Full brain tracts segmented using multiple fluid sources/sinks.]]
|[[Image:FMModuleScreenshot.png|thumb|320px|Screenshot of Slicer Module for Fluid Mechanics Tractography.]]
|}

===Key Investigators===
* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D
* Isomics: Steve Pieper and Alex Yarmarkovich

<div style="margin: 20px;">

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

<h1>Objective</h1>
Computational fluid dynamics is a rich field and its application to the analysis of diffusion tensor imaging (DTI) datasets has yielded possible applications to tractography, image registration, and white matter pathology. We are developing several useful and novel diffusion tensor imaging (DTI) analysis algorithms modeled on the principles of fluid mechanics for inclusion within the NA-MIC framework. The goal of this project is to develop these methods, make them compatible with the NA-MIC ITK-based software infrastructure (i.e. Slicer), and promote their dissemination to the scientific community.

See our [[hageman:NAMICFluidMechDTITractography|Project Page]] for more information.

</div>

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

<h1>Approach, Plan</h1>

We have developed and initially validated a DTI tractography method based on Navier-Stokes fluid mechanics. See the papers listed in the reference section for complete details on the method. Our approach for this project week will focus on the following:
* Building the our current CL Slicer module into an interactive GUI in Slicer 3. Our method is currently integrated as a CL Slicer module in a custom build of Slicer 3. The module has the following functionalities:
**reconstruction of the diffusion tensor and computation of common DTI scalar volumes (FA, LI, RGB). In addition, if users prefer using their own tensor reconstruction methods, the module can be run with any arbitrary set of tensor volumes.
**computation of fluid velocity vector field volume
**reconstruction of tracts based on the above fluid velocity volume
** Optimizing initial coding of method in ITK (better use of multithreading)
** Specialized visualization using VTK:
*** Fluid velocity vector field animation
*** Layout for Slicer 3 Plug-in
*** Interactive (real-time) manipulation of sources/sinks (ROIs) on steady-state fluid solution (possible application for intra-operative DTI)
* Working with the interested groups in analyzing control and white matter pathology data. Specifically, we have seen promising results when looking at the flow perturbation around white matter lesions seen in multiple sclerosis or stroke that may suggest a novel method for automatic lesion detection in DTI.
</div>

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

<h1>Progress</h1>
* Command line fluid mechanics tractography module integrated into Slicer 3 (see snapshot above)
* VTK module for fluid mechanics visualization completed.
** Discussion of possibly including module in next stable Slicer release.
** Progress made on (near) real time fluid velocity vector field animation but not yet stable for release.
* Arrangements made to include FM tractography method as part of DTI validation effort.
</div>

<br style="clear: both;" />

</div>

===References===
* Hageman NS, Shattuck DW, Narr K, Toga AW (2006). A diffusion tensor imaging tractography method based on Navier-Stokes fluid mechanics. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2006), Arlington, VA, USA, 6-9 April 2006. p. 798-801
* Hageman NS, Toga AW, Narr K, Shattuck DW (2009). A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics. IEEE Trans. in Medicial Imaging, 28(3): 348-360.

2010 Summer Project Week Diffusion

2010-06-10T19:41:57Z

Nhageman:

{|
|[[Image:PW-MIT2010.png|thumb|320px|[[2010_Summer_Project_Week#Projects|Project Week Main Page]] ]]
|[[Image:Hageman_cspfig4NAMIC_07-06-22.png|thumb|320px|Corticospinal tracts segmented using our fluid mechanics based tractography method.]]
|[[Image:Hageman_FullBrainSlicerTractography.jpg|thumb|320px|Full brain tracts segmented using multiple fluid sources/sinks.]]
|[[Image:FMModuleScreenshot.png|thumb|320px|Screenshot of Slicer Module for Fluid Mechanics Tractography.]]
|}

__NOTOC__

===Key Investigators===
* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D
* Isomics: Steve Pieper and Alex Yarmarkovich

<div style="margin: 20px;">

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

<h1>Objective</h1>
Computational fluid dynamics is a rich field and its application to the analysis of diffusion tensor imaging (DTI) datasets has yielded possible applications to tractography, image registration, and white matter pathology. We are developing several useful and novel diffusion tensor imaging (DTI) analysis algorithms modeled on the principles of fluid mechanics for inclusion within the NA-MIC framework. The goal of this project is to develop these methods, make them compatible with the NA-MIC ITK-based software infrastructure (i.e. Slicer), and promote their dissemination to the scientific community.

See our [[hageman:NAMICFluidMechDTITractography|Project Page]] for more information.

</div>

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

<h1>Approach, Plan</h1>

We have developed and initially validated a DTI tractography method based on Navier-Stokes fluid mechanics. See the papers listed in the reference section for complete details on the method. Our approach for this project week will focus on the following:
* Building the our current CL Slicer module into an interactive GUI in Slicer 3. Our method is currently integrated as a CL Slicer module in a custom build of Slicer 3. The module has the following functionalities:
**reconstruction of the diffusion tensor and computation of common DTI scalar volumes (FA, LI, RGB). In addition, if users prefer using their own tensor reconstruction methods, the module can be run with any arbitrary set of tensor volumes.
**computation of fluid velocity vector field volume
**reconstruction of tracts based on the above fluid velocity volume
** Optimizing initial coding of method in ITK (better use of multithreading)
** Specialized visualization using VTK:
*** Fluid velocity vector field animation
*** Layout for Slicer 3 Plug-in
*** Interactive (real-time) manipulation of sources/sinks (ROIs) on steady-state fluid solution (possible application for intra-operative DTI)
* Working with the interested groups in analyzing control and white matter pathology data. Specifically, we have seen promising results when looking at the flow perturbation around white matter lesions seen in multiple sclerosis or stroke that may suggest a novel method for automatic lesion detection in DTI.
</div>

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

<h1>Progress</h1>
* Command line fluid mechanics tractography module integrated into Slicer 3 (see snapshot above)
* VTK module for fluid mechanics visualization completed.
** Discussion of possibly including module in next stable Slicer release.
** Progress made on (near) real time fluid velocity vector field animation but not yet stable for release.
* Arrangements made to include FM tractography method as part of DTI validation effort.
</div>

<br style="clear: both;" />

</div>

===References===
* Hageman NS, Shattuck DW, Narr K, Toga AW (2006). A diffusion tensor imaging tractography method based on Navier-Stokes fluid mechanics. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2006), Arlington, VA, USA, 6-9 April 2006. p. 798-801
* Hageman NS, Toga AW, Narr K, Shattuck DW (2009). A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics. IEEE Trans. in Medicial Imaging, 28(3): 348-360.

2010 Summer Project Week Diffusion

2010-06-10T19:39:51Z

Nhageman: Created page with '{| |Project Week Main Page ]] |[[Image:Hageman_cspfig4NAMIC_07-06-22.png|thumb|320px|Corticospinal tracts …'

{|
|[[Image:PW2010-v3.png|thumb|320px|[[2010_Summer_Project_Week#Projects|Project Week Main Page]] ]]
|[[Image:Hageman_cspfig4NAMIC_07-06-22.png|thumb|320px|Corticospinal tracts segmented using our fluid mechanics based tractography method.]]
|[[Image:Hageman_FullBrainSlicerTractography.jpg|thumb|320px|Full brain tracts segmented using multiple fluid sources/sinks.]]
|[[Image:FMModuleScreenshot.png|thumb|320px|Screenshot of Slicer Module for Fluid Mechanics Tractography.]]
|}

__NOTOC__

===Key Investigators===
* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D
* Isomics: Steve Pieper and Alex Yarmarkovich

<div style="margin: 20px;">

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

<h1>Objective</h1>
Computational fluid dynamics is a rich field and its application to the analysis of diffusion tensor imaging (DTI) datasets has yielded possible applications to tractography, image registration, and white matter pathology. We are developing several useful and novel diffusion tensor imaging (DTI) analysis algorithms modeled on the principles of fluid mechanics for inclusion within the NA-MIC framework. The goal of this project is to develop these methods, make them compatible with the NA-MIC ITK-based software infrastructure (i.e. Slicer), and promote their dissemination to the scientific community.

See our [[hageman:NAMICFluidMechDTITractography|Project Page]] for more information.

</div>

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

<h1>Approach, Plan</h1>

We have developed and initially validated a DTI tractography method based on Navier-Stokes fluid mechanics. See the papers listed in the reference section for complete details on the method. Our approach for this project week will focus on the following:
* Building the our current CL Slicer module into an interactive GUI in Slicer 3. Our method is currently integrated as a CL Slicer module in a custom build of Slicer 3. The module has the following functionalities:
**reconstruction of the diffusion tensor and computation of common DTI scalar volumes (FA, LI, RGB). In addition, if users prefer using their own tensor reconstruction methods, the module can be run with any arbitrary set of tensor volumes.
**computation of fluid velocity vector field volume
**reconstruction of tracts based on the above fluid velocity volume
** Optimizing initial coding of method in ITK (better use of multithreading)
** Specialized visualization using VTK:
*** Fluid velocity vector field animation
*** Layout for Slicer 3 Plug-in
*** Interactive (real-time) manipulation of sources/sinks (ROIs) on steady-state fluid solution (possible application for intra-operative DTI)
* Working with the interested groups in analyzing control and white matter pathology data. Specifically, we have seen promising results when looking at the flow perturbation around white matter lesions seen in multiple sclerosis or stroke that may suggest a novel method for automatic lesion detection in DTI.
</div>

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

<h1>Progress</h1>
* Command line fluid mechanics tractography module integrated into Slicer 3 (see snapshot above)
* VTK module for fluid mechanics visualization completed.
** Discussion of possibly including module in next stable Slicer release.
** Progress made on (near) real time fluid velocity vector field animation but not yet stable for release.
* Arrangements made to include FM tractography method as part of DTI validation effort.
</div>

<br style="clear: both;" />

</div>

===References===
* Hageman NS, Shattuck DW, Narr K, Toga AW (2006). A diffusion tensor imaging tractography method based on Navier-Stokes fluid mechanics. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2006), Arlington, VA, USA, 6-9 April 2006. p. 798-801
* Hageman NS, Toga AW, Narr K, Shattuck DW (2009). A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics. IEEE Trans. in Medicial Imaging, 28(3): 348-360.

2010 Summer Project Week

2010-06-10T19:38:24Z

Nhageman: /* Projects */

__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==
=== Monday, June 21, 2010 ===
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)

=== Tuesday, June 22, 2010 ===
** 8:30am breakfast
**9-9:45am: NA-MIC Kit Update (Jim Miller) - include Module nomenclature (Extensions: cmdline vs loadable, Built-in), QT, Include Superbuild demo by Dave P.
**9:45-10:30am 3D Slicer Update (Steve Pieper)
**10:30-11am OpenIGTLink Update (Junichi Tokuda)
**11-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
** noon lunch
** 1-3pm: Breakout Session: QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)
** 3pm: [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
** 4-5pm [[2010 Summer Project Week Breakout Session: Data Management]] (Dan Marcus, Stephen Aylward)
** 5:30pm adjourn for day

=== Wednesday, June 23, 2010 ===
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2010 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
**12:45pm: [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
**1-3pm: Breakout Session: [[Microscopy_Image_Analysis]] (Sean Megason)
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:QA Training]] (Luis Ibanez)
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:VTK Widget]] (Nicole, Kilian, JC)
** 5:30pm adjourn for day

=== Thursday, June 24, 2010 ===
** 8:30am breakfast

** 9am-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
** noon lunch
** 1-2pm: [[2010 Summer Project Week Breakout Session:GWE]] (Marco Ruiz)
** 2-2:30pm: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)
** 5:30pm adjourn for day

=== Friday, June 25, 2010 ===
** 8:30am breakfast
** 10am-noon: [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. 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, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)

=== IGT ===
*[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Planning|MR to CT Registration for Prostate Brachytherapy Planning]] (Andriy Fedorov, Dominik Meier, Hans Johnson)
*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 ===
*Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
*Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, 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)
*[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
*[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)

===[[Microscopy Image Analysis]] ===
* Malaterre, Gouaillard: DICOM supplement [ftp://medical.nema.org/medical/dicom/supps/sup145_09.pdf 145]: Microscopy Image in the Dicom Standard
* Laehman, Gouaillard: Microscopy pre-processing extension of ITK: convolution, deconvolution, wavelets and more
* Gouaillard: Flow Cytometry
* [[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)
* [[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)

=== Shape Analysis ===
*[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)
* [[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)

=== Informatics ===
* Computer Aided Photodynamic Therapy (Pietka, Spinczyk)

=== 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)

=== NA-MIC Kit Internals ===
*Module Inventory (Steve, Jim)
*Viewer Manager Factory (Alex Y., 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:XNATE_Client_For_Slicer|XNAT Enterprise webservices client for Slicer]] (Wendy Plesniak, Mark Anderson)
*[[2010_NAMIC_Project_week:Slicer4Icons|Consistent visual language for Slicer4: icon rework marathon]] (Wendy Plesniak)
*[[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)
*Superbuild (Dave Partika, 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>

# Nicole Aucoin , BWH
# Michel Audette , Kitware
# Stephen Aylward , Kitware, Inc
# 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
# 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
# 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.
# Leslie Holton , Medtronic Navigation
# Luis Ibanez , KITWARE Inc.
# Jayender Jagadeesan , SPL
# Hans Johnson , University of Iowa
# Tina Kapur , Brigham and Women's Hospital
# Ron Kikinis , Brigham and Women's Hospital
# Minjeong Kim , UNC-Chapel Hill
# Ivan Kolesov , Georgia Institute of Technology
# Garrett Larson , UNC-CH
# Rui Li , MGH
# Curtis Lisle , KnowledgeVis, LLC
# Haiying Liu , Brigham and Women's Hospital
# 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
# Daniel Marcus , Washington University
# 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
# Raghav Padmanabhan , RPI
# Kannappan Palaniappan , university of Missouri
# Beatriz Paniagua , University of North Caolina at Chapel Hill
# Xenophon Papademetris , Yale University
# David Partyka , Kitware Inc
# Pratik Patel ,
# Sudhir Pathak , Univeristy Of Pittsburgh
# 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
# William Schroeder , Kitware
# Mark Scully , The Mind Research Network
# 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
# Junichi Tokuda , Brigham and Women's Hospital
# Tamas Ungi , Queen's University
# Clement Vachet , UNC Chapel Hill
# Gopalkrishna Veni , SCI Institute
# Demian Wassermann , SPL/LMI/PNL
# Adam Weinrich , Nokia
# Sandy Wells , BWH
# Guorong Wu , University of North Carolina at Chapel Hill
# Alexander Yarmarkovich , ISOMICS
# Alexander Zaitsev , Brigham and Womens Hospital

2010 Summer Project Week

2010-05-14T21:26:55Z

Nhageman: /* Diffusion */

Engineering:UCLA

2009-08-27T20:20:06Z

Nhageman:

#Completed Slicer command-line module for fluid mechanics DTI tractography method (beta testing; release date: September 2009)
#Slicer-BrainLab UCLA Neurosurgery Pilot Study (Initial Meeting with IGT group)
#Attended NAMIC Programming Project Week @ MIT, June 2009
#Attended NAMIC AHM, SLC Utah, January 2009
#Attended NAMIC Programming Project Week @ MIT, June 2008
#Completed ITK compatible fluid mechanics DTI tractography method
#Attended NAMIC AHM, SLC Utah, January 2008
#Attended NAMIC Programming Project Week @ MIT, June 2007
#Attended NAMIC AHM, SLC Utah, January 2007
#Attended NAMIC Programming Project Week @ MIT, June 2006
#Pipeline version 4.0 with Client-Server capabilities now available
#Scalable server which handles 1000's of inputs
#Default visualization component in Pipeline package
#Pipeline Batch mode available - Slicer can now invoke Pipeline in batch-mode with pre-bound workflows
#Integration with IDA, other protocol/software suites in progress
# built NAMIC software [[InstallationPipelines|installation pipelines]]
# attended dissemination workshops [[Dissemination:Workshop_Dec9-10_Boston|2004-12-9 Boston]] and [[Dissemination:Workshop_Feb17-18_2005|2005-2-18 UCSD]]
# attended NAMIC AHM at SLC Utah, January 2006
#Latest build/documentation available at: [http://pipeline.loni.ucla.edu/]
--

Engineering:UCLA

2009-08-27T20:16:49Z

Nhageman:

#Slicer-BrainLab UCLA Neurosurgery Pilot Study (Initial Meeting)
#Attended NAMIC Programming Project Week @ MIT, June 2009
#Attended NAMIC AHM, SLC Utah, January 2009
#Completed Slicer command-line module for fluid mechanics DTI tractography method (beta testing; release date: September 2009)
#Attended NAMIC Programming Project Week @ MIT, June 2008
#Completed ITK compatible fluid mechanics DTI tractography method
#Attended NAMIC AHM, SLC Utah, January 2008
#Attended NAMIC Programming Project Week @ MIT, June 2007
#Attended NAMIC AHM, SLC Utah, January 2007
#Attended NAMIC Programming Project Week @ MIT, June 2006
#Pipeline version 4.0 with Client-Server capabilities now available
#Scalable server which handles 1000's of inputs
#Default visualization component in Pipeline package
#Pipeline Batch mode available - Slicer can now invoke Pipeline in batch-mode with pre-bound workflows
#Integration with IDA, other protocol/software suites in progress
# built NAMIC software [[InstallationPipelines|installation pipelines]]
# attended dissemination workshops [[Dissemination:Workshop_Dec9-10_Boston|2004-12-9 Boston]] and [[Dissemination:Workshop_Feb17-18_2005|2005-2-18 UCSD]]
# attended NAMIC AHM at SLC Utah, January 2006
#Latest build/documentation available at: [http://pipeline.loni.ucla.edu/]
--

2009 Summer Project Week Hageman DTIDigitalPhantom

2009-07-13T14:12:18Z

Nhageman: /* Key Investigators */

{|
|[[Image:PW2009-v3.png|thumb|320px|[[2009_Summer_Project_Week#Projects|Project Week Main Page]] ]]
|[[Image:Hageman_DWIPhantomWebPage4NAMIC_09-06-13.jpg|thumb|320px|Web service for DWI phantom generator hosted by UCLA]]
|[[Image:Hageman_DWIPhantomForm4NAMIC_09-06-13.jpg|thumb|320px|Form used by web service to generate phantom DWI dataset]]
|}

__NOTOC__

===Key Investigators===
* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D

<div style="margin: 20px;">

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

<h1>Objective</h1>
Imaging datasets constructed from digital phantom models continue to be valuable resource for validating image analysis algorithms. There is a need for such resources for the validation of DTI analysis algorithms, especially for those methods that involve measures of WM integrity or segmentation of WM tracts. Although some fixed digital DTI phantom models exist, we have created a software tool that allows users to generate a DWI dataset from a ground truth WM shape based on their own chosen experimental paradigm. This will provide users with the flexibility to define the parameters of each validation dataset, which is not available with current digital DTI phantom validation resources.

The current version of the program that will generate a DWI dataset based on a single or double helix ground truth that simulates a white matter tract. The user is free to specify desired dimensions, experimental parameters, and level of Rician or Gaussian noise in the final dataset. We will host this program via a webservice from the Laboratory of Neuroimaging at UCLA.
</div>

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

<h1>Approach, Plan</h1>
The functioning webservice and binaries are scheduled for an external release in July 2009. For this project week,
*We will demo the program and webservice utility or generate specific datasets for any interested groups. Pre-release binaries are available upon request.
*We will discuss possible links to the webservice as part of Slicer and NAMIC Wiki.

</div>

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

<h1>Progress</h1>
*Interested collaborators met concerning release date of web service and binaries.
*Discussion about incorporation of web service into Slicer and NAMIC Wiki.
</div>

<br style="clear: both;" />

</div>

===References===
* Hageman NS, Shattuck DW, Narr K, Toga AW (2006). A diffusion tensor imaging tractography method based on Navier-Stokes fluid mechanics. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2006), Arlington, VA, USA, 6-9 April 2006. p. 798-801
* Hageman NS, Toga AW, Narr K, Shattuck DW (2009). A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics. IEEE Trans. in Medicial Imaging 28(3): 348-360.

2009 Summer Project Week Hageman FMTractography

2009-07-13T14:02:49Z

Nhageman: /* Key Investigators */

{|
|[[Image:PW2009-v3.png|thumb|320px|[[2009_Summer_Project_Week#Projects|Project Week Main Page]] ]]
|[[Image:Hageman_cspfig4NAMIC_07-06-22.png|thumb|320px|Corticospinal tracts segmented using our fluid mechanics based tractography method.]]
|[[Image:Hageman_FullBrainSlicerTractography.jpg|thumb|320px|Full brain tracts segmented using multiple fluid sources/sinks.]]
|[[Image:FMModuleScreenshot.png|thumb|320px|Screenshot of Slicer Module for Fluid Mechanics Tractography.]]
|}

__NOTOC__

===Key Investigators===
* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D
* Isomics: Steve Pieper and Alex Yarmarkovich

<div style="margin: 20px;">

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

<h1>Objective</h1>
Computational fluid dynamics is a rich field and its application to the analysis of diffusion tensor imaging (DTI) datasets has yielded possible applications to tractography, image registration, and white matter pathology. We are developing several useful and novel diffusion tensor imaging (DTI) analysis algorithms modeled on the principles of fluid mechanics for inclusion within the NA-MIC framework. The goal of this project is to develop these methods, make them compatible with the NA-MIC ITK-based software infrastructure (i.e. Slicer), and promote their dissemination to the scientific community.

See our [[hageman:NAMICFluidMechDTITractography|Project Page]] for more information.

</div>

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

<h1>Approach, Plan</h1>

We have developed and initially validated a DTI tractography method based on Navier-Stokes fluid mechanics. See the papers listed in the reference section for complete details on the method. Our approach for this project week will focus on the following:
* Building the our current CL Slicer module into an interactive GUI in Slicer 3. Our method is currently integrated as a CL Slicer module in a custom build of Slicer 3. The module has the following functionalities:
**reconstruction of the diffusion tensor and computation of common DTI scalar volumes (FA, LI, RGB). In addition, if users prefer using their own tensor reconstruction methods, the module can be run with any arbitrary set of tensor volumes.
**computation of fluid velocity vector field volume
**reconstruction of tracts based on the above fluid velocity volume
** Optimizing initial coding of method in ITK (better use of multithreading)
** Specialized visualization using VTK:
*** Fluid velocity vector field animation
*** Layout for Slicer 3 Plug-in
*** Interactive (real-time) manipulation of sources/sinks (ROIs) on steady-state fluid solution (possible application for intra-operative DTI)
* Working with the interested groups in analyzing control and white matter pathology data. Specifically, we have seen promising results when looking at the flow perturbation around white matter lesions seen in multiple sclerosis or stroke that may suggest a novel method for automatic lesion detection in DTI.
</div>

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

<h1>Progress</h1>
* Command line fluid mechanics tractography module integrated into Slicer 3 (see snapshot above)
* VTK module for fluid mechanics visualization completed.
** Discussion of possibly including module in next stable Slicer release.
** Progress made on (near) real time fluid velocity vector field animation but not yet stable for release.
* Arrangements made to include FM tractography method as part of DTI validation effort.
</div>

<br style="clear: both;" />

</div>

===References===
* Hageman NS, Shattuck DW, Narr K, Toga AW (2006). A diffusion tensor imaging tractography method based on Navier-Stokes fluid mechanics. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2006), Arlington, VA, USA, 6-9 April 2006. p. 798-801
* Hageman NS, Toga AW, Narr K, Shattuck DW (2009). A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics. IEEE Trans. in Medicial Imaging, 28(3): 348-360.

2009 Summer Project Week Hageman FMTractography

2009-06-21T08:57:04Z

Nhageman:

{|
|[[Image:PW2009-v3.png|thumb|320px|[[2009_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:Hageman_cspfig4NAMIC_07-06-22.png|thumb|320px|Corticospinal tracts segmented using our fluid mechanics based tractography method.]]
|[[Image:Hageman_FullBrainSlicerTractography.jpg|thumb|320px|Full brain tracts segmented using multiple fluid sources/sinks.]]
|[[Image:FMModuleScreenshot.png|thumb|320px|Screenshot of Slicer Module for Fluid Mechanics Tractography.]]
|}

__NOTOC__

===Key Investigators===
* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D
* Isomics: Steve Pieper and Alex Yarmarkovich

<div style="margin: 20px;">

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

<h1>Objective</h1>
Computational fluid dynamics is a rich field and its application to the analysis of diffusion tensor imaging (DTI) datasets has yielded possible applications to tractography, image registration, and white matter pathology. We are developing several useful and novel diffusion tensor imaging (DTI) analysis algorithms modeled on the principles of fluid mechanics for inclusion within the NA-MIC framework. The goal of this project is to develop these methods, make them compatible with the NA-MIC ITK-based software infrastructure (i.e. Slicer), and promote their dissemination to the scientific community.

See our [[hageman:NAMICFluidMechDTITractography|Project Page]] for more information.

</div>

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

<h1>Approach, Plan</h1>

We have developed and initially validated a DTI tractography method based on Navier-Stokes fluid mechanics. See the papers listed in the reference section for complete details on the method. Our approach for this project week will focus on the following:
* Building the our current CL Slicer module into an interactive GUI in Slicer 3. Our method is currently integrated as a CL Slicer module in a custom build of Slicer 3. The module has the following functionalities:
**reconstruction of the diffusion tensor and computation of common DTI scalar volumes (FA, LI, RGB). In addition, if users prefer using their own tensor reconstruction methods, the module can be run with any arbitrary set of tensor volumes.
**computation of fluid velocity vector field volume
**reconstruction of tracts based on the above fluid velocity volume
** Optimizing initial coding of method in ITK (better use of multithreading)
** Specialized visualization using VTK:
*** Fluid velocity vector field animation
*** Layout for Slicer 3 Plug-in
*** Interactive (real-time) manipulation of sources/sinks (ROIs) on steady-state fluid solution (possible application for intra-operative DTI)
* Working with the interested groups in analyzing control and white matter pathology data. Specifically, we have seen promising results when looking at the flow perturbation around white matter lesions seen in multiple sclerosis or stroke that may suggest a novel method for automatic lesion detection in DTI.
</div>

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

<h1>Progress</h1>
</div>

<br style="clear: both;" />

</div>

===References===
* Hageman NS, Shattuck DW, Narr K, Toga AW (2006). A diffusion tensor imaging tractography method based on Navier-Stokes fluid mechanics. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2006), Arlington, VA, USA, 6-9 April 2006. p. 798-801
* Hageman NS, Toga AW, Narr K, Shattuck DW (2009). A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics. IEEE Trans. in Medicial Imaging, 28(3): 348-360.

2009 Summer Project Week Hageman FMTractography

2009-06-21T08:55:24Z

Nhageman:

{|
|[[Image:PW2009-v3.png|thumb|320px|[[2009_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:Hageman_cspfig4NAMIC_07-06-22.png|thumb|320px|Corticospinal tracts segmented using our fluid mechanics based tractography method.]]
|[[Image:Hageman_FullBrainSlicerTractography.jpg|thumb|320px|Full brain tracts segmented using multiple fluid sources/sinks.]]
|[[Image:FMModuleScreenshot.png|thumb|320px|Screenshot of Slicer Module for Fluid Mechanics Tractography.]]
|}

__NOTOC__

===Key Investigators===
* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D
* Isomics: Steve Pieper and Alex Yarmarkovich

<div style="margin: 20px;">

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

<h1>Objective</h1>
Computational fluid dynamics is a rich field and its application to the analysis of diffusion tensor imaging (DTI) datasets has yielded possible applications to tractography, image registration, and white matter pathology. We are developing several useful and novel diffusion tensor imaging (DTI) analysis algorithms modeled on the principles of fluid mechanics for inclusion within the NA-MIC framework. The goal of this project is to develop these methods, make them compatible with the NA-MIC ITK-based software infrastructure (i.e. Slicer), and promote their dissemination to the scientific community.

See our [[hageman:NAMICFluidMechDTITractography|Project Page]] for more information.

</div>

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

<h1>Approach, Plan</h1>

We have developed and initially validated a DTI tractography method based on Navier-Stokes fluid mechanics. See the papers listed in the reference section for complete details on the method. Our approach for this project week will focus on the following:
* Building the our current CL Slicer module into an interactive GUI in Slicer 3. Our method is currently integrated as a CL Slicer module in a custom build of Slicer 3. The module has the following functionalities:
**reconstruction of the diffusion tensor and computation of common DTI scalar volumes (FA, LI, RGB). In addition, if users prefer using their own tensor reconstruction methods, the module can be run with any arbitrary set of tensor volumes.
**computation of fluid velocity vector field volume
**reconstruction of tracts based on the above fluid velocity volume
** Optimizing initial coding of method in ITK (better use of multithreading)
** Specialized visualization using VTK:
*** Fluid velocity vector field animation
*** Layout for Slicer 3 Plug-in
*** Interactive (real-time) manipulation of sources/sinks (ROIs) on steady-state fluid solution (possible application for intra-operative DTI)
* Working with the interested groups in analyzing control and white matter pathology data. Specifically, we have seen promising results when looking at the flow perturbation around white matter lesions seen in multiple sclerosis or stroke that may suggest a novel method for automatic lesion detection in DTI.
</div>

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

<h1>Progress</h1>
* Command line fluid mechanics tractography module integrated into Slicer 3 (see snapshot above)
* VTK module for fluid mechanics visualization completed.
** Discussion of possibly including module in next stable Slicer release.
** Progress made on (near) real time fluid velocity vector field animation but not yet stable for release.
* Arrangements made to include FM tractography method as part of DTI validation effort.
</div>

<br style="clear: both;" />

</div>

===References===
* Hageman NS, Shattuck DW, Narr K, Toga AW (2006). A diffusion tensor imaging tractography method based on Navier-Stokes fluid mechanics. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2006), Arlington, VA, USA, 6-9 April 2006. p. 798-801
* Hageman NS, Toga AW, Narr K, Shattuck DW (2009). A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics. IEEE Trans. in Medicial Imaging, 28(3): 348-360.

2009 Summer Project Week Hageman DTIDigitalPhantom

2009-06-21T08:49:36Z

Nhageman:

{|
|[[Image:PW2009-v3.png|thumb|320px|[[2009_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:Hageman_DWIPhantomWebPage4NAMIC_09-06-13.jpg|thumb|320px|Web service for DWI phantom generator hosted by UCLA]]
|[[Image:Hageman_DWIPhantomForm4NAMIC_09-06-13.jpg|thumb|320px|Form used by web service to generate phantom DWI dataset]]
|}

__NOTOC__

===Key Investigators===
* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D

<div style="margin: 20px;">

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

<h1>Objective</h1>
Imaging datasets constructed from digital phantom models continue to be valuable resource for validating image analysis algorithms. There is a need for such resources for the validation of DTI analysis algorithms, especially for those methods that involve measures of WM integrity or segmentation of WM tracts. Although some fixed digital DTI phantom models exist, we have created a software tool that allows users to generate a DWI dataset from a ground truth WM shape based on their own chosen experimental paradigm. This will provide users with the flexibility to define the parameters of each validation dataset, which is not available with current digital DTI phantom validation resources.

The current version of the program that will generate a DWI dataset based on a single or double helix ground truth that simulates a white matter tract. The user is free to specify desired dimensions, experimental parameters, and level of Rician or Gaussian noise in the final dataset. We will host this program via a webservice from the Laboratory of Neuroimaging at UCLA.
</div>

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

<h1>Approach, Plan</h1>
The functioning webservice and binaries are scheduled for an external release in early July 2009. For this project week,
*We will demo the program and webservice utility or generate specific datasets for any interested groups. Pre-release binaries are available upon request.
*We will discuss possible links to the webservice as part of Slicer and NAMIC Wiki.

</div>

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

<h1>Progress</h1>

</div>

<br style="clear: both;" />

</div>

===References===
* Hageman NS, Shattuck DW, Narr K, Toga AW (2006). A diffusion tensor imaging tractography method based on Navier-Stokes fluid mechanics. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2006), Arlington, VA, USA, 6-9 April 2006. p. 798-801
* Hageman NS, Toga AW, Narr K, Shattuck DW (2009). A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics. IEEE Trans. in Medicial Imaging 28(3): 348-360.

2009 Summer Project Week Hageman DTIDigitalPhantom

2009-06-21T08:35:56Z

Nhageman:

2009 Summer Project Week Hageman DTIDigitalPhantom

2009-06-21T08:32:23Z

Nhageman:

File:Hageman DWIPhantomForm4NAMIC 09-06-13.jpg

2009-06-21T08:27:24Z

Nhageman:

2009 Summer Project Week Hageman DTIDigitalPhantom

2009-06-21T08:25:56Z

Nhageman:

{|
|[[Image:PW2009-v3.png|thumb|320px|[[2009_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:Hageman_DWIPhantomWebPage4NAMIC_09-06-13.jpg|thumb|320px|Web service for DWI phantom generator hosted by UCLA]]
|}

__NOTOC__

===Key Investigators===
* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D

<div style="margin: 20px;">

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

<h1>Objective</h1>
We have created a software tool to generate DWI datasets from a predefined phantom shape.
</div>

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

<h1>Approach, Plan</h1>

</div>

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

<h1>Progress</h1>

</div>

<br style="clear: both;" />

</div>

===References===
* Hageman NS, Shattuck DW, Narr K, Toga AW (2006). A diffusion tensor imaging tractography method based on Navier-Stokes fluid mechanics. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2006), Arlington, VA, USA, 6-9 April 2006. p. 798-801
* Hageman NS, Toga AW, Narr K, Shattuck DW (2008). A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics. IEEE Trans. in Medicial Imaging, In Submission.

File:Hageman DWIPhantomWebPage4NAMIC 09-06-13.jpg

2009-06-21T08:23:13Z

Nhageman:

2009 Summer Project Week Hageman DTIDigitalPhantom

2009-06-21T08:21:10Z

Nhageman:

2009 Summer Project Week

2009-06-18T11:47:55Z

Nhageman: /* Attendee List */

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

[[Image:PW2009-v3.png|300px]]

*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. 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 will begin on''' Thursday, April 16th 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 that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

== Agenda==
* Monday
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
**9:30-10am: NA-MIC Kit Overview (Jim Miller)
** 10-10:30am Slicer 3.4 Update (Steve Pieper)
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)
** noon lunch
** 2:30pm-4pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis)
** 4:30pm CIMIT Forum (at BWH Shapiro Center) Open Source Software for Translational IGT Research and Commercial Use, Clif Burdette, Acoustic MedSystems, Inc.
At BWH / Carl J. and Ruth Shapiro Cardiovascular Cente

** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (Alex G.)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** 9-11am [[Events:TutorialContestJune2009|Tutorial Contest Presentations]]
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT for Programmers]] (Dan M.)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. 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_2010|in Utah, January 4-8, 2010]]

== Projects ==

#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline]] (Clement Vachet UNC)
#[[2009_Summer_Project_Week_Lupus_Lesion_Segmentation |Lupus Lesion Segmentation]] (Jeremy Bockholt MRN)
#[[Summer2009:VCFS|Stochastic Tractography to study VCFS and Schizophrenia]] (Marek Kubicki BWH)
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images|Segmentation of Knee Structures]] (Harish Doddi Stanford)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Ziv Yaniv Georgetown)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan Virginia Tech)
#[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim UNC)
#[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Snehasish Roy JHU)
# [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt Lisle Knowledge Vis)
#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp MGH)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|SLicer3, BioImage Suite and Brainlab - Introduction and Demo to UCLA]] (Haiying Liu BWH)
#[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Segmentation of thalamic nuclei from DTI]] (Ion-Florin Talos BWH)
#[[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev BWH)
#[[2009_Summer_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep | DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu UNC)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom | DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao Utah)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Andrey Fedorov BWH)
#[[EMSegment|EM Segment]] (Sylvain Jaume MIT, Nicolas Rannou BWH)
#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Andrey Fedorov BWH)
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel Prastawa Utah)
#[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu UNC)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez Kitware)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber Utah)
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze MIT)
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer |Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace Robarts Institute)
# [[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian Robarts Institute)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor Robarts Institute)
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve Pieper BWH)
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal BWH)
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with Slicer python]] (Julien de Siebenthal BWH)
# [[Summer2009:Using_cython| Accelerating python with cython: application to stochastic tractography]] (Julien de Siebenthal BWH)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole Aucoin BWH)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole Aucoin BWH)
# [[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang Siemens Research)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wendy Plesniak BWH)
# [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andrey Fedorov BWH)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn BWH)
# [[Summer2009:Extension of the Command Line XML Syntax/Interface | Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)
#[[2009_Summer_Project_Week_Slicer3_XNAT_UI | XNAT user interface improvements for NA-MIC]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNATFS | XNAT File System with FUSE]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong Harvard)
#[[2009_Summer_Project_Week_GWE_XNAT | GWE-XNAT Integration]] (Marco Ruiz UCSD)
#[[2009_Summer_Project_Week_Slicer3_registration| Slicer 3 registration ]] (Andrew Rausch)
#[[2009_Summer_Project_Week_Transrectal_Prostate_biopsy|Transrectal Prostate Biopsy]] (Andras Lasso Queen's)
#[[2009_Summer_Project_Week_3DGRASE|3D GRASE]] (Scott Hoge BWH)
#[[2009_Summer_Project_Week_TrigeminalNerve|Atlas to CT Registration in Trigeminal Neuralgia]] (Marta Peroni PoliMI, Maria Francesca Spadea UMG, Greg Sharp MGH)
#[[2009_Summer_Project_Week_FunctionalClusteringAnalysis|Functional Analysis of White Matter in Whole Brain Clustering of Schizophrenic Patients]] (Doug Terry, Marek Kubicki BWH)
#[[2009_Summer_Project_Week_Slicer|Integration of Flexible Surgical Instrument Modeling and Virtual Catheter with Slicer]] (Jayender Jagadeesan BWH)
#[[2009_Summer_Project_Week_Orthogonal_Reformat_Widget|Orthogonal Planes in Reformat Widget]] (Michal Depa MIT)
#[[2009_Summer_Project_Week_New_ITK_Level_Set_Framework|New Level Framework in ITK]] (Arnaud Gelas, Harvard Medical School)
#[[2009_Summer_Project_Week_TubularSurfaceSeg|Tubular Surface Segmentation in Slicer]] (Vandana Mohan, Georgia Tech)
#[[2009_Summer_project_week_prostate_registration|Prostate Registration Slicer Module]] (Yi Gao, Georgia Tech)
#[[2009_Summer_Project_Week_RTHawk_MR_Navigation|Using RTHawk to Implement MR Navigation]]

===CUDA Projects===

This is a list of candidate cuda projects that will be discussed with Joe Stam shortly:

#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Tina Kapur BWH)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor Robarts Institute)
#[[2009_Summer_Project_Week_Dose_Calculation |accelerate calculation for LDR seeds]] (Jack Blevins Acousticmed)
#[[2009_Summer_Project_Week_Cone_Beam_backprojection]](Zhou Shen U Michigan)
#[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan U Michigan)
#[[Summer2009:Using_CUDA_for_stochastic_tractography|Developing interactive stochastic tractography using CUDA]] (Julien de Siebenthal BWH)
#acceleration of parallel real time processing of strain and elasticity images for monitoring of ablative therapy (Clif Burdette Acousticmed)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 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 18, 2009: 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. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# 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-3-4/#dirlist Slicer-3-4 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].

== Logistics ==
*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.
*'''Registration Method''' Add your name to the Attendee List section of this page
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.
*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.
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]
==Attendee List==

'''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''

{|
|-
|
{|
!#
|----
|1
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|2
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|}
|
{| class="wikitable sortable"
!First
!Last
!Affiliation
|----
|John
|Melonakos
|AccelerEyes (Wed & Thu morning)
|----
|Jack
|Blevins
|Acoustic Med
|----
|Clif
|Burdette
|Acoustic Med (Mon-Wed)
|----
|Dana
|Peters
|Beth Israel Deaconess
|----
|Nicole
|Aucoin
|BWH (NAMIC)
|----
|Giovanna
|Danagoulian
|BWH (NCIGT Collaborator)
|----
|Haytham
|Elhawary
|BWH (NCIGT Collaborator)
|----
|Andriy
|Fedorov
|BWH (NAMIC Collaborator)
|----
|Daniel
|Haehn
|BWH (NAC)
|----
|Michael
|Halle
|BWH (NAC)
|----
|Nobuhiko
|Hata
|BWH (NCIGT)
|----
|Katie
|Hayes
|BWH (NAMIC)
|----
|Scott
|Hoge
|BWH (NCIGT)
|----
|Tina
|Kapur
|BWH (NCIGT, NAMIC)
|----
|Ron
|Kikinis
|BWH (NAMIC, NAC, NCIGT)
|----
|Jayender
|Jagadeesan
|BWH (NCIGT Collaborator)
|----
|Haying
|Liu
|BWH (NCIGT)
|----
|Lauren
|O'Donnell
|BWH (NCIGT)
|----
|Wendy
|Plesniak
|BWH (NAC)
|----
|Megumi
|Nakao
|BWH (NAIST)
|----
|Sonia
|Pujol
|BWH (NAMIC)
|----
|Lei
|Qin
|BWH (NCIGT Collaborator)
|----
|Nicolas
|Rannou
|BWH (NAC)
|----
|Petter
|Risholm
|BWH (NCIGT)
|----
|Florin
|Talos
|BWH (NAC)
|----
|Clare
|Tempany
|BWH (NCIGT)
|----
|Junichi
|Tokuda
|BWH (NCIGT)
|----
|Demian
|Wasserman
|BWH (INRIA)
|----
|Carl-Fredrik
|Westin
|BWH (NAC)
|----
|Sandy
|Wells
|BWH (NAC, NCIGT)
|----
|Lilla
|Zollei
|MGH (NAC)
|----
|Padma
|Akella
|BWH (NCIGT)
|----
|Sylvain
|Bouix
|BWH (PNL)
|----
|Julien
|de Siebenthal
|BWH (PNL)
|----
|Marek
|Kubicki
|BWH (NAMIC DBP PNL)
|----
|Juhana
|Frosen
|BWH Tues only
|----
|Sun Woo
|Lee
|BWH (PNL)
|----
|Jimi
|Malcolm
|BWH (PNL)
|----
|Eric
|Melonakos
|BWH (PNL)
|----
|Yogesh
|Rathi
|BWH (PNL)
|----
|Peter
|Savadjiev
|BWH (PNL)
|----
|Doug
|Terry
|BWH (PNL)
|----
|Andrew
|Rausch
|BWH (Mon only)
|----
|Cal
|Hisley
|Des Moines Unive
|----
|Jim
|Miller
|GE
|----
|Xiaodong
|Tao
|GE
|----
|Vandana
|Mohan
|GA Tech
|----
|Yi
|Gao
|GA Tech
|----
|Ivan
|Kolosev
|GA Tech
|----
|Behnood
|Gholami
|GA Tech
|----
|Ziv
|Yaniv
|Georgetown
|----
|Alex
|Gouaillard
|Harvard Systems Biology
|----
|Arnaud
|Gelas
|Harvard Systems Biology
|----
|Sean
|Megason
|Harvard Systems Biology (Wed only)
|----
|Lydie
|Souhait
|Harvard Systems Biology
|----
|Moti
|Freiman
|Hebrew University of Jerusalem
|----
|Amanda
|Peters
|Harvard SEAS
|----
|Maria Francesca
|Spadea
|Italy
|----
|Curtis
|Lisle
|KnowledgeVis
|----
|Steve
|Pieper
|Isomics
|----
|Alex
|Yarmarkovich
|Isomics
|----
|Nathan
|Cho
|JHU
|----
|Bennett
|Landman
|JHU
|----
|Snehashis
|Roy
|JHU
|----
|Sam
|Song
|JHU
|----
|Sebastien
|Barre
|Kitware
|----
|Luis
|Ibanez
|Kitware
|----
|Daniel
|Blezek
|Mayo
|----
|Yong
|Gao
|MGH
|----
|Randy
|Gollub
|MGH
|----
|Rui
|Li
|MGH
|----
|Greg
|Sharp
|MGH
|----
|Robert
|Yaffe
|MGH - Mon
|----
|Sylvain
|Jaume
|MIT
|----
|Bjoern
|Menze
|MIT
|----
|Jeremy
|Bockholt
|MRN (NAMIC Lupus DBP)
|----
|Mark
|Scully
|MRN (NAMIC Lupus DBP) Tue-Th
|----
|Joe
|Stam
|NVIDIA (Wed & Thurs)
|----
|Kimberly
|Powell
|NVIDIA (Wed)
|----
|Marta
|Peroni
|Politecnico di Milano
|----
|Andras
|Lasso
|Queen's (NAMIC DBP)
|----
|Yanling
|Liu
|SAIC/NCI-Frederick
|----
|Melanie
|Grebe
|Siemens Corporate Research
|----
|Lining
|Yang
|Siemens Corporate Research
|----
|Harish
|Doddi
|Stanford University
|----
|Marco
|Ruiz
|UCSD
|----
|Nathan
|Hageman
|UCLA (Mon-Thurs)
|----
|Hans
|Johnson
|U Iowa
|----
|Vincent
|Magnotta
|U Iowa
|----
|Jeffrey
|Yager
|U Iowa
|----
|Manasi
|Ramachandran
|U Iowa
|----
|Dave
|Welch
|U Iowa
|----
|Andrzej
|Przybyszewski
|UMass Med (Mon)
|----
|James
|Balter
|U Michigan
|----
|Dan
|McShan
|U Michigan
|----
|Zhou
|Shen
|U Michigan
|----
|Beatriz
|Paniagua
|UNC
|----
|Minjeong
|Kim
|UNC
|----
|Zhexing
|Liu
|UNC
|----
|Clement
|Vachet
|UNC (NAMIC DBP)
|----
|Guorong
|Wu
|UNC
|----
|Samuel
|Gerber
|SCI, Utah
|----
|Ran
|Tao
|SCI, Utah
|----
|Marcel
|Prastawa
|SCI, Utah
|----
|Ross
|Whitaker
|SCI, Utah
|----
|Curtis
|Rueden
|UW-Madison
|----
|Dan
|Marcus
|WUSTL
|----
|Misha
|Milchenko
|WUSTL
|----
|Kevin
|Archie
|WUSTL
|----
|Tim
|Olsen
|WUSTL
|----
|Mehdi
|Esteghamatian
|Robarts Research Inst. / Western Ontario
|----
|Diego
|Cantor
|Robarts Research Inst. / Western Ontario
|----
|Danielle
|Pace
|Robarts Research Inst. / Western Ontario
|----
|Vidya
|Rajagopalan
|VA Tech
|----
|Gregory
|Fischer
|WPI
|----
|Dominique
|Belhachemi
|Yale U (Tu & Wed)
|----
|Alark
|Joshi
|Yale U (Tu & Wed)
|----
|Xenios
|Papademetris
|Yale U (Tu & Wed)
|----
|Dustin
|Scheinost
|Yale U (Tu & Wed)
|----
|Michelle
|Borkin
|Harvard SEAS (Mon only)
|----
|Renxin
|Chu
|BWH (NCIGT) (Mon, Tue)
|----
|Ben
|Schwartz
|BWH (NCIGT) (Mon, Tue)
|----
|Marianna
|Jakab
|BWH (NCIGT, NAC) (Mon, Tue)
|----
|Viswanath
|Avasarala
|GE (Wed, Thurs)
|}
|}

'''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''

The following was used to convert from excel to mediawiki markup: http://area23.brightbyte.de/csv2wp.php

2009 Summer Project Week Hageman DTIDigitalPhantom

2009-06-04T17:13:03Z

Nhageman:

{|
|[[Image:PW2009-v3.png|thumb|320px|[[2009_Summer_Project_Week|Project Week Main Page]] ]]
|}

__NOTOC__

===Key Investigators===
* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D

<div style="margin: 20px;">

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

<h1>Objective</h1>
We have created a software tool to generate DWI datasets from a predefined phantom shape.
</div>

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

<h1>Approach, Plan</h1>

</div>

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

<h1>Progress</h1>

</div>

<br style="clear: both;" />

</div>

===References===
* Hageman NS, Shattuck DW, Narr K, Toga AW (2006). A diffusion tensor imaging tractography method based on Navier-Stokes fluid mechanics. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2006), Arlington, VA, USA, 6-9 April 2006. p. 798-801
* Hageman NS, Toga AW, Narr K, Shattuck DW (2008). A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics. IEEE Trans. in Medicial Imaging, In Submission.

2009 Summer Project Week Hageman FMTractography

2009-06-04T17:10:08Z

Nhageman:

{|
|[[Image:PW2009-v3.png|thumb|320px|[[2009_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:Hageman_cspfig4NAMIC_07-06-22.png|thumb|320px|Corticospinal tracts segmented using our fluid mechanics based tractography method.]]
|[[Image:Hageman_FullBrainSlicerTractography.jpg|thumb|320px|Full brain tracts segmented using multiple fluid sources/sinks.]]
|[[Image:FMModuleScreenshot.png|thumb|320px|Screenshot of Slicer Module for Fluid Mechanics Tractography.]]
|}

__NOTOC__

===Key Investigators===
* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D
* Isomics: Steve Pieper and Alex Yarmarkovich

<div style="margin: 20px;">

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

<h1>Objective</h1>
Computational fluid dynamics is a rich field and its application to the analysis of diffusion tensor imaging (DTI) datasets has yielded possible applications to tractography, image registration, and white matter pathology. We are developing several useful and novel diffusion tensor imaging (DTI) analysis algorithms modeled on the principles of fluid mechanics for inclusion within the NA-MIC framework. The goal of this project is to develop these methods, make them compatible with the NA-MIC ITK-based software infrastructure (i.e. Slicer), and promote their dissemination to the scientific community.

See our [[hageman:NAMICFluidMechDTITractography|Project Page]] for more information.

</div>

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

<h1>Approach, Plan</h1>

We have developed and initially validated a DTI tractography method based on Navier-Stokes fluid mechanics. See the papers listed in the reference section for complete details on the method. Our approach for this project week will focus on the following:
* Building the our current CL Slicer module into an interactive GUI in Slicer 3. Our method is currently integrated as a CL Slicer module in a custom build of Slicer 3. The module has the following functionalities:
**reconstruction of the diffusion tensor and computation of common DTI scalar volumes (FA, LI, RGB). In addition, if users prefer using their own tensor reconstruction methods, the module can be run with any arbitrary set of tensor volumes.
**computation of fluid velocity vector field volume
**reconstruction of tracts based on the above fluid velocity volume
** Optimizing initial coding of method in ITK (better use of multithreading)
** Specialized visualization using VTK:
*** Fluid velocity vector field animation
*** Layout for Slicer 3 Plug-in
*** Interactive (real-time) manipulation of sources/sinks (ROIs) on steady-state fluid solution (possible application for intra-operative DTI)
* Working with the interested groups in analyzing control and white matter pathology data. Specifically, we have seen promising results when looking at the flow perturbation around white matter lesions seen in multiple sclerosis or stroke that may suggest a novel method for automatic lesion detection in DTI.
</div>

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

<h1>Progress</h1>
* Command line fluid mechanics tractography module integrated into Slicer 3 (see snapshot above)
* VTK module for fluid mechanics visualization completed.
** Discussion of possibly including module in next stable Slicer release.
** Progress made on (near) real time fluid velocity vector field animation but not yet stable for release.
* Arrangements made to include FM tractography method as part of DTI validation effort.
</div>

<br style="clear: both;" />

</div>

===References===
* Hageman NS, Shattuck DW, Narr K, Toga AW (2006). A diffusion tensor imaging tractography method based on Navier-Stokes fluid mechanics. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2006), Arlington, VA, USA, 6-9 April 2006. p. 798-801
* Hageman NS, Toga AW, Narr K, Shattuck DW (2008). A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics. IEEE Trans. in Medicial Imaging, In Submission.
* Hamilton L, Nuechterlein K, Hageman NS, Woods R, Asarnow R, Alger J, Gaser C, Toga AW, Narr K (2008). Mean Diffusivity and Fractional Anisotropy as Indicators of Schizophrenia and Genetic Vulnerability, Neuroimage, In Submission.

2009 Summer Project Week Hageman FMTractography

2009-06-04T17:09:50Z

Nhageman:

{|
|[[Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:Hageman_cspfig4NAMIC_07-06-22.png|thumb|320px|Corticospinal tracts segmented using our fluid mechanics based tractography method.]]
|[[Image:Hageman_FullBrainSlicerTractography.jpg|thumb|320px|Full brain tracts segmented using multiple fluid sources/sinks.]]
|[[Image:FMModuleScreenshot.png|thumb|320px|Screenshot of Slicer Module for Fluid Mechanics Tractography.]]
|}

__NOTOC__

===Key Investigators===
* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D
* Isomics: Steve Pieper and Alex Yarmarkovich

<div style="margin: 20px;">

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

<h1>Objective</h1>
Computational fluid dynamics is a rich field and its application to the analysis of diffusion tensor imaging (DTI) datasets has yielded possible applications to tractography, image registration, and white matter pathology. We are developing several useful and novel diffusion tensor imaging (DTI) analysis algorithms modeled on the principles of fluid mechanics for inclusion within the NA-MIC framework. The goal of this project is to develop these methods, make them compatible with the NA-MIC ITK-based software infrastructure (i.e. Slicer), and promote their dissemination to the scientific community.

See our [[hageman:NAMICFluidMechDTITractography|Project Page]] for more information.

</div>

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

<h1>Approach, Plan</h1>

We have developed and initially validated a DTI tractography method based on Navier-Stokes fluid mechanics. See the papers listed in the reference section for complete details on the method. Our approach for this project week will focus on the following:
* Building the our current CL Slicer module into an interactive GUI in Slicer 3. Our method is currently integrated as a CL Slicer module in a custom build of Slicer 3. The module has the following functionalities:
**reconstruction of the diffusion tensor and computation of common DTI scalar volumes (FA, LI, RGB). In addition, if users prefer using their own tensor reconstruction methods, the module can be run with any arbitrary set of tensor volumes.
**computation of fluid velocity vector field volume
**reconstruction of tracts based on the above fluid velocity volume
** Optimizing initial coding of method in ITK (better use of multithreading)
** Specialized visualization using VTK:
*** Fluid velocity vector field animation
*** Layout for Slicer 3 Plug-in
*** Interactive (real-time) manipulation of sources/sinks (ROIs) on steady-state fluid solution (possible application for intra-operative DTI)
* Working with the interested groups in analyzing control and white matter pathology data. Specifically, we have seen promising results when looking at the flow perturbation around white matter lesions seen in multiple sclerosis or stroke that may suggest a novel method for automatic lesion detection in DTI.
</div>

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

<h1>Progress</h1>
* Command line fluid mechanics tractography module integrated into Slicer 3 (see snapshot above)
* VTK module for fluid mechanics visualization completed.
** Discussion of possibly including module in next stable Slicer release.
** Progress made on (near) real time fluid velocity vector field animation but not yet stable for release.
* Arrangements made to include FM tractography method as part of DTI validation effort.
</div>

<br style="clear: both;" />

</div>

===References===
* Hageman NS, Shattuck DW, Narr K, Toga AW (2006). A diffusion tensor imaging tractography method based on Navier-Stokes fluid mechanics. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2006), Arlington, VA, USA, 6-9 April 2006. p. 798-801
* Hageman NS, Toga AW, Narr K, Shattuck DW (2008). A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics. IEEE Trans. in Medicial Imaging, In Submission.
* Hamilton L, Nuechterlein K, Hageman NS, Woods R, Asarnow R, Alger J, Gaser C, Toga AW, Narr K (2008). Mean Diffusivity and Fractional Anisotropy as Indicators of Schizophrenia and Genetic Vulnerability, Neuroimage, In Submission.

2009 Summer Project Week Hageman FMTractography

2009-06-04T17:08:22Z

Nhageman: Created page with '{| |Project Week Main Page ]] |[[Image:Hageman_cspfig4NAMIC_07-06-22.png|thumb|320px|Corticospinal tracts...'

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:Hageman_cspfig4NAMIC_07-06-22.png|thumb|320px|Corticospinal tracts segmented using our fluid mechanics based tractography method.]]
|[[Image:Hageman_FullBrainSlicerTractography.jpg|thumb|320px|Full brain tracts segmented using multiple fluid sources/sinks.]]
|[[Image:FMModuleScreenshot.png|thumb|320px|Screenshot of Slicer Module for Fluid Mechanics Tractography.]]
|}

__NOTOC__

===Key Investigators===
* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D
* Isomics: Steve Pieper and Alex Yarmarkovich

<div style="margin: 20px;">

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

<h1>Objective</h1>
Computational fluid dynamics is a rich field and its application to the analysis of diffusion tensor imaging (DTI) datasets has yielded possible applications to tractography, image registration, and white matter pathology. We are developing several useful and novel diffusion tensor imaging (DTI) analysis algorithms modeled on the principles of fluid mechanics for inclusion within the NA-MIC framework. The goal of this project is to develop these methods, make them compatible with the NA-MIC ITK-based software infrastructure (i.e. Slicer), and promote their dissemination to the scientific community.

See our [[hageman:NAMICFluidMechDTITractography|Project Page]] for more information.

</div>

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

<h1>Approach, Plan</h1>

We have developed and initially validated a DTI tractography method based on Navier-Stokes fluid mechanics. See the papers listed in the reference section for complete details on the method. Our approach for this project week will focus on the following:
* Building the our current CL Slicer module into an interactive GUI in Slicer 3. Our method is currently integrated as a CL Slicer module in a custom build of Slicer 3. The module has the following functionalities:
**reconstruction of the diffusion tensor and computation of common DTI scalar volumes (FA, LI, RGB). In addition, if users prefer using their own tensor reconstruction methods, the module can be run with any arbitrary set of tensor volumes.
**computation of fluid velocity vector field volume
**reconstruction of tracts based on the above fluid velocity volume
** Optimizing initial coding of method in ITK (better use of multithreading)
** Specialized visualization using VTK:
*** Fluid velocity vector field animation
*** Layout for Slicer 3 Plug-in
*** Interactive (real-time) manipulation of sources/sinks (ROIs) on steady-state fluid solution (possible application for intra-operative DTI)
* Working with the interested groups in analyzing control and white matter pathology data. Specifically, we have seen promising results when looking at the flow perturbation around white matter lesions seen in multiple sclerosis or stroke that may suggest a novel method for automatic lesion detection in DTI.
</div>

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

<h1>Progress</h1>
* Command line fluid mechanics tractography module integrated into Slicer 3 (see snapshot above)
* VTK module for fluid mechanics visualization completed.
** Discussion of possibly including module in next stable Slicer release.
** Progress made on (near) real time fluid velocity vector field animation but not yet stable for release.
* Arrangements made to include FM tractography method as part of DTI validation effort.
</div>

<br style="clear: both;" />

</div>

===References===
* Hageman NS, Shattuck DW, Narr K, Toga AW (2006). A diffusion tensor imaging tractography method based on Navier-Stokes fluid mechanics. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2006), Arlington, VA, USA, 6-9 April 2006. p. 798-801
* Hageman NS, Toga AW, Narr K, Shattuck DW (2008). A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics. IEEE Trans. in Medicial Imaging, In Submission.
* Hamilton L, Nuechterlein K, Hageman NS, Woods R, Asarnow R, Alger J, Gaser C, Toga AW, Narr K (2008). Mean Diffusivity and Fractional Anisotropy as Indicators of Schizophrenia and Genetic Vulnerability, Neuroimage, In Submission.

2009 Summer Project Week Hageman DTIDigitalPhantom

2009-06-04T17:07:07Z

Nhageman: Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png|Project Week Main Page </gallery> ==Key Investigators== * BWH: Junichi Tokuda, Wendy Plesniak, Nobuhiko Hata...'

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
</gallery>

==Key Investigators==
* BWH: Junichi Tokuda, Wendy Plesniak, Nobuhiko Hata
* WFU:Craig A. Hamilton

<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>

==References==
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .

2009 Summer Project Week

2009-06-04T17:03:14Z

Nhageman: /* Collaboration Projects */

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

*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. 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 will begin on''' Thursday, April 16th 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 that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

== Agenda==
* Monday
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
**9:30-10am: NA-MIC Kit Overview (Jim Miller)
** 10-10:30am Slicer 3.4 Update (Steve Pieper)
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)
** noon lunch
** 2:30pm-5pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis)
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (Alex G.)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** 9-11pm Tutorial Contest Presentations
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT]] (Dan M.)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. 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_2010|in Utah, January 4-8, 2010]]

== Projects ==

The list of projects for this week will go here.
=== Collaboration Projects ===
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]]
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi, Dan Blezek?, Steve, Alex G?)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer (Haiying, Ziv, Noby)]]
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|SLicer3, BioImage Suite and Brainlab - Introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)]]
#Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)
#Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)
#Slicer module for the computation of fibre dispersion and curving measures (Peter Savadjiev, C-F Westin)
#Xnat user interface improvements for NA-MIC (Dan M, Florin, Ron, Wendy)
#xnat and DICOMRT (Greg Sharp, Dan M) - might be done?
#Grid Wizard+xnat clinic (Clement Vachet)
#[[2009_Summer_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom | DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
#Cortical Thickness Pipeline (Clement Vachet, Ipek Oguz)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Demo|Demo Brainlab-BioImage Suite-Slicer in BWH OR (Haiying, Isaiah, Nathan Hageman)]]
#[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Xiaodong, Snehashis Roy)
#[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Fedorov, GeorgiaTech)
#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Fedorov, Marcel, Ron)
#Automatic brain MRI processing pipeline (Marcel, Hans)
#XNAT integration into Harvard Catalyst i2b2 framework(Gao, Yong)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze, Jeff Yager, Vince Magnotta)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan, Andrey Fedorov)
#DWI/DTI QC and Preparation Tool: DTIPrep (Zhexing Liu)

===IGT Projects:===
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#port 4d gated ultrasound code to Slicer - (Danielle)
#integration of stereo video into Slicer (Mehdi)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)
#neuroendoscope workflow presentation (sebastien barre)
#breakout session on Dynamic Patient Models (James Balter)
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Sandy Wells, Jim Balter, and others)

===NA-MIC Engineering Projects===
# DICOM Validation and Cleanup Tool (Luis, Sid, Steve, Greg)
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal, Sylvain Bouix)
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with python]] (Julien de Siebenthal, Sylvain Bouix)
# [[Summer2009:Using_CUDA_for_stochastic_tractography| Developing realtime feedback using CUDA]] (Julien de Siebenthal, Sylvain Bouix)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)
# [[EM_Segmenter|EM Segmenter]] (Sylvain Jaume, Nicolas Rannou)
# Plug-in 3D Viewer based on XIP (Lining)
# [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt, Steve, Vince)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien de Siebenthal)
# [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andriy, Luis, Bill, Jim, Steve)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 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 18, 2009: 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. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# 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-3-4/#dirlist Slicer-3-4 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==
If you plan to attend, please add your name here.

#Ron Kikinis, BWH (NA-MIC, NAC, NCIGT)
#Ferenc Jolesz, BWH (NCIGT, NAC)
#Clare Tempany, BWH (NCIGT)
#Tina Kapur, BWH (NA-MIC, NCIGT)
#Steve Pieper, Isomics Inc
#Jim Miller, GE Research
#Xiaodong Tao, GE Research
#Randy Gollub, MGH
#Nicole Aucoin, BWH (NA-MIC)
#Dan Marcus, WUSTL
#Junichi Tokuda, BWH (NCIGT)
#Alex Gouaillard, Harvard Systems Biology
#Arnaud Gelas, Harvard Systems Biology
#Kishore Mosanliganti, Harvard Systems Biology
#Lydie Souhait, Harvard Systems Biology
#Luis Ibanez, Kitware Inc
#Vincent Magnotta, UIowa
#Hans Johnson, UIowa
#Xenios Papademetris, Yale
#Gregory S. Fischer, WPI (Mon, Tue, Wed)
#Daniel Blezek, Mayo (Tue-Fri)
#Danielle Pace, Robarts Research Institute / UWO
#Clement Vachet, UNC-Chapel Hill
#Dave Welch, UIowa
#Demian Wassermann, Odyssée lab, INRIA, France
#Manasi Ramachandran, UIowa
#Greg Sharp, MGH
#Rui Li, MGH
#Mehdi Esteghamatian, Robarts Research Institute / UWO
#Misha Milchenko, WUSTL
#Kevin Archie, WUSTL
#Tim Olsen, WUSTL
#Wendy Plesniak BWH (NAC)
#Haiying Liu BWH (NCIGT)
#Curtis Lisle, KnowledgeVis / Isomics
#Diego Cantor, Robarts Research Institute / UWO
#Daniel Haehn, BWH
#Nicolas Rannou, BWH
#Sylvain Jaume, MIT
#Alex Yarmarkovich, Isomics
#Marco Ruiz, UCSD
#Andriy Fedorov, BWH (NA-MIC)
#Harish Doddi, Stanford University
#Saikat Pal, Stanford University
#Scott Hoge, BWH (NCIGT)
#Vandana Mohan, Georgia Tech
#Ivan Kolosev, Georgia Tech
#Behnood Gholami, Georgia Tech
#James Balter, U Michigan
#Dan McShan, U Michigan
#Zhou Shen, U Michigan
#Maria Francesca Spadea, Italy
#Lining Yang, Siemens Corporate Research
#Beatriz Paniagua, UNC-Chapel Hill
#Bennett Landman, Johns Hopkins University
#Snehashis Roy, Johns Hopkins University
#Marta Peroni, Politecnico di Milano
#Sebastien Barre, Kitware, Inc.
#Samuel Gerber, SCI University of Utah
#Ran Tao, SCI University of Utah
#Marcel Prastawa, SCI University of Utah
#Katie Hayes, BWH (NA-MIC)
#Sonia Pujol, BWH (NA-MIC)
#Andras Lasso, Queen's University
#Yong Gao, MGH
#Minjeong Kim, UNC-Chapel Hill
#Guorong Wu, UNC-Chapel Hill
#Jeffrey Yager, UIowa
#Yanling Liu, SAIC/NCI-Frederick
#Ziv Yaniv, Georgetown
#Bjoern Menze, MIT
#Vidya Rajagopalan, Virginia Tech
#Sandy Wells, BWH (NAC, NCIGT)
#Lilla Zollei, MGH (NAC)
#Lauren O'Donnell, BWH
#Florin Talos, BWH (NAC)
#Nobuhiko Hata, BWH (NCIGT)
#Alark Joshi, Yale
#Yogesh Rathi, BWH
#Jimi Malcolm, BWH
#Dustin Scheinost, Yale
#Dominique Belhachemi, Yale
#Sam Song, JHU
#Nathan Cho, JHU
#Julien de Siebenthal, BWH
#Peter Savadjiev, BWH
#Carl-Fredrik Westin, BWH
#John Melonakos, AccelerEyes (Wed & Thu morning)
#Yi Gao, Georgia Tech
#Sylvain Bouix, BWH
#Zhexing Liu, UNC-CH
#Eric Melonakos, BWH
#Lei Qin, BWH
#Giovanna Danagoulian, BWH
#Andrew Rausch, BWH (1st day only)
#Haytham Elhawary, BWH
#Jayender Jagadeesan, BWH
#Marek Kubicki, BWH
#Doug Terry, BWH
#Nathan Hageman, LONI (UCLA)

== Logistics ==
*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.
*'''Registration Method''' Add your name to the Attendee List section of this page
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.
*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.
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

Hageman:NAMICFluidMechDTITractography

2009-06-04T16:58:27Z

Nhageman: /* Links */

__NOTOC__
<br>
= Fluid Mechanics Based DTI Tractography =

== Overview ==

Currently, our project is focused on developing a novel method for diffusion tensor imaging (DTI) tractography modeled on the dynamics of a viscous fluid described by the second order non-linear Navier-Stokes equations. Even though these equations are most commonly seen in the context of fluid mechanics, they have been shown to be successful in modeling a large number of diverse physical phenomena. Our second order nonlinear-based approach is an extension of previous linear PDE methods, but our model contains a viscous force not present in previous methods, represented as an additional convection term in the PDE. We model local viscosity of the fluid as a function of the local intervoxel and intravoxel anisotropy in the corresponding DTI image volume. The incorporation of this convection term in our flow field calculation allows us to closely couple the magnitude of the fluid velocity to the magnitude of the underlying anisotropy of the DTI tensor field, providing a dampening force in background areas, such as gray matter and CSF. This eliminates the need for the white matter mask used by other PDE-based methods to prevent the model from entering these areas. To compute an estimate of the most likely connection path between two regions in the brain, we simulate the flow of an artificial fluid between those two points through a volume whose dimensions, pressure, and local viscosity are derived from the underlying DTI data. We then numerically solve for the fluid velocity vector field. The estimated connection path is then computed by finding the optimal path through the fluid velocity that simultaneously maximizes both the fluid velocity and its gradient.

Computational fluid dynamics is a rich field and, in addition to this tractography method, we are investigating its application to the analysis of diffusion tensor imaging (DTI) datasets for registration and analysis of white matter pathology. We are currently developing several useful and novel diffusion tensor imaging (DTI) analysis algorithms modeled on the principles of fluid mechanics for inclusion within the NA-MIC framework. The goal of this project is to fully develop these methods, make them compatible with the NA-MIC ITK-based software infrastructure (i.e. Slicer), and promote their dissemination to the scientific community.

== Description ==

Our algorithm simulates the flow of an artificial fluid through a volume whose dimensions, viscosity, and pressure tensor field are derived from a DTI volume. Specific regions of interest are chosen as sources and/or sinks, and we simulate the flow of an artificial fluid governed by the Navier-Stokes equations. The most likely connection path is then estimated using a generalized gradient vector flow (GGVF) based approach to compute the trajectory through the fluid velocity vector field that simultaneously maximizes the magnitude of the fluid velocity and its gradient along the path. Our fluid model is valid only as a theoretical framework for generating a connectivity metric and does not try to model any aspect of the underlying diffusion process.

[[Image:NAMICFMech_VisFig.jpg|Viscosity Map]]

Viscosity maps derived from 2D slices of DTI data from human control subjects. Viscosity values were calculated from the corresponding diffusion tensor image and are color-coded according to the legend bar seen on the right side of the figure. A. Axial slice taken at the level of the internal capsule. The corpus callosum, marked with a star is a highly organized white matter tract and is therefore characterized by low viscosity. Conversely, the lateral ventricle, marked with a delta contains CSF and is highly viscous. B. A mid-sagittal slice. As in A, the corpus callosum is marked with a star and is characterized by low viscosity. In contrast, the lateral ventricular space, marked with a delta contains CSF and therefore has no architecture. Consequently, it is highly viscous.

[[Image:NAMICFMech_PressureFig.jpg|Pressure Map]]

Representations of the pressure tensor derived from 2D slices from human control subjects. At each voxel in the image, the pressure force is represented by a tensor glyph, an ellipsoid whose axis is obtained from a diagonalization of the corresponding pressure tensor. The color of the ellipsoid represents the dominant diffusion direction, according to the color coded axes in the figure with the superior-inferior z-axis (blue) coming out of the page, the anterior-posterior y-axis (green) vertical, and the left-right x-axis (red) horizontal. A. A 2D axial slice taken at the level of the internal capsule. The white box marks the enlarged area shown in B. B. Enlarged view from A. The posterior limb of the corpus callosum, marked with a star is a highly organized white matter tract, and the pressure force acts on the artificial fluid co-linear with the fiber tract. In contrast, the lateral ventricular space, marked with a delta contains little structure. Consequently, the pressure force is isotropic in that region.

[[Image:NAMICflowfieldlesion.JPG|400 px|Fluid Velocity Field Solution]]

We solve our modified Navier-Stokes fluid mechanics model with these variables to get a fluid velocity field which is then used as a metric of regional connectivity. Tracts are generated using a modified method based on a generalized gradient vector field approach.

[[Image:NAMICFMech_CspFig.jpg|Human Corticospinal Tracts]]

Segmentation results of the corticospinal tracts using our method in human control DTI images. ROIs were placed within the brainstem below the level of the crossing pontine fibers and within the corona radiata above the level of the corpus callosum. Cross-sections of the approximate location of these ROIs are shown Figure 8D, drawn in white, superimposed on the corresponding axial DEC slices. Figure 8A shows the estimated connection paths between these ROIs generated by our method. An axial slice of the tensor glyphs at the level of the mid-brain is shown for spatial reference. The tracts show a prominent lateral course at the level of the mid-pons (Figure 8A: white arrow). This corresponds to a strong lateral diffusion component at that point as seen in the directionally encoded color (DEC) image of the axial slice at the mid-pontine level (Figure 8B, 8C: white arrow). The tensor glyphs and DEC image are color-coded by the axes shown in the figure.

[[Image:Hageman_FullBrainSlicerTractography.jpg|Full brain tracts segmented using our fluid mechanics based tractography method.]]

== Key Investigators ==

* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D

== Publications ==

''In Print''
* [http://www.na-mic.org/Special:Publications?text=Projects:MultiscaleShapeSegmentation&submit=Search&keywords=checked NA-MIC Publications Database].



''In Submission''
* Hageman NS, Toga AW, Narr K, Shattuck DW (2008). A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics. ''IEEE Trans. in Medicial Imaging'', In Submission.
* Hamilton L, Nuechterlein K, Hageman NS, Woods R, Asarnow R, Alger J, Gaser C, Toga AW, Narr K (2008). Mean Diffusivity and Fractional Anisotropy as Indicators of Schizophrenia and Genetic Vulnerability, ''Neuroimage'', In Submission.

== Links ==

* Hageman NS, Shattuck DW, Narr K, Toga AW (2006). A diffusion tensor imaging tractography method based on Navier-Stokes fluid mechanics. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2006), Arlington, VA, USA, 6-9 April 2006. p. 798-801 ([[media:Hageman-Toga2006.pdf|PDF]])
* [http://www.loni.ucla.edu LONI Website]

Project Week Results: [[2008_Winter_Project_Week:Fluid_Mechanics_Tractography|2008 Winter]], [[2008_Summer_Project_Week|2008 Summer]], [[2009_Winter_Project_Week|2009 Winter]], [[2009_Summer_Project_Week|2009 Summer]]

2009 Winter Project Week Hageman FMTractography

2009-06-04T16:56:19Z

Nhageman:

{|
|[[Image:PW2009-v3.png|thumb|320px|[[2009_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:Hageman_cspfig4NAMIC_07-06-22.png|thumb|320px|Corticospinal tracts segmented using our fluid mechanics based tractography method.]]
|[[Image:Hageman_FullBrainSlicerTractography.jpg|thumb|320px|Full brain tracts segmented using multiple fluid sources/sinks.]]
|[[Image:FMModuleScreenshot.png|thumb|320px|Screenshot of Slicer Module for Fluid Mechanics Tractography.]]
|}

__NOTOC__

===Key Investigators===
* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D
* Isomics: Steve Pieper and Alex Yarmarkovich

<div style="margin: 20px;">

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

<h1>Objective</h1>
Computational fluid dynamics is a rich field and its application to the analysis of diffusion tensor imaging (DTI) datasets has yielded possible applications to tractography, image registration, and white matter pathology. We are developing several useful and novel diffusion tensor imaging (DTI) analysis algorithms modeled on the principles of fluid mechanics for inclusion within the NA-MIC framework. The goal of this project is to develop these methods, make them compatible with the NA-MIC ITK-based software infrastructure (i.e. Slicer), and promote their dissemination to the scientific community.

See our [[hageman:NAMICFluidMechDTITractography|Project Page]] for more information.

</div>

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

<h1>Approach, Plan</h1>

We have developed and initially validated a DTI tractography method based on Navier-Stokes fluid mechanics. See the papers listed in the reference section for complete details on the method. Our approach for this project week will focus on the following:
* Building the our current CL Slicer module into an interactive GUI in Slicer 3. Our method is currently integrated as a CL Slicer module in a custom build of Slicer 3. The module has the following functionalities:
**reconstruction of the diffusion tensor and computation of common DTI scalar volumes (FA, LI, RGB). In addition, if users prefer using their own tensor reconstruction methods, the module can be run with any arbitrary set of tensor volumes.
**computation of fluid velocity vector field volume
**reconstruction of tracts based on the above fluid velocity volume
** Optimizing initial coding of method in ITK (better use of multithreading)
** Specialized visualization using VTK:
*** Fluid velocity vector field animation
*** Layout for Slicer 3 Plug-in
*** Interactive (real-time) manipulation of sources/sinks (ROIs) on steady-state fluid solution (possible application for intra-operative DTI)
* Working with the interested groups in analyzing control and white matter pathology data. Specifically, we have seen promising results when looking at the flow perturbation around white matter lesions seen in multiple sclerosis or stroke that may suggest a novel method for automatic lesion detection in DTI.
</div>

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

<h1>Progress</h1>
* Command line fluid mechanics tractography module integrated into Slicer 3 (see snapshot above)
* VTK module for fluid mechanics visualization completed.
** Discussion of possibly including module in next stable Slicer release.
** Progress made on (near) real time fluid velocity vector field animation but not yet stable for release.
* Arrangements made to include FM tractography method as part of DTI validation effort.
</div>

<br style="clear: both;" />

</div>

===References===
* Hageman NS, Shattuck DW, Narr K, Toga AW (2006). A diffusion tensor imaging tractography method based on Navier-Stokes fluid mechanics. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2006), Arlington, VA, USA, 6-9 April 2006. p. 798-801
* Hageman NS, Toga AW, Narr K, Shattuck DW (2008). A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics. IEEE Trans. in Medicial Imaging, In Submission.
* Hamilton L, Nuechterlein K, Hageman NS, Woods R, Asarnow R, Alger J, Gaser C, Toga AW, Narr K (2008). Mean Diffusivity and Fractional Anisotropy as Indicators of Schizophrenia and Genetic Vulnerability, Neuroimage, In Submission.

2009 Summer Project Week

2009-06-04T16:51:07Z

Nhageman: /* Collaboration Projects */

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

*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. 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 will begin on''' Thursday, April 16th 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 that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

== Agenda==
* Monday
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
**9:30-10am: NA-MIC Kit Overview (Jim Miller)
** 10-10:30am Slicer 3.4 Update (Steve Pieper)
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)
** noon lunch
** 2:30pm-5pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis)
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (Alex G.)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** 9-11pm Tutorial Contest Presentations
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT]] (Dan M.)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. 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_2010|in Utah, January 4-8, 2010]]

== Projects ==

The list of projects for this week will go here.
=== Collaboration Projects ===
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]]
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi, Dan Blezek?, Steve, Alex G?)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer (Haiying, Ziv, Noby)]]
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|SLicer3, BioImage Suite and Brainlab - Introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)]]
#Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)
#Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)
#Slicer module for the computation of fibre dispersion and curving measures (Peter Savadjiev, C-F Westin)
#Xnat user interface improvements for NA-MIC (Dan M, Florin, Ron, Wendy)
#xnat and DICOMRT (Greg Sharp, Dan M) - might be done?
#Grid Wizard+xnat clinic (Clement Vachet)
#[[2009_Summer_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#?DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA (Nathan Hageman)
#Cortical Thickness Pipeline (Clement Vachet, Ipek Oguz)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Demo|Demo Brainlab-BioImage Suite-Slicer in BWH OR (Haiying, Isaiah, Nathan Hageman)]]
#[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Xiaodong, Snehashis Roy)
#[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Fedorov, GeorgiaTech)
#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Fedorov, Marcel, Ron)
#Automatic brain MRI processing pipeline (Marcel, Hans)
#XNAT integration into Harvard Catalyst i2b2 framework(Gao, Yong)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze, Jeff Yager, Vince Magnotta)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan, Andrey Fedorov)
#DWI/DTI QC and Preparation Tool: DTIPrep (Zhexing Liu)

===IGT Projects:===
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#port 4d gated ultrasound code to Slicer - (Danielle)
#integration of stereo video into Slicer (Mehdi)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)
#neuroendoscope workflow presentation (sebastien barre)
#breakout session on Dynamic Patient Models (James Balter)
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Sandy Wells, Jim Balter, and others)

===NA-MIC Engineering Projects===
# DICOM Validation and Cleanup Tool (Luis, Sid, Steve, Greg)
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal, Sylvain Bouix)
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with python]] (Julien de Siebenthal, Sylvain Bouix)
# [[Summer2009:Using_CUDA_for_stochastic_tractography| Developing realtime feedback using CUDA]] (Julien de Siebenthal, Sylvain Bouix)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)
# [[EM_Segmenter|EM Segmenter]] (Sylvain Jaume, Nicolas Rannou)
# Plug-in 3D Viewer based on XIP (Lining)
# [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt, Steve, Vince)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien de Siebenthal)
# [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andriy, Luis, Bill, Jim, Steve)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 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 18, 2009: 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. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# 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-3-4/#dirlist Slicer-3-4 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==
If you plan to attend, please add your name here.

#Ron Kikinis, BWH (NA-MIC, NAC, NCIGT)
#Ferenc Jolesz, BWH (NCIGT, NAC)
#Clare Tempany, BWH (NCIGT)
#Tina Kapur, BWH (NA-MIC, NCIGT)
#Steve Pieper, Isomics Inc
#Jim Miller, GE Research
#Xiaodong Tao, GE Research
#Randy Gollub, MGH
#Nicole Aucoin, BWH (NA-MIC)
#Dan Marcus, WUSTL
#Junichi Tokuda, BWH (NCIGT)
#Alex Gouaillard, Harvard Systems Biology
#Arnaud Gelas, Harvard Systems Biology
#Kishore Mosanliganti, Harvard Systems Biology
#Lydie Souhait, Harvard Systems Biology
#Luis Ibanez, Kitware Inc
#Vincent Magnotta, UIowa
#Hans Johnson, UIowa
#Xenios Papademetris, Yale
#Gregory S. Fischer, WPI (Mon, Tue, Wed)
#Daniel Blezek, Mayo (Tue-Fri)
#Danielle Pace, Robarts Research Institute / UWO
#Clement Vachet, UNC-Chapel Hill
#Dave Welch, UIowa
#Demian Wassermann, Odyssée lab, INRIA, France
#Manasi Ramachandran, UIowa
#Greg Sharp, MGH
#Rui Li, MGH
#Mehdi Esteghamatian, Robarts Research Institute / UWO
#Misha Milchenko, WUSTL
#Kevin Archie, WUSTL
#Tim Olsen, WUSTL
#Wendy Plesniak BWH (NAC)
#Haiying Liu BWH (NCIGT)
#Curtis Lisle, KnowledgeVis / Isomics
#Diego Cantor, Robarts Research Institute / UWO
#Daniel Haehn, BWH
#Nicolas Rannou, BWH
#Sylvain Jaume, MIT
#Alex Yarmarkovich, Isomics
#Marco Ruiz, UCSD
#Andriy Fedorov, BWH (NA-MIC)
#Harish Doddi, Stanford University
#Saikat Pal, Stanford University
#Scott Hoge, BWH (NCIGT)
#Vandana Mohan, Georgia Tech
#Ivan Kolosev, Georgia Tech
#Behnood Gholami, Georgia Tech
#James Balter, U Michigan
#Dan McShan, U Michigan
#Zhou Shen, U Michigan
#Maria Francesca Spadea, Italy
#Lining Yang, Siemens Corporate Research
#Beatriz Paniagua, UNC-Chapel Hill
#Bennett Landman, Johns Hopkins University
#Snehashis Roy, Johns Hopkins University
#Marta Peroni, Politecnico di Milano
#Sebastien Barre, Kitware, Inc.
#Samuel Gerber, SCI University of Utah
#Ran Tao, SCI University of Utah
#Marcel Prastawa, SCI University of Utah
#Katie Hayes, BWH (NA-MIC)
#Sonia Pujol, BWH (NA-MIC)
#Andras Lasso, Queen's University
#Yong Gao, MGH
#Minjeong Kim, UNC-Chapel Hill
#Guorong Wu, UNC-Chapel Hill
#Jeffrey Yager, UIowa
#Yanling Liu, SAIC/NCI-Frederick
#Ziv Yaniv, Georgetown
#Bjoern Menze, MIT
#Vidya Rajagopalan, Virginia Tech
#Sandy Wells, BWH (NAC, NCIGT)
#Lilla Zollei, MGH (NAC)
#Lauren O'Donnell, BWH
#Florin Talos, BWH (NAC)
#Nobuhiko Hata, BWH (NCIGT)
#Alark Joshi, Yale
#Yogesh Rathi, BWH
#Jimi Malcolm, BWH
#Dustin Scheinost, Yale
#Dominique Belhachemi, Yale
#Sam Song, JHU
#Nathan Cho, JHU
#Julien de Siebenthal, BWH
#Peter Savadjiev, BWH
#Carl-Fredrik Westin, BWH
#John Melonakos, AccelerEyes (Wed & Thu morning)
#Yi Gao, Georgia Tech
#Sylvain Bouix, BWH
#Zhexing Liu, UNC-CH
#Eric Melonakos, BWH
#Lei Qin, BWH
#Giovanna Danagoulian, BWH
#Andrew Rausch, BWH (1st day only)
#Haytham Elhawary, BWH
#Jayender Jagadeesan, BWH
#Marek Kubicki, BWH
#Doug Terry, BWH
#Nathan Hageman, LONI (UCLA)

== Logistics ==
*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.
*'''Registration Method''' Add your name to the Attendee List section of this page
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.
*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.
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

2009 Summer Project Week

2009-06-04T16:44:39Z

Nhageman: /* Attendee List */

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

*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. 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 will begin on''' Thursday, April 16th 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 that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

== Agenda==
* Monday
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
**9:30-10am: NA-MIC Kit Overview (Jim Miller)
** 10-10:30am Slicer 3.4 Update (Steve Pieper)
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)
** noon lunch
** 2:30pm-5pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis)
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (Alex G.)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** 9-11pm Tutorial Contest Presentations
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT]] (Dan M.)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. 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_2010|in Utah, January 4-8, 2010]]

== Projects ==

The list of projects for this week will go here.
=== Collaboration Projects ===
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]]
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi, Dan Blezek?, Steve, Alex G?)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer (Haiying, Ziv, Noby)]]
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|SLicer3, BioImage Suite and Brainlab - Introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)]]
#Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)
#Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)
#Slicer module for the computation of fibre dispersion and curving measures (Peter Savadjiev, C-F Westin)
#Xnat user interface improvements for NA-MIC (Dan M, Florin, Ron, Wendy)
#xnat and DICOMRT (Greg Sharp, Dan M) - might be done?
#Grid Wizard+xnat clinic (Clement Vachet)
#?Fluid Mechanincs Module (Nathan Hageman)
#?DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA (Nathan Hageman)
#Cortical Thickness Pipeline (Clement Vachet, Ipek Oguz)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Demo|Demo Brainlab-BioImage Suite-Slicer in BWH OR (Haiying, Isaiah, Nathan Hageman)]]
#[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Xiaodong, Snehashis Roy)
#[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Fedorov, GeorgiaTech)
#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Fedorov, Marcel, Ron)
#Automatic brain MRI processing pipeline (Marcel, Hans)
#XNAT integration into Harvard Catalyst i2b2 framework(Gao, Yong)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze, Jeff Yager, Vince Magnotta)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan, Andrey Fedorov)
#DWI/DTI QC and Preparation Tool: DTIPrep (Zhexing Liu)

===IGT Projects:===
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#port 4d gated ultrasound code to Slicer - (Danielle)
#integration of stereo video into Slicer (Mehdi)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)
#neuroendoscope workflow presentation (sebastien barre)
#breakout session on Dynamic Patient Models (James Balter)
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Sandy Wells, Jim Balter, and others)

===NA-MIC Engineering Projects===
# DICOM Validation and Cleanup Tool (Luis, Sid, Steve, Greg)
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal, Sylvain Bouix)
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with python]] (Julien de Siebenthal, Sylvain Bouix)
# [[Summer2009:Using_CUDA_for_stochastic_tractography| Developing realtime feedback using CUDA]] (Julien de Siebenthal, Sylvain Bouix)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)
# [[EM_Segmenter|EM Segmenter]] (Sylvain Jaume, Nicolas Rannou)
# Plug-in 3D Viewer based on XIP (Lining)
# [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt, Steve, Vince)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien de Siebenthal)
# [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andriy, Luis, Bill, Jim, Steve)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 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 18, 2009: 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. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# 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-3-4/#dirlist Slicer-3-4 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==
If you plan to attend, please add your name here.

#Ron Kikinis, BWH (NA-MIC, NAC, NCIGT)
#Ferenc Jolesz, BWH (NCIGT, NAC)
#Clare Tempany, BWH (NCIGT)
#Tina Kapur, BWH (NA-MIC, NCIGT)
#Steve Pieper, Isomics Inc
#Jim Miller, GE Research
#Xiaodong Tao, GE Research
#Randy Gollub, MGH
#Nicole Aucoin, BWH (NA-MIC)
#Dan Marcus, WUSTL
#Junichi Tokuda, BWH (NCIGT)
#Alex Gouaillard, Harvard Systems Biology
#Arnaud Gelas, Harvard Systems Biology
#Kishore Mosanliganti, Harvard Systems Biology
#Lydie Souhait, Harvard Systems Biology
#Luis Ibanez, Kitware Inc
#Vincent Magnotta, UIowa
#Hans Johnson, UIowa
#Xenios Papademetris, Yale
#Gregory S. Fischer, WPI (Mon, Tue, Wed)
#Daniel Blezek, Mayo (Tue-Fri)
#Danielle Pace, Robarts Research Institute / UWO
#Clement Vachet, UNC-Chapel Hill
#Dave Welch, UIowa
#Demian Wassermann, Odyssée lab, INRIA, France
#Manasi Ramachandran, UIowa
#Greg Sharp, MGH
#Rui Li, MGH
#Mehdi Esteghamatian, Robarts Research Institute / UWO
#Misha Milchenko, WUSTL
#Kevin Archie, WUSTL
#Tim Olsen, WUSTL
#Wendy Plesniak BWH (NAC)
#Haiying Liu BWH (NCIGT)
#Curtis Lisle, KnowledgeVis / Isomics
#Diego Cantor, Robarts Research Institute / UWO
#Daniel Haehn, BWH
#Nicolas Rannou, BWH
#Sylvain Jaume, MIT
#Alex Yarmarkovich, Isomics
#Marco Ruiz, UCSD
#Andriy Fedorov, BWH (NA-MIC)
#Harish Doddi, Stanford University
#Saikat Pal, Stanford University
#Scott Hoge, BWH (NCIGT)
#Vandana Mohan, Georgia Tech
#Ivan Kolosev, Georgia Tech
#Behnood Gholami, Georgia Tech
#James Balter, U Michigan
#Dan McShan, U Michigan
#Zhou Shen, U Michigan
#Maria Francesca Spadea, Italy
#Lining Yang, Siemens Corporate Research
#Beatriz Paniagua, UNC-Chapel Hill
#Bennett Landman, Johns Hopkins University
#Snehashis Roy, Johns Hopkins University
#Marta Peroni, Politecnico di Milano
#Sebastien Barre, Kitware, Inc.
#Samuel Gerber, SCI University of Utah
#Ran Tao, SCI University of Utah
#Marcel Prastawa, SCI University of Utah
#Katie Hayes, BWH (NA-MIC)
#Sonia Pujol, BWH (NA-MIC)
#Andras Lasso, Queen's University
#Yong Gao, MGH
#Minjeong Kim, UNC-Chapel Hill
#Guorong Wu, UNC-Chapel Hill
#Jeffrey Yager, UIowa
#Yanling Liu, SAIC/NCI-Frederick
#Ziv Yaniv, Georgetown
#Bjoern Menze, MIT
#Vidya Rajagopalan, Virginia Tech
#Sandy Wells, BWH (NAC, NCIGT)
#Lilla Zollei, MGH (NAC)
#Lauren O'Donnell, BWH
#Florin Talos, BWH (NAC)
#Nobuhiko Hata, BWH (NCIGT)
#Alark Joshi, Yale
#Yogesh Rathi, BWH
#Jimi Malcolm, BWH
#Dustin Scheinost, Yale
#Dominique Belhachemi, Yale
#Sam Song, JHU
#Nathan Cho, JHU
#Julien de Siebenthal, BWH
#Peter Savadjiev, BWH
#Carl-Fredrik Westin, BWH
#John Melonakos, AccelerEyes (Wed & Thu morning)
#Yi Gao, Georgia Tech
#Sylvain Bouix, BWH
#Zhexing Liu, UNC-CH
#Eric Melonakos, BWH
#Lei Qin, BWH
#Giovanna Danagoulian, BWH
#Andrew Rausch, BWH (1st day only)
#Haytham Elhawary, BWH
#Jayender Jagadeesan, BWH
#Marek Kubicki, BWH
#Doug Terry, BWH
#Nathan Hageman, LONI (UCLA)

== Logistics ==
*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.
*'''Registration Method''' Add your name to the Attendee List section of this page
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.
*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.
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

2009 Annual Scientific Report

2009-05-08T01:01:48Z

Nhageman: /* Key Investigators */

Back to [[2009_Progress_Report]]

=Guidelines for preparation=

*[[2009_Progress_Report#Scientific Report Timeline]] - Main point is that May 15 is the date by which all sections below need to be completed. No extensions are possible.
*DBPs - If there is work outside of the roadmap projects that you would like to report, you are welcome to create a separate section for it under "Other".
*The outline for this report is similar to the 2008 and 2007 reports, which are provided here for reference: [[2008_Annual_Scientific_Report]], [[2007_Annual_Scientific_Report]].
*In preparing summaries for each of the 8 topics in this report, please leverage the detailed pages for projects provided here: [[NA-MIC_Internal_Collaborations]].
*Publications will be mined from the SPL publications database. All core PIs need to ensure that all NA-MIC publications are in the publications database by May 15.

=Introduction (Tannenbaum)=

The National Alliance for Medical Imaging Computing (NA-MIC) is now completing its fifth year. The Center is comprised of a multi-institutional, interdisciplinary team of computer scientists, software engineers, and medical investigators who have come together to develop and apply computational tools for the analysis and visualization of medical imaging data. A further purpose of the Center is to provide infrastructure and environmental support for the development of computational algorithms and open source technologies, as well as to oversee the training and dissemination of these tools to the medical research community. We are currently in year two of our second set of Driving Biological Projects (DBP), three of which involve diseases of the brain: (a) brain lesion analysis in neuropschiatric systemic lupus erythematosus; (b) a study of cortical thickness for autism; and (c) stochastic tractography for velocardiofacial syndrome (VCFS). The fourth DBP takes the Center in a very new direction, (d) the prostate: brachytherapy needle positioning robot integration.

Over the past five years, NA-MIC has made substantial progress toward the attainment of its major objectives. In year one, the Center focused on forging alliances amongst its various cores and constituent groups to assure that the efforts of the cores were well integrated toward the attainment of common and specific goals. To that end a great deal of effort went into defining the kinds of tools that would be needed for specific imaging applications. The second year emphasized the identification of key research thrusts that cut across all cores and were driven by the needs and requirements of the DBPs. This led to the formulation of the Center's four main technical themes: Diffusion Tensor Analysis, Structural Analysis, Functional MRI Analysis, and the integration of newly developed tools into the NA-MIC Tool Kit. The third year of Center activity was devoted to the continuation of collaborative work to develop solutions for the various brain-oriented DBPs. The fourth year was focused on translating collaborative knowledge and work to a new set of DBPs. In the current fifth year, a number of projects have made sufficient progress to warrant introduction as modules in Slicer, thereby making the Core 1 algorithms available to the general medical imaging community. Some of these algorithms are quite general and can be used for purposes far broader than the original DBPs. For example, a new point cloud registration algorithm developed for the prostate brachytherapy needle positioning project also can be used for DWI registration. Likewise, work on DTI/DWI tractography has been applied to the segmentation of blood vessels and soft plaque detection in the coronary arteries.

Year five progress with respect to the current DBPs is relevant to the scope of this Annual Progress Report. As mentioned, we currently have three projects in the area of neuropsychiatric disorders: Systemic Lupus Erythematosis (MIND Institute, University of New Mexico), Velocardiofacial Syndrome (Harvard), and Autism (University of North Carolina, Chapel Hill). A fourth project from Johns Hopkins and Queens Universities involves the application of core technologies to imaging/robotics-guided treatments in prostate cancer. A number of papers have been published that specifically acknowledge the NA-MIC, and significant software development is continuing as well.

Section 3 outlines specific aims fulfilled this year by the four roadmap projects: Section 3.1 describes the Stochastic Tractography Approach for Velocardiofacial Syndrome; Section 3.2 details the application of our work to Brachytherapy Needle Positioning for the Prostate; Section 3.3 outlines the Brain Lesion Analysis in Neuropsychiatric Systemic Lupus Erythematosus project; and Section 3.4 documents the Cortical Thickness for Autism project. For all of these projects, a synergism of effort has produced working computer modules that are user friendly and accessible to both medical researchers and clinicians.

Section 4 describes year five work on the four infrastructure topics. These include: Diffusion Image Analysis (Section 4.1), Structural Analysis (Section 4.2), Functional MRI Analysis (Section 4.3), and the NA-MIC Toolkit (Section 4.4). Many of the algorithms produced by Cores 1-3 have been integrated into ITK and Slicer, including those concerning shape analysis (e.g., spherical wavelets), new segmentation algorithms (for DTI/DWI tractography and the segmentation of the prostate), and new approaches to registration (e.g., based on particle filtering).

Finally, the last three sections of this Annual Progress Report highlight some of the work that the the Scientific Leadership believes is particularly significant to the the overall goals of the Center. Section 5 summarizes the benefits of several advanced algorithms, gives a description of the growing NAMIC-Toolkit, and documents the scope of our efforts in technology transfer and outreach. It is essential to emphasize that although the algorithms emanating from this Center were developed to solve specific clinical problems raised by the DBPs, in application, most of these algorithms have far more general utility and far greater potential impact on the medical imaging technical base. To this end, Section 6 draws attention to the impact and value of our work on biocomputing imaging at three different levels: within the Center, within the NIH-funded research community, and externally in the national and international community. To further illustrate the impact of our work, Section 7 provides some updated timelines with specific milestones achieved by the various NA-MIC cores. Section 8 lists publications pertinent to the current reporting period that acknowledge NA-MIC support, and Section 9 provides the External Advisory Report and our considered response.

=Clinical Roadmap Projects=
==Roadmap Project: Stochastic Tractography for VCFS (Kubicki)==
===Overview (Kubicki)===
The goal of this project is to create an end-to-end application that would be useful in evaluating anatomical connectivity between segmented cortical regions of the brain. The ultimate goal of our program is to understand anatomical connectivity similarities and differences between genetically related schizophrenia and velocardio-facial syndrome. Thus we plan to use the "stochastic tractography" tool for the analysis of abnormalities in integrity, or connectivity, provided by arcuate fasciculus, fiber bundle involved in language processing, in schizophrenia and VCFS.

===Algorithm Component (Golland)===
At the core of this project is the stochastic tractography algorithm
developed and implemented in collaboration between MIT and
BWH. Stochastic Tractography is a Bayesian approach to estimating
nerve fiber tracts from DTI images.

We first use the diffusion tensor at each voxel in the volume to
construct a local probability distribution for the fiber direction
around the principal direction of diffusion. We then sample the tracts
between two user-selected ROIs, by simulating a random walk between
the regions, based the local transition probabilities inferred from
the DTI image.

The resulting collection of fibers and the associated FA values
provide useful statistics on the properties of connections between the
two regions. To constrain the sampling process to the relevant white
matter region, we use atlas-based segmentation to label ventricles and
gray matter and to exclude them from the search space. As such, this
step relies heavily on the registration and segmentation functionality
in Slicer.

Over the last year, we have been working on applying several pre- and postprocessing steps to the algorithm pipeline. These steps include eddy current and geometric distortion correction that have been made available to us by Utah group, as well as DTI filtering (BWH). White matter masks can also now be created based on T2 thresholding within the slicer stochastic tractography module, which makes them more precise, since they do not rely on MRI to DTI co-registration.

At the same time we are working on the datasets where fMRI activations as well as gray matter segmentations need to be registered to DTI data, in order to seed within the predefined gray matter regions. We have made a significant progress in between modality registration, additional improvement is expected when distortion correction become part of the analysis pipeline.

We are also working on improved ways to visualize and quantify stochastic tractography output, not only by parametrizing fiber tracts, but also by creating connection probability distribution maps.

===Engineering Component (Davis)===
Stochastic Tractography slicer module has been rewritten in python now, and new module released in December 2008, and presented at the AHM in SLC. Its now part of the slicer3. Module documentation have been also created. Current engineering efforts are concentrated on maintaining the module, optimizing it for working with other data formats, and adding new functionality, such as better registration, distortion correction and ways of extracting and measuring FA along the tracts.

Also, because of the fact that the new data is much more computationally demanding (higher spatial resolution, more diffusion directions), and cortical ROIs usually much larger than the previously used WM ROIs, there is general need for performance improvement. This issue is highlighted especially by our stochastic way of tracking connections, where hundreds, instead of just one, (as in deterministic tractography) tracts are being generated from one seed. Thus some of our efforts go towards multithreading, and utilizing parallel processing. Version of our algorithm that uses large computer clusters have been developed and can be downloaded and installed by individual users with minimal knowledge of parallel computing now.

===Clinical Component (Kubicki)===
Over the last year, we tested the algorithm on newly released 3T NAMIC data, which contains high resolution DTI as well as structural RM data, plus automatic anatomical segmentations. Data is already co-registered, so cortical ROIs can be used as seeding points for stochastic tractography.

Using this dataset, we have completed a clinical study, where we looked at the connections between inferior frontal and superior temporal lobes, sites of the language network. Connections of these two regions, obtained with stochastic tractography, have been measured, and compared between group of 20 chronic schizophrenia patients and 20 controls. We have also looked at gray matter volumes of destination regions, trying to estimate relationship between gray and white matter abnormalities in schizophrenia. Results of this study have been presented at World Psychiatry Congress in Florence, Italy in April of 2009, as well as at Harvard Psychiatry MYSELL conference also in April 2009.

Another clinical study that is under way, is the application of stochastic tractography to define connections involved in emotional processing. For this purpose, we use cortical segmentations of anterior cingulated gyrus, orbital-frontal gyrus and amygdala, and trace as well as quantify connections between there regions in healthy controls as well in schizophrenia patients. Results of this preliminary study have been presented at MYSELL in April 2009, and will be presented at Biological Psychiatry conference later this year.

We are also involved in two collaborative studies. In one, use DTI data acquired in at UCI, and apply stochastic method to segment and measure arcuate fasciculus in subjects with schizophrenia and language impairment, as evinced in ERP data. In another collaboration, we combine resting state fMRI data with DTI in order to measure connectivity between regions forming functional network. Both these projects are under way.

Finally, stochastic tractography have been used qualitatively in one publication that is in press in Human Brain Mapping. Here, we combined fMRI with DTI whole brain data analysis, and found regions that were expressing abnormal functional connectivity in schizophrenia. These regions were then assigned to certain anatomical structures (white mater tracts), based on their location, and relationship to stochastic tractography output.

===Additional Information===
Additional Information for this project is available [http://wiki.na-mic.org/Wiki/index.php/DBP2:Harvard:Brain_Segmentation_Roadmap here on the NA-MIC wiki].
==Roadmap Project: MR-guided Prostate Biopsy Needle Positioning Robot Integration (Fichtinger)==
===Overview (Fichtinger)===
Numerous studies have demonstrated the efficacy of image-guided needle-based therapy and biopsy in the management of prostate cancer. The accuracy of traditional prostate interventions performed using transrectal ultrasound (TRUS) is limited by image fidelity, needle template guides, needle deflection and tissue deformation. Magnetic Resonance
Imaging (MRI) is an ideal modality for guiding and monitoring such interventions due to its excellent visualization of the prostate, its sub-structure and surrounding tissues.

We have designed a comprehensive robotic assistant system that allows prostate biopsy and brachytherapy procedures to be performed entirely inside a 3T closed MRI scanner. The current system applies transrectal approach to the prostate: an endorectal coil and steerable needle guide, both tuned to 3T magnets and invariable to any particular scanner, are integrated into the MRI compatible manipulator.

Under the NAMIC initiative, the image computing, visualization, intervention planning, and kinematic planning interface is being accomplished with open source system built on the NAMIC toolkit and its components, such as Slicer3 and ITK. These are complemented by a collection of unsupervised prostate segmentation and registration methods that are of great importance to the clinical performance of the interventional system as a whole.

===Algorithm Component (Tannenbaum)===

We have worked on both the segmentation and the registration of the prostate from MRI and ultrasound data. We explain each of the steps below.

'''Prostate Segmentation'''

We must first extract the prostate. We provided two methods: a shape based method and a semi-automatic method. More details are given below and images and further details may be found [http://www.na-mic.org/Wiki/index.php/Projects:ProstateSegmentation here]

# ''A shape based algorithm''. This begins with learning a group of shapes, obtained from manually segmenting a set of prostate 3D images. With the shapes represented as the hyperbolic tangent of the signed distance functions, principle component analysis is employed to learn the shapes. Further, given a new prostate image, we search the learned shape space in order to find one shape best segment the given image. The fitness of one shape to segment the image is evaluated by an energy functional measuring the discrepancy of the statistical characteristics inside and outside the current segmentation boundary. Such method is robust to the noise in the images. Moreover, the whole algorithm pipeline has been integrated into the Slicer3 through the command line module.
# ''Semi-automatic method''. This method is based on a random walk segmentation algorithm. With user provided initial seed regions inside and out side the object (prostate), the algorithm computes a probability distribution over the image domain by solving a boundary value partial differential equation where the value at seed regions are fixed at 1.0 or 0.0, depending or whether they are object or background seeds. The resulting distribution indicates the probability of each voxel belonging to the object. Simply threshold by 0.5 gives the segmentation of the object. Moreover, if the result is not suitable, the user can edit the seed regions, and the new result is computed based on this previous result. This algorithm has been integrated into the transrectal prostate MRI module of Slier3.

'''Prostate Registration'''

We developed a nonlinear (affine) prostate registration method by treating prostate images as point sets. Then the iterative closest point algorithm is improved to register the point sets generated by the two images to be registered. The proposed method shows robustness to long distance transition and partial image structure. Moreover, such representation is much sparser than sampling image on the uniform grid thus the registration is very fast comparing two 3D volumetric
image registration.

Furthermore, the registration is viewed as a posterior estimation problem, in which the distributions of the affine and translation parameters are to be estimated. This can naturally be estimated using a particle filter framework. Through this, the method can handle the otherwise difficult cases where the two prostates are one supine and
one prone.

More details are given [[Projects:pfPtSetImgReg|here...]]

===Engineering Component (Hayes)===
<Note Progress in the last year>

===Clinical Component (Fichtinger)===
<Note Progress in the last year>

===Additional Information===
Additional Information for this project is available [http://wiki.na-mic.org/Wiki/index.php/DBP2:JHU:Roadmap here on the NA-MIC wiki].
==Roadmap Project: Brain Lesion Analysis in Neuropsychiatric Systemic Lupus Erythematosus (Bockholt)==
===Overview (Bockholt)===
The primary goal of the MIND DPB is to examine changes in white matter lesions in adults with Neuropsychiatric Systemic Lupus Erythematosus (SLE). We want to be able to characterize lesion location, size, and intensity, and would also like to examine longitudinal changes of lesions in an SLE cohort. To accomplish this goal, we will create an end-to-end application entirely within NA-MIC Kit allowing individual analysis of white matter lesions. Such a workflow will then be applied to a clinical sample in the process of being collected.

===Algorithm Component (Whitaker)===
The basic steps necessary for the white matter lesion analysis application entail first registration of T1, T2, and FLAIR images, second tissue classification into gray, white, csf, or lesion, thirdly clustering lesion for anatomical localization, and finally a summarization of lesion size and image intensity parameters within each unique lesion.

<Note Progress in the last year>

===Engineering Component (Pieper)===

At the [http://www.na-mic.org/Wiki/index.php/2009_Winter_Project_Week January 2009 NA-MIC project week] a first pass of a lesion segmentation tutorial was provided to the community. This was the first end-to-end workflow for this project and represented a significant step in the project. Based on feedback from the community and the target clinical users of these tools, we identified additional steps to improve the system.

The primary engineering effort has been directed to the following projects:

'''Interface Improvements'''

We have begun to look at the creation of a [[2009_Winter_Project_Week:HighLevelWizard| high level wizard]] as a front end to the processing task. This interface would allow users to go through the steps without directly navigating the slicer modules and can also provide state management that will simplify the visualization efforts.

'''Modularity and Deployment'''

The current tutorial has been difficult for some users to implement due to the requirement that the lesion detection module be compiled locally on the user's machine. Non-developers understandably find this to be a difficult requirement, so we are integrating the lesion segmentation code into the [http://www.slicer.org/slicerWiki/index.php/Slicer3:Loadable_Modules:Status Slicer3 loadable module project] so that pre-compiled versions of the module are available for users. To implement this, we are following the templates provided by the [http://www.nitrc.org/projects/slicer3examples/ slicer example modules] provided on the nitrc.org website. This infrastructure was created via a supplement to NA-MIC provided by the NITRC project. The [http://www.nitrc.org/projects/lupuslesion/ project page on nitrc.org] is being updated as new features are added to the modules.

'''Core Implementation Support'''

During this period we have also worked on [[2009_Winter_Project_Week:LesionSegmentationEfficiency|optimizing the implementation]] of the core ITK code. This effort has primarily been accomplished by the MIND group, with interactions as needed with the rest of the NA-MIC community.

In addition, ongoing discussions with the rest of the NA-MIC community are encouraging code sharing among projects through modularization of common processing tasks and development of 'best of breed' routines for lesion detection and quantification. These tools are then embodied as slicer modules for use in other applications such as brain tumor change tracking.

===Clinical Component (Bockholt)===
<Note Progress in the last year>
===Additional Information===
Additional Information for this project is available [http://wiki.na-mic.org/Wiki/index.php/DBP2:MIND:Roadmap here on the NA-MIC wiki].
==Roadmap Project: Cortical Thickness for Autism(Hazlett)==
===Overview (Hazlett)===

A primary goal of the UNC DPB is to examine changes in cortical thicknes in children with autism compared to typical controls. We want to examine group differences in both local and regional cortical thickness, and would also like to examine longitudinal changes in the cortex from ages 2-4 years. To accomplish this goal, this project will create an end-to-end application within Slicer3 allowing individual and group analysis of regional and local cortical thickness. Such a workflow will then be applied to our study data (already collected).

===Algorithm Component (Styner)===

The basic steps necessary for the cortical thickness application entail first tissue segmentation in order to separate white and gray matter regions, second cortical thickness measurement, thirdly cortical correspondence to compare measurements across subjects and finally a statistical analysis to locally compute group differences.

<Note Progress in the last year>

===Engineering Component (Miller, Vachet)===

<Note Progress in the last year>

===Clinical Component (Hazlett)===
<Note Progress in the last year>

===Additional Information===
Additional Information for this project is available [http://wiki.na-mic.org/Wiki/index.php/DBP2:UNC:Cortical_Thickness_Roadmap here on the NA-MIC wiki].

=Four Infrastructure Topics=
==Diffusion Image Analysis (Gerig)==
<Note Progress in the last year>
===Key Investigators===

<Need to update the list below>

* BWH: Marek Kubicki, Martha Shenton, Sylvain Bouix, Julien von Siebenthal, Thomas Whitford, Jennifer Fitzsimmons, Doug Terry, Jorge Alverado, Eric Melonakos, Carl-Fredrik Westin.
* MIT: Lauren O'Donnell, Polina Golland
* UCI: James Fallon, Judi Ford
* Utah I: Tom Fletcher, Ross Whitaker, Ran Tao, Yongsheng Pan
* Utah II: Casey Goodlett, Sylvain Gouttard, Guido Gerig
* GA Tech: John Melonakos, Vandana Mohan, Shawn Lankton, Allen Tannenbaum
* GE: Xiaodong Tao, Jim Miller, Mahnaz Mandah
* UCLA: Nathan Hageman
* Isomics: Steve Pieper
* Kitware: Luis Ibanez

===Additional Information===
Additional Information for this topic is available [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_Internal_Collaborations:DiffusionImageAnalysis here on the NA-MIC wiki].

==Structural Analysis(Tannenbaum)==
===Progress===
Under Structural Analysis, the main topics of research for NAMIC are structural segmentation, registration techniques and shape analysis. These topics are correlated and hence research in one often finds application in another. For example, shape analysis can yield useful priors for segmentation, or segmentation and registration can provide structural correspondences for use in shape analysis and so on.

An overview of selected progress highlights under these broad topics follows:

Segmentation

* Geodesic Tractography Segmentation: We proposed an image segmentation technique based on augmenting the conformal (or geodesic) active contour framework with directional information. This has been applied successfully to the segmentation of neural fiber bundles such as the Cingulum Bundle. This framework has now been integrated into Slicer and is being tested on a population of brain data sets.

* Tubular Surface Segmentation: We have proposed a new model for tubular surfaces that transforms the problem of detecting a surface in 3D space, to detecting a curve in 4D space. Besides allowing us to impose a "soft" tubular shape prior, this also leads to computational efficiency over conventional surface segmentation approaches. We have also developed the moving end points implementation of this framework wherein the required input is only a few points in the interior of the structure of interest. This yields the additional advantage that the framework simulatenously returns both the 3D segmentation and the 3D skeleton of the structure eliminating the need for apriori knowledge of end points, and an expensive skeletonization step. The framework is applicable to different tubular anatomical structures in the body. We have so far applied it successfully to the Cingulum Bundle, and blood vessels.

* Local-global Segmentation: We have proposed a novel segmentation approach that combines the advantages of local and global approaches to segmentation, by using statistics over regions that are local to each point on the evolving countour. This makes it well suited to applications with contrast differences within the structure of interest such as in blood vessel segmentation, as well as applications like the neural fiber bundles where the diffusion profiles of voxels within the structure are locally similar but vary along the length of the fiber bundle itself.

* Shape-based segmentation: Standard image based segmentation approaches perform poorly when there is little or no contrast along boundaries of different regions. In such cases segmentation is mostly performed manually using prior knowledge of the shape and relative location of the underlying structures combined with partially discernible boundaries. We have presented an automated approach guided by covariant shape deformations of neighboring structures, which is an additional source of prior knowledge. Captured by a shape atlas, these deformations are transformed into a statistical model using the logistic function. The mapping between atlas and image space, structure boundaries, anatomical labels, and image inhomogeneities are estimated simultaneously within an Expectation-Maximization formulation of the Maximum A posteriori Probability (MAP) estimation problem. These results are then fed into an Active Mean Field approach, which views the results as priors to a Mean Field approximation with a curve length prior. We have applied the algorithm successfully to real MRI images, and we have also implemented it into 3D Slicer.

* Re-Orientation Approach for Segmentation of DW-MRI: This work proposes a methodology to segment tubular fiber bundles from diffusion weighted magnetic resonance images (DW-MRI). Segmentation is simplified by locally reorienting diffusion information based on large-scale fiber bundle geometry. Segmentation is achieved through simple global statistical modeling of diffusion orientation which allows for a convex optimization formulation of the segmentation problem, combining orientation statistics and spatial regularization. The approach compares very favorably with segmentation by full-brain streamline tractography.

Registration

* Optimal Mass Transport based Registration: We have provided a computationaly efficient non-rigid/elastic image registration algorithm based on the Optimal Mass Transport theory. We use the Monge-Kantorovich formulation of the Optimal Mass Transport problem and implement the solution proposed by Haker et al. using multi-resolution and multigrid techniques to speed up the convergence. We also leverage the computation power of general purpose graphics processing units available on standard desktop computing machines to exploit the inherent parallelism in our algorithm. We extend the work by Haker et al. who compute the optimal warp from a first order partial differential equation, an improvement over earlier proposed higher order methods and those based on linear programming, and further implement the algorithm using a coarse-to-fine strategy resulting in phenomenol improvement in convergence. We have applied it successfully to the registration of 3D brain MRI datasets (preoperative and intra-operative), and are currently extending it to the non-rigid registration of baseline DWI to brain MRI data.

* Atlas Regularization for Image Segmentation: Atlas-based approaches have demonstrated the ability to automatically identify detailed brain structures from 3-D magnetic resonance (MR) brain images. Unfortunately, the accuracy of this type of method often degrades when processing data acquired on a different scanner platform or pulse sequence than the data used for the atlas training. In this paper, we improve the performance of an atlas-based whole brain segmentation method by introducing an intensity renormalization procedure that automatically adjusts the prior atlas intensity model to new input data. Validation using manually labeled test datasets has shown that the new procedure improves the segmentation accuracy (as measured by the Dice coefficient) by 10% or more for several structures including hippocampus, amygdala, caudate, and pallidum. The results verify that this new procedure reduces the sensitivity of the whole brain segmentation method to changes in scanner platforms and improves its accuracy and robustness, which can thus facilitate multicenter or multisite neuroanatomical imaging studies.

* Point-set Rigid Registration: We have proposed a particle filtering scheme for the registration of 2D and 3D point set undergoing a rigid body transformation. Moreover, we incorporate stochastic dynamics to model the uncertainity of the registration process. We treat motion as a local variation in the pose parameters obatined from running a few iterations of the standard Iterative Closest Point (ICP) algorithm. Employing this idea, we introduce stochastic motion dynamics to widen the narrow band of convergence as well as provide a dynamical model of uncertainity. In contrast with other techniques, our approach requires no annealing schedule, which results in a reduction in computational complexity as well as maintains the temoral coherency of the state (no loss of information). Also, unlike most alternative approaches for point set registration, we make no geometric assumptions on the two data sets.We applied the algorithm to different alignments of point clouds and it successfully found the correct optimal transformation that aligns two given point clouds despite the differing geometry around the local neighborhood of a point within their respective sets.

* Regularization for Optimal Mass Transport: To extend the flexibility of the existing OMT algorithm, we added a regularization term to the functional being minimized. This term controls the tradeoff between how well two images match after registration versus how warped the transformation map can become. A weighted sum of squared differences is used to penalize having to move mass over long distances; this addition also helps to keep the transformation physically accurate by reducing the likelihood that the transformation grid will fold over itself and keeping the grid smooth.

* Registration of DW-MRI to structural MRI: Optimal Mass Transport was applied to the problem of correcting EPI distortion in DW-MRI. A mask for white matter in DW-MRI was registered to the white matter mask extracted from the structural MRI for the same patient. Prior to registration, it is important to normalize intensities in the two masks; this was done by dividing the images into regions and uniformly normalizing over each region to assure the sum of the intensities is equal. Then, once a transformation between the white matter masks was calculated, this transformation was applied to the original DW-MRI image.

Shape Analysis

* Shape Analysis Framework using SPHARM-PDM: We have provided an analysis framework of objects with spherical topology, described by sampled spherical harmonics SPHARM-PDM. The input is a set of binary segmentations of a single brain structure, such as the hippocampus or caudate. These segmentations are first processed to fill any interior holes. The processed binary segmentations are converted to surface meshes, and a spherical parametrization is computed for the surface meshes using a area-preserving, distortion minimizing spherical mapping. The SPHARM description is computed from the mesh and its spherical parametrization. Using the first order ellipsoid from the spherical harmonic coefficients, the spherical parametrizations are aligned to establish correspondence across all surfaces. The SPHARM description is then sampled into a triangulated surfaces (SPHARM-PDM) via icosahedron subdivision of the spherical parametrization. These SPHARM-PDM surfaces are all spatially aligned using rigid Procrustes alignment. Group differences between groups of surfaces are computed using the standard robust Hotelling T 2 two sample metric. Statistical p-values, both raw and corrected for multiple comparisons, result in significance maps. We provide additional visualization of the group tests via mean difference magnitude and vector maps, as well as maps of the group covariance information. We have a stable implementation, and current development focuses on integrating the current command line tools into Slicer (v3) via the Slicer execution model.

* Population studies using Tubular Surface Model: We have proposed a tubular shape model for the Cingulum Bundle which models a tubular surface as a center-line coupled with a radius function at every point along the center-line. This model shows potential for population studies on the Cingulum Bundle which is believed to be involved in Schizophrenia, since it provides a natural way of sampling the structure to build a feature representation of it. We are currently segmenting the Cingulum Bundle from a population of brain data sets, towards performing this population analysis using the Pott's Model.

* Automatic Outlining of Sulci on a Brain Surface: We present a method to automatically extract certain key features on a surface. We apply this technique to outline sulci on the cortical surface of a brain, where the data is taken to be a 3D triangulated mesh formed from the segmentation of MR image slices. The problem is posed as energy minimization using penalizing the arc-length of segmenting curve using conformal factor involving the mean curvature of the underlying surface. The computation is made practical for dense meshes via the use of a sparse-field method to track the level set interfaces and regularized least-squares estimation of geometric quantities.

===Key Investigators===

Needs to be updated:

* MIT: Polina Golland, Kilian Pohl, Sandy Wells, Eric Grimson, Mert R. Sabuncu
* UNC: Martin Styner, Ipek Oguz, Xavier Barbero
* Utah: Ross Whitaker, Guido Gerig, Suyash Awate, Tolga Tasdizen, Tom Fletcher, Joshua Cates, Miriah Meyer
* GaTech: Allen Tannenbaum, John Melonakos, Vandana Mohan, Tauseef ur Rehman, Shawn Lankton, Samuel Dambreville, Yi Gao, Romeil Sandhu, Xavier Le Faucheur, James Malcolm, Ivan Kolosev
* Isomics: Steve Pieper
* GE: Bill Lorensen, Jim Miller
* Kitware: Luis Ibanez, Karthik Krishnan
* UCLA: Arthur Toga, Michael J. Pan, Jagadeeswaran Rajendiran
* BWH: Sylvain Bouix, Motoaki Nakamura, Min-Seong Koo, Martha Shenton, Marc Niethammer, Jim Levitt, Yogesh Rathi, Marek Kubicki, Steven Haker

===Additional Information===
Additional Information for this topic is available [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_Internal_Collaborations:StructuralImageAnalysis here on the NA-MIC wiki].
==fMRI Analysis (Golland)==
===Progress===
One of the major goals in analysis of fMRI data is the detection of
functionally homogeneous networks in the brain.

<note progress here>

===Key Investigators===

Need to update this list:

# MIT: Polina Golland, Danial Lashkari, Bryce Kim
# Harvard/BWH: Sylvain Bouix, Martha Shenton, Marek Kubicki

===Additional Information===
Additional Information for this topic is available [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_Internal_Collaborations:fMRIAnalysis here on the NA-MIC wiki].
==NA-MIC Kit Theme (Schroeder)==
===Progress===
The NAMIC-Kit consists of a framework of advanced computational components, as well as the support infrastructure for testing, documenting, and deploying leading edge medical imaging algorithms and software tools. The framework has been carefully constructed to provide low-level access to libraries and modules for advanced users, plus high-level application access that non-computer professionals can use to address a variety of problems in biomedical computing. In this fifth year of the NA-MIC projects <summary of progress>

===Software Releases===
The NAMIC-Kit can be represented as a pyramid of capabilities, with the base consisting of toolkits and libraries, and the apex standing in for the Slicer3 user application. In between, Slicer modules are stand-alone executables that can be integrated directly into the Slicer3 application, including GUI integration, while work-flows are groups of modules that are integrated together to manifest sophisticated segmentation, registration and biomedical computing algorithms. In a coordinated NAMIC effort, major releases of these many components were realized over the past year. This includes, but is not limited to:
*
*

===Slicer3 and the Software Framework===
One of the major achievements of the past year has been the release of [http://www.slicer.org/slicerWiki/index.php/Documentation-3.4 version 3.4 of 3D Slicer] in May of 2009. A number of important improvements have been made by the Engineering Core and significant new functionality has been added throug other NA-MIC cores and collaborators since the release of version 3.2 in August of 2008. A few notable examples include:

* [http://www.slicer.org/slicerWiki/index.php/Modules:Saving-Documentation-3.4 An Integrated Data Save Dialog]
* [http://www.slicer.org/slicerWiki/index.php/Modules:Fiducials-Documentation-3.4 Significant Rework of the Fiducials Interface]
* [http://www.slicer.org/slicerWiki/index.php/Modules:Slices-Documentation-3.4 A Slices Module to Support Advanced Visualization Modes]
* [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation Significant Improvements to the Interactive Label Map Editor]
* [http://www.slicer.org/slicerWiki/index.php/Modules:ChangeTracker-Documentation-3.4 Integration of a Brain Tumor Change Tracking Module in collaboration with the Brain Science Foundation]
* [http://www.slicer.org/slicerWiki/index.php/Modules:IA_FEMesh-Documentation-3.4 Integration of a Finite Element Meshing Module as a deliverable of the NA-MIC Collaboration Grant at the University of Iowa]
* [http://www.slicer.org/slicerWiki/index.php/Modules:FetchMI-Documentation-3.4 A Medical Informatics Interface to XNAT in collaboration with BIRN]
* [http://www.slicer.org/slicerWiki/index.php/Slicer3:Python The Ability to Interactively Script Slicer in Python as well as Tcl]

In addition, there have been major extensions to the diffusion imaging tools, registration tools, filters, image guided therapy, and other core changes that enhance the utility and applicability of the software.

===Software Process===
One of the challenges facing developers has been the requirement to implement, test and deploy software systems across multiple computing platforms. NAMIC continues to push the state of the art with further development of the CMake, CTest, and CPack tools for cross-platform development, testing, and packaging, respectively...

===Key Investigators===
THis list needs to be updated:

* Kitware - Will Schroeder (Core 2 PI), Sebastien Barre, Luis Ibanez, Bill Hoffman
* GE - Jim Miller, Xiaodong Tao
* Isomics - Steve Pieper, Alex Yarmarkovich, Curt Lisle, Terry Lorber

===Additional Information===
Additional Information for this topic is available [http://wiki.na-mic.org/Wiki/index.php/NA-MIC-Kit here on the NA-MIC wiki].

=Highlights(Schroeder)=
===Advanced Algorithms===

===NAMIC-Kit===

===Outreach and Technology Transfer===
Cores 4-5-6 continue to support, train and dissemniate to the NAMIC community, and the broader biomedical computing community.
* The Slicer community held several workshops and tutorials. In xxx a satellite event was held for the international Organization for Human Brain Mapping at the annual meeting in xxx. The xx workshop on xx hosted xx participants representing xx countries from around the world, xx states within the US and xxdifferent laboratories including xx NIH institutes. In addition, <note how many slicer tutorials were held and where etc>
* Project Week continues to be a successful NAMIC venue. These semi-annual events are held in Boston in June, and January in Salt Lake City. These events are well attended with approximately 100 participants, of which about a third are outside collaborators. At the last Project Week in Salt Lake City, approximately xx projects were realized.
* NAMIC continues to participate in conferences and other technical venues. For example, NAMIC hosted xxx

=Impact and Value to Biocomputing (Miller)=
NA-MIC impacts Biocomputing through a variety of mechanisms. First,
NA-MIC produces scientific results, methodologies, workflows,
algorithms, imaging platforms, and software engineering tools and
paradigms in an open enviroment that contributes directly to the body of
knowledge available to the field. Second, NA-MIC science and
technology enables the entire medical imaging community to build on
NA-MIC results, methods, and techniques, to concentrate on the new
science instead of developing supporting infrastructure, to leverage
NA-MIC scientists and engineers to adapt NA-MIC technology to new
problem domains, and to leverage NA-MIC infrastructure to distribute
their own technology to a larger community.

===Impact within the Center===

===Impact within NIH Funded Research===

===National and International Impact===

= Timeline (Ross)=

<The table needs to be updated>

This section of the report gives the milestones for years 1 through 5 that are associated with the timelines in the original proposal. We have organized the milestones by core. For each milestone we have indicated the proposed year of completion and a very brief description of the current status. In some cases the milestones include ongoing work, and we have try to indicate that in the status. We have also included tables that list any significant changes to the proposed timelines. On the wiki page, we have links to the notes from the various PIs that give more details on their progress and the status of the milestones.

'''These tables demonstrate that the project is, on the whole, proceeding according to the originally planned schedule.'''

== Core 1: Algorithms ==

=== Timelines and Milestones ===

{| border="1"
| '''Group'''
| '''Aim'''
| '''Milestone'''
| '''Proposed time of completion'''
| '''Status'''
|-
| '''MIT'''
| 1
| '''Shape-based segmentation'''
|
|
|-
| '''MIT'''
| 1.1
| Methods to learn shape representations
| Year 2
| Completed
|-
| '''MIT'''
| 1.2
| Shape in atlas-driven segmentation
| Year 4
| Completed
|-
| '''MIT'''
| 1.3
| Validate and refine approach
| Year 5
| In Progress
|-
| '''MIT'''
| 2
| '''Shape analysis'''
|
|
|-
| '''MIT'''
| 2.1
| Methods to compute statistics of shapes
| Year 4
| Completed
|-
| '''MIT'''
| 2.3
| Validation of shape methods on application data
| Year 5
| Completed, refinements ongoing
|-
| '''MIT'''
| 3
| '''Analysis of DTI data'''
|
|
|-
| '''MIT'''
| 3.1
| Fiber geometry
| Year 3
| Completed
|-
| '''MIT'''
| 3.2
| Fiber statistics
| Year 5
| Completed, new developments ongoing
|-
| '''MIT'''
| 3.3
| Validation on real data
| Year 5
| Completed, refinements ongoing
|-
| '''Utah'''
| 1
| '''Processing of DTI data'''
|
|
|-
| '''Utah'''
| 1.1
| Filtering of DTI
| Year 2
| Completed
|-
| '''Utah'''
| 1.2
| Quantitative analysis of DTI
| Year 3
| Completed, refinements ongoing
|-
| '''Utah'''
| 1.3
| Segmentation of cortex/WM
| Year 3
| Completed partially, modified below
|-
| '''Utah'''
| 1.4
| Segmentation analysis of white matter tracts
| Year 3
| Completed, applications ongoing
|-
| '''Utah'''
| 1.5
| Joint analysis of DTI and functional data
| Year 5
| Initiated
|-
| '''Utah'''
| 2
| Nonparametric Shape Analysis
| Year 5
| Completed
|-
| '''Utah'''
| 2.1
| Framework in place
| Year 3
| Complete
|-
| '''Utah'''
| 2.2
| Demonstration on shape of neuranatomy (from Core 3)
| Year 4
| Complete
|-
| '''Utah'''
| 2.3
| Development for multiobject complexes
| Year 4
| Complete
|-
| '''Utah'''
| 2.4
| Demonstration of NP shape representations on clinical hypotheses from Core 3
| Year 5
| Complete, publications in progress
|-
| '''Utah'''
| 2.6
| Integration into NAMIC-kit
| Year 5
| Incomplete (initiated)
|-
| '''Utah'''
| 2.7
| Shape regression
| Year 5
| Incomplete
|-

|-
| '''UNC'''
| 1
| '''Statistical shape analysis'''
|
|
|-
| '''UNC'''
| 1.1
| Comparative anal. of shape anal. schemes
| Year 2
| Completed
|-
| '''UNC'''
| 1.3
| Statistical shape analysis incl. patient variable
| Year 5
| Complete, refinements ongoing
|-
| '''UNC'''
| 2
| '''Structural analysis of DW-MRI'''
|
|
|-
| '''UNC'''
| 2.1
| DTI tractography tools
| Year 4
| Completed
|-
| '''UNC'''
| 2.2
| Geometric characterization of fiber tracts
| Year 5
| Completed
|-
| '''UNC'''
| 2.3
| Quant. anal. of diffusion along fiber tracts
| Year 5
| Completed.
|-
| '''GaTech'''
| 1.1
| ITK Implementation of PDEs
| Year 2
| Completed
|-
| '''GaTech'''
| 1.1
| Applications to Core 3 data
| Year 4
| Completed
|-
| '''GaTech'''
| 1.2
| New statistic models
| Year 4
| Completed
|-
| '''GaTech'''
| 1.2
| Shape anaylsis
| Year 4
| Completed, refinements ongoing
|-
| '''GaTech'''
| 2.0
| Integration in to Slicer
| Year 4-5
| Preliminary results and ongoing
|-
| '''MGH'''
| 1
| '''Registration'''
|
|
|-
| '''MGH'''
| 1.1
| Collect DTI/QBALL data
| Year 2
| Completed
|-
| '''MGH'''
| 1.2
| Develop registration method
| Year 2
| Completed
|-
| '''MGH'''
| 1.3
| Test/optimize registration method
| Year 3
| In Progress
|-
| '''MGH'''
| 1.4
| Apply registration on core 3 data
| Year 5
| In Queue
|-
| '''MGH'''
| 2
| '''Group DTI Statistics'''
|
|
|-
| '''MGH'''
| 2.1
| Develop group statistic method
| Year 2
| Partially Complete
|-
| '''MGH'''
| 2.2
| Apply on core 3 data
| Year 5
| In Queue
|-
| '''MGH'''
| 3
| '''Diffusion Segmentation '''
|
|
|-
| '''MGH'''
| 3.1
| Collect DTI/QBALL data
| Year 2
| Completed
|-
| '''MGH'''
| 3.2
| Develop/optimize segmentation algorithm
| Year 3
| Modified
|-
| '''MGH'''
| 3.3
| Integrate w/ tractography
| Year 4
| Modified
|-
| '''MGH'''
| 3.4
| Apply on core 3 data
| Year 5
| Modified
|-
| '''MGH'''
| 4
| '''Group Morphometry Statistics'''
|
|
|-
| '''MGH'''
| 4.1
| Develop/optimize statistics algorithms
| Year 3
| Modified
|-
| '''MGH'''
| 4.2
| Develop GUI for Linux
| Year 3
| Modified
|-
| '''MGH'''
| 4.3
| Slicer integration
| Year 3
| Modified
|-
| '''MGH'''
| 4.4
| Compile application on Windows
| Year 4
| Modified
|-
| '''MGH'''
| 5
| XNAT Desktop
| Years 4-5
|
|-
| '''MGH'''
| 5.1
| Establish requirements for desktop version of XNAT
| Years 4-5
| Complete
|-
| '''MGH'''
| 5.2
| Develop implementation plan for prototype
| Years 4-5
| Complete
|-
| '''MGH'''
| 5.3
| Implement prototype version
| Years 4-5
| Incomplete (in progress)
|-
| '''MGH'''
| 5.4
| Implement alpha version
| Year 5
| Incomplete
|-
| '''MGH'''
| 6
| XNAT Central
| Years 4-5
|
|-
| '''MGH'''
| 6.1
| Deploy XNAT Central, a public access XNAT host
| Years 4-5
| Complete
|-
| '''MGH'''
| 6.2
| Coordinate with NAMIC sites to upload project data
| Years 4-5
| Incomplete (ongoing)
|-
| '''MGH'''
| 6.3
| Continue developing XNAT Central based on feedback from NAMIC sites
| Years 4-5
| Incomplete (ongoing)
|-
| '''MGH'''
| 7
| NAMIC Kit integration
| Years 4-5
|
|-
| '''MGH'''
| 7.1
| Implement web services to exchange data with Slicer, Batchmake, and other client applications
| Years 4-5
| Incomplete (ongoing)
|-
| '''MGH'''
| 7.2
| Add XNAT Desktop to standard NAMIC kit distribution
| Year 5
| Incomplete
|-
|}

=== Timeline Modifications ===

{| border="1"
| '''Group'''
| '''Aim'''
| '''Milestone'''
| '''Modification'''
|-
| '''MIT'''
| 2.2
| Methods to compare shape statistics
| Removed, the effort refocused on registration necessary for population studies
|-
| '''MIT'''
| 2.4
| Software infrastructure to integrate shape analysis tools into the pipeline for population studies.
| New, morphed into collaboration with XNAT to provide more general population analysis tools. Partially completed.
|-
| '''MIT'''
| 4
| fMRI analysis including local and atlas-based priors for quantifying activation.
| New, partially completed. Refinements in progress. Clinical study with Core 1 is in progress.
|-
| '''Utah'''
| 2.2 (removed)
| Feature-based brain image registration.
| Shift emphasis to shape-based analysis/registration
|-
| '''Utah'''
| 2.1 (removed)
| Cortical filtering and feature detection
| Effort is subsumed by other Core 1 partners (e.g. see MGH/Freesurfer)
|-
| '''Utah'''
| 1.3 (removed)
| Segmentation of cortex/WM
| Effort is subsumed by other Core 1-2 partners (e.g. see EM-Segmenter)
|-
| '''Utah'''
| 3.0 (removed)
| Fast implmentations of PDEs
| Real-time filtering is demphasized in favor of shape/DTI analysis
|-
| '''Utah'''
| 1.5 (added)
| Joint analysis of DTI and functional data
| Opportunities/needs within various collaborations
|-
| '''Utah'''
| 2.1-2.3 (added, in place of cortical analysis)
| Shape analysis
| Nonparametric shape analysis added to address needs of core 3.
|-
| '''Utah'''
| 2.7
| Shape regression
| Extension/completion of framework. Opportunities/needs within various collaborations.
|-
| '''UNC'''
| 1.2
| Develop medially-based shape representation
| Remove
|-
| '''UNC'''
| 1.4
| Develop generic cortical correspondence framework (Years 3-5)
| New
|-
| '''UNC'''
| 2.4
| DTI Atlas Building (Years 2--4)
| New
|-
| '''GaTech'''
| 2.1
| FA analysis
| New
|-
| '''MGH'''
| 4.1 - 4.4
| Group Morphometry Statistics
| Added and then removed, based on personnel changes
|-
| '''MGH'''
| 5-7
| XNAT
| Added to support remote image database capabilities
|}

=== [[Core_1_Timeline_Notes|Core 1 Timeline Notes ]] ===

== Core 2: Engineering ==

=== Core 2 Timelines and Milestones ===

{| border="1"
| '''Group'''
| '''Aim'''
| '''Milestone'''
| '''Proposed time of completion'''
| '''Status'''
|-
| '''GE'''
| 1
| '''Define software architecture'''
|
|
|-
| '''GE'''
| 1
| Object design
| Yr 1
| Completed
|-
| '''GE'''
| 1
| Identify patterns
| Yr 3
| Patterns for processing scalar and vector images, models, fiducials complete. Patterns for diffusion weighted completed, fMRI ongoing.
|-
| '''GE'''
| 1
| Create frameworks
| Yr 3
| Frameworks for processing scalar and vector images, models, fiducials complete. Frameworks for diffusion weighted completed, fMRI ongoing.
|-
| '''GE'''
| 2
| '''Software engineering process'''
|
|
|-
| '''GE'''
| 2
| Extreme programming
| Yr 1-5
| On schedule, ongoing
|-
| '''GE'''
| 2
| Process automatiion
| Yr 3
| On schedule, ongoing
|-
| '''GE'''
| 2
| Refactoring
| Yr 3
| Complete
|-
| '''GE'''
| 3
| '''Automated quality system'''
|
|
|-
| '''GE'''
| 3
| DART deployment
| Yr 2
| Complete
|-
| '''GE'''
| 3
| Persistent testing system
| Yr 5
| Incomplete
|-
| '''GE'''
| 3
| Automatic defect detection
| Yr 5
| Incomplete
|-
| '''Kitware'''
| 1
| '''Cross-platform development'''
|
|
|-
| '''Kitware'''
| 1
| Deploy environment (CMake, CTest)
| Yr 1
| Complete
|-
| '''Kitware'''
| 1
| DART Integration and testing
| Yr 1
| Complete
|-
| '''Kitware'''
| 1
| Documentation tools
| Yr 2
| Complete
|-
| '''Kitware'''
| 2
| '''Integration tools'''
|
|
|-
| '''Kitware'''
| 2
| File Formats/IO facilities
| Yr 2
| Complete
|-
| '''Kitware'''
| 2
| CableSWIG deployment
| Yr 3
| Complete (integration ongoing)
|-
| '''Kitware'''
| 2
| Establish XML schema
| Yr 4
| Complete, refinements ongoing
|-
| '''Kitware'''
| 3
| '''Technology delivery'''
|
|
|-
| '''Kitware'''
| 3
| Deploy applications
| Yr 1
| Complete (ongoing)
|-
| '''Kitware'''
| 3
| Establish plug-in repository
| Yr 2
| Incomplete
|-
| '''Kitware'''
| 3
| Cpack
| Yr 4-5
| Incomplete
|-
| '''Isomics'''
| 1
| NAMIC builds of slicer
| Years 2--5
| Complete
|-
| '''Isomics'''
| 1
| Schizophrenia and DBP intefaces
| Year 3---5
| Completed (refinements ongoing)
|-
| '''Isomics'''
| 2
| ITK Integration tools
| Year 1---3
| Completed
|-
| '''Isomics'''
| 2
| Experiment Control Interfaces
| Year 2---5
| Migration from LONI to BatchMake Underway
|-
| '''Isomics'''
| 2
| fMRI/DTI algorithm support
| Year 2---5
| Completed DTI, fMRI Ongoing
|-
| '''Isomics'''
| 2
| New DBP algorithm support
| Year 2---5
| Ongoing
|-
| '''Isomics'''
| 3
| Compatible build process
| Year 1---3
| Completed
|-
| '''Isomics'''
| 3
| Dart Integration
| Year 1---2
| Completed (upgrades ongoing)
|-
| '''Isomics'''
| 3
| Test scripts for new code
| Year 2---5
| Ongoing
|-
| '''UCSD'''
| 1
| Grid computing---base
| Year 1
| Completed
|-
| '''UCSD'''
| 1
| Grid enabled algorithms
| Year 3
| First version (GWiz alpha) available - initial integration with Slicer3 and execution model.
|-
| '''UCSD'''
| 1
| Testing infrastructure
| Year 4
| Initiated
|-
| '''UCSD'''
| 2
| Data grid --- compatibility
| Year 2
| Completed
|-
| '''UCSD'''
| 2
| Data grid --- slicer access
| Year 2
| Completed for version 2.6. In progress for Slicer3
|-
| '''UCSD'''
| 3
| Data mediation --- deploy
| Year 1
| Incomplete (modfication below)
|-
| '''UCLA'''
| 1
| Debabeler functionality
| Year 1
| Continued Progress
|-
| '''UCLA'''
| 2
| SLIPIE Interpretation (Layer 1)
| Year 1--Year2
| In Progress
|-
| '''UCLA'''
| 3
| SLIPIE Interpretation (Layer 2)
| Year 1--Year2
| On Schedule
|-
| '''UCLA'''
| 3
| Developing ITK Modules
| Year2
| In Progress
|-
| '''UCLA'''
| 4
| Integrating SRB (GSI-enabled)
| Year2
| Completed
|-
| '''UCLA'''
| 5
| Integrating IDA
| Year2
| Completed
|-
| '''UCLA'''
| 5
| Integrating External Visualization Applications
| Year2
| Completed
|}

=== Core 2 Timeline Modifications ===

{| border="1"
| '''Group'''
| '''Aim'''
| '''Milestone'''
| '''Modification'''
|-
| '''Isomics'''
| 3
| Data mediation
| Delayed pending integration of databases into NAMIC infractructure
|}

=== [[Core_2_Timeline_Notes|Core 2 Timeline Notes ]] ===

== Core 3: Driving Biological Problems ==

The Core 3 projects submitted R01 style proposals, as specified in the RFA, and did not submit timelines.

== Core 4: Service ==

=== Core 4 Timelines and Milestones ===

{| border="1"
| '''Group'''
| '''Aim'''
| '''Milestone'''
| '''Proposed time of completion'''
| '''Status'''
|-
| '''Kitware'''
| 1
| '''Implement Development Farms'''
|
|
|-
| '''Kitware'''
| 1
| Deploy platforms
| Yrs 1
| Complete
|-
| '''Kitware'''
| 1
| Communications
| Yrs 1
| Complete, ongoing
|-
| '''Kitware'''
| 2
| '''Establish software process'''
|
|
|-
| '''Kitware'''
| 2
| Secure developer database
| Yr 1
| Complete, ongoing
|-
| '''Kitware'''
| 2
| Collect guidelines
| Yr 1
| Complete
|-
| '''Kitware'''
| 2
| Manage software submission process
| Yr 1
| Complete
|-
| '''Kitware'''
| 2
| Configure process tools
| Yr 1
| Complete
|-
| '''Kitware'''
| 2
| Survey community
| Yr 1
| Complete
|-
| '''Kitware'''
| 3
| '''Deploy NAMIC Tools'''
|
|
|-
| '''Kitware'''
| 3
| Toolkits
| Yr 1
| Complete
|-
| '''Kitware'''
| 3
| Integration tools
| Yr 1
| Complete
|-
| '''Kitware'''
| 3
| Applications
| Yr 1
| Complete
|-
| '''Kitware'''
| 3
| Integrate new computing resources
| Yr 1
| Complete
|-
| '''Kitware'''
| 4
| '''Provide support'''
|
|
|-
| '''Kitware'''
| 4
| Esablish support infrastructure
| Yrs 1--5
| On schedule, ongoing
|-
| '''Kitware'''
| 4
| NAMIC support
| Yr 1
| Complete
|-
| '''Kitware'''
| 5
| Manage NAMIC Software Releases
| Yrs 1--5
| On schedule, ongoing
|}

=== Core 4 Timeline Modifications ===

{| border="1"
| '''Group'''
| '''Aim'''
| '''Milestone'''
| '''Modification'''
|-
| Kitware
| 2-5
| Various
| Refined/modified the sub aims
|}

=== [[Core_4_Timeline_Notes|Core 4 Timeline Notes ]] ===

== Core 5: Training ==

=== Core 5 Timelines and Milestones ===

{| border="1"
| '''Group'''
| '''Aim'''
| '''Milestone'''
| '''Proposed time of completion'''
| '''Status'''
|-
| '''Harvard'''
| 1
| '''Formal Training Guidllines'''
|
|
|-
| '''Harvard'''
| 1
| Functional neuroanatomy
| Yr 1
| Complete
|-
| '''Harvard'''
| 1
| Clinical correlations
| Yr 1
| Complete
|-
| '''Harvard'''
| 2
| '''Mentoring'''
|
|
|-
| '''Harvard'''
| 2
| Programming workshops
| Yrs 1-5
| On schedule, ongoing
|-
| '''Harvard'''
| 2
| One-on-one mentoring, Cores 1, 2, 3
| Yrs 1-5
| On schedule, ongoing
|-
| '''Harvard'''
| 3
| '''Collaborative work environment'''
|
|
|-
| '''Harvard'''
| 3
| Wiki
| Yrs 1
| Complete
|-
| '''Harvard'''
| 3
| Mailing lists
| Yrs 1
| Complete
|-
| '''Harvard'''
| 3
| Regular telephone conferences
| Yrs 1-5
| On schedule, ongoing
|-
| '''Harvard'''
| 4
| '''Educational component for tools'''
|
|
|-
| '''Harvard'''
| 4
| Slicer training modules
| Yr 2-5
| Slicer 2.x tutorials complete, Two Slicer 3 tutorials complete, translation of 2.x tutorials to 3 is ongoing and on schedule
|-
| '''Harvard'''
| 5
| '''Demonstrations and hands-on training'''
|
|
|-
| '''Harvard'''
| 5
| Various workshops and conferences
| Yrs 1--5
| On schedule, ongoing
|}

=== Core 5 Timeline Modifications ===

None.

=== [[Core_5_Timeline_Notes|Core 5 Timeline Notes ]] ===

== Core 6: Dissemination ==

=== Core 6 Timelines and Milestones ===

{| border="1"
| '''Group'''
| '''Aim'''
| '''Milestone'''
| '''Proposed time of completion'''
| '''Status'''
|-
| Isomics
| 1
| Create a collaboration metholdology for NA-MIC
|
|
|-
| Isomics
| 1.1
| develop a selection process
| Yr 1
| Complete
|-
| Isomics
| 1.2
| guidelines to govern the collaborations
| Yr 1-2
| Complete
|-
| Isomics
| 1.3
| Provide on-site training
| Yr 1-5
| Complete for current tools (ongoing for tool refinement)
|-
| Isomics
| 1.4
| develop a web site infrastructure
| Yr 1
| Complete
|-
| Isomics
| 2
| Facilitate communication between NA-MIC developers and wider research community
|
|
|-
| Isomics
| 2.1
| develop materials describing NAMIC technology
| Yr 1-5
| On Schedule
|-
| Isomics
| 2.2
| participate in scientific meetings
| Yr 2-5
| On Schedule
|-
| Isomics
| 2.3
| Document interactions with external researchers
| Yr 2-5
| On Schedule
|-
| Isomics
| 2.4
| Coordinate publication strategies
| Yr 3-5
| On Schedule
|-
| Isomics
| 3
| Develop a publicly accessible internet resource of data, software, documentation, and publication of new discoveries
|
|
|-
| Isomics
| 3.1
| On-line repository of NAMIC related publications and presentations
| Yr 1-5
| On Schedule
|-
| Isomics
| 3.2
| On-line repository of NAMIC tutorial and training material
| Yr 1-5
| On Schedule
|-
| Isomics
| 3.3
| Index and a searchable database
| Yr 1-2
| Done
|-
| Isomics
| 3.4
| Automated feedback systems that track software downloads
| Yr 3
| Done
|}

=== Core 6 Timeline Modifications ===

None.

=== [[Core_6_Timeline_Notes|Core 6 Timeline Notes ]] ===

=Appendix A Publications (Mastrogiacomo)=
A list should be mined from the publications database and attached here in MS word format.

=Appendix B EAB Report and Response (Kapur)=
===EAB Report===

===Response to EAB Report===

2009 Winter Project Week Hageman FMTractography

2009-01-09T17:51:29Z

Nhageman: /* Key Investigators */

2009 Winter Project Week Hageman FMTractography

2009-01-09T17:50:38Z

Nhageman: /* Key Investigators */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:Hageman_cspfig4NAMIC_07-06-22.png|thumb|320px|Corticospinal tracts segmented using our fluid mechanics based tractography method.]]
|[[Image:Hageman_FullBrainSlicerTractography.jpg|thumb|320px|Full brain tracts segmented using multiple fluid sources/sinks.]]
|[[Image:FMModuleScreenshot.png|thumb|320px|Screenshot of Slicer Module for Fluid Mechanics Tractography.]]
|}

__NOTOC__

===Key Investigators===
* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D
* Isomics: Steve Pieper and Alex Yarmarkovich

<div style="margin: 20px;">

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

<h1>Objective</h1>
Computational fluid dynamics is a rich field and its application to the analysis of diffusion tensor imaging (DTI) datasets has yielded possible applications to tractography, image registration, and white matter pathology. We are developing several useful and novel diffusion tensor imaging (DTI) analysis algorithms modeled on the principles of fluid mechanics for inclusion within the NA-MIC framework. The goal of this project is to develop these methods, make them compatible with the NA-MIC ITK-based software infrastructure (i.e. Slicer), and promote their dissemination to the scientific community.

See our [[hageman:NAMICFluidMechDTITractography|Project Page]] for more information.

</div>

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

<h1>Approach, Plan</h1>

We have developed and initially validated a DTI tractography method based on Navier-Stokes fluid mechanics. See the papers listed in the reference section for complete details on the method. Our approach for this project week will focus on the following:
* Building the our current CL Slicer module into an interactive GUI in Slicer 3. Our method is currently integrated as a CL Slicer module in a custom build of Slicer 3. The module has the following functionalities:
**reconstruction of the diffusion tensor and computation of common DTI scalar volumes (FA, LI, RGB). In addition, if users prefer using their own tensor reconstruction methods, the module can be run with any arbitrary set of tensor volumes.
**computation of fluid velocity vector field volume
**reconstruction of tracts based on the above fluid velocity volume
** Optimizing initial coding of method in ITK (better use of multithreading)
** Specialized visualization using VTK:
*** Fluid velocity vector field animation
*** Layout for Slicer 3 Plug-in
*** Interactive (real-time) manipulation of sources/sinks (ROIs) on steady-state fluid solution (possible application for intra-operative DTI)
* Working with the interested groups in analyzing control and white matter pathology data. Specifically, we have seen promising results when looking at the flow perturbation around white matter lesions seen in multiple sclerosis or stroke that may suggest a novel method for automatic lesion detection in DTI.
</div>

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

<h1>Progress</h1>
* Command line fluid mechanics tractography module integrated into Slicer 3.
* VTK module for fluid mechanics visualization completed.
** Discussion of possibly including module in next stable Slicer release.
** Progress made on (near) real time fluid velocity vector field animation but not yet stable for release.
* Arrangements made to include FM tractography method as part of DTI validation effort.
</div>

<br style="clear: both;" />

</div>

===References===
* Hageman NS, Shattuck DW, Narr K, Toga AW (2006). A diffusion tensor imaging tractography method based on Navier-Stokes fluid mechanics. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2006), Arlington, VA, USA, 6-9 April 2006. p. 798-801
* Hageman NS, Toga AW, Narr K, Shattuck DW (2008). A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics. IEEE Trans. in Medicial Imaging, In Submission.
* Hamilton L, Nuechterlein K, Hageman NS, Woods R, Asarnow R, Alger J, Gaser C, Toga AW, Narr K (2008). Mean Diffusivity and Fractional Anisotropy as Indicators of Schizophrenia and Genetic Vulnerability, Neuroimage, In Submission.

2009 Winter Project Week Hageman UCLANSBrainLab

2009-01-09T17:46:20Z

Nhageman: /* Key Investigators */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|}

__NOTOC__

===Key Investigators===
* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D

<div style="margin: 20px;">

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

<h1>Objective</h1>
Preoperative mapping of the brain is an important step in tumor resection involving functionally critical areas of the brain. Visualization of the location of gray and white matter structures with respect to the tumor mass helps the surgeon plan an operative approach that will minimize post-operative deficits. While functional areas have successfully been localized via fMRI, recently diffusion tensor imaging (DTI) has been shown to be successful in localizing critical white matter structures as well. The neurosurgery department at UCLA has been using BrainLab to do this type of preoperative planning in tumor patients. The recent link of BrainLab to Slicer allows us to take advantage of the alogithms in Slicer in the clinical research setting. The goal of this project is to develop a successful link between BrainLab and Slicer for the UCLA neurosugery department to assist in preoperative planning of tumor resection.

</div>

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

<h1>Approach, Plan</h1>
* Establishment of successful link between Slicer and BrainLab for the UCLA neurosurgery department
* Clinical study of preoperative planning of tumor resection using Slicer methods
</div>

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

<h1>Progress</h1>
* Successful segmentation of tumor data (WM tractography and tumor boundaries) from UCLA neurosurgery in Slicer.
** Visualization will currently be used in pre-operative planning of tumor resection.
** Analysis of tracts (via scalar metrics) will be correlated with clinical outcome.
* Discussion of ways to include fMRI and DTI data analysis via Slicer into BrainLab through the IGT link.
</div>

<br style="clear: both;" />

</div>

===References===

http://www.slicer.org/slicerWiki/index.php/Slicer3:BrainLab_Integration

2009 Winter Project Week Hageman FEMSolverLib

2009-01-09T17:41:01Z

Nhageman: /* Key Investigators */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|}

__NOTOC__

===Key Investigators===
* UCLA: Nathan Hageman
* Isomics: Steve Pieper
* UIowa: Vince Magnotta, Nicole Grosland
* Mario Negri: Luca Antiga
* Kitware: Luis Ibanez

<div style="margin: 20px;">

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

<h1>Objective</h1>
Finite element method (FEM) and finite volume method (FVM) approaches are common ways to obtain numerical estimates to differential equations which do not lend themselves to analytical solutions. These varied methods can be computationally difficult and time-consuming to code and optimize. Therefore, a library of standard algorithmic approaches would save redundant effort and help to standardize approaches. The goal of this project is to develop and compile these methods within an ITK-compatible framework and make them available for use to the general scientific community.

</div>

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

<h1>Approach, Plan</h1>
* Creation of an FEM/FVM solver library within ITK from which standard FEM/FVM methods can be used
* Above FEM/FVM library will allow users to create novel methods derived from standard approaches
* Creation of Slicer module that provides a GUI for FEM/FVM solvers
</div>

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

<h1>Progress</h1>
* Preliminary coding/planning of FVM ITK class
* Commitment to continue class/module development via inclusion as part of weekly engineering tcons
</div>

<br style="clear: both;" />

</div>

===References===

2009 Winter Project Week Hageman UCLANSBrainLab

2009-01-09T17:31:24Z

Nhageman: /* Key Investigators */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|}

__NOTOC__

===Key Investigators===
* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D

<div style="margin: 20px;">

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

<h1>Objective</h1>
Preoperative mapping of the brain is an important step in tumor resection involving functionally critical areas of the brain. Visualization of the location of gray and white matter structures with respect to the tumor mass helps the surgeon plan an operative approach that will minimize post-operative deficits. While functional areas have successfully been localized via fMRI, recently diffusion tensor imaging (DTI) has been shown to be successful in localizing critical white matter structures as well. The neurosurgery department at UCLA has been using BrainLab to do this type of preoperative planning in tumor patients. The recent link of BrainLab to Slicer allows us to take advantage of the alogithms in Slicer in the clinical research setting. The goal of this project is to develop a successful link between BrainLab and Slicer for the UCLA neurosugery department to assist in preoperative planning of tumor resection.

</div>

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

<h1>Approach, Plan</h1>
* Establishment of successful link between Slicer and BrainLab for the UCLA neurosurgery department
* Clinical study of preoperative planning of tumor resection using Slicer methods
</div>

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

<h1>Progress</h1>
* Successful segmentation of tumor data from UCLA neurosurgery in Slicer.
</div>

<br style="clear: both;" />

</div>

===References===

http://www.slicer.org/slicerWiki/index.php/Slicer3:BrainLab_Integration

2009 Winter Project Week Hageman FMTractography

2009-01-09T17:27:30Z

Nhageman: /* Key Investigators */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:Hageman_cspfig4NAMIC_07-06-22.png|thumb|320px|Corticospinal tracts segmented using our fluid mechanics based tractography method.]]
|[[Image:Hageman_FullBrainSlicerTractography.jpg|thumb|320px|Full brain tracts segmented using multiple fluid sources/sinks.]]
|[[Image:FMModuleScreenshot.png|thumb|320px|Screenshot of Slicer Module for Fluid Mechanics Tractography.]]
|}

__NOTOC__

===Key Investigators===
* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D
* Isomics: Steve Pieper and Alex Yarmarkovich

<div style="margin: 20px;">

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

<h1>Objective</h1>
Computational fluid dynamics is a rich field and its application to the analysis of diffusion tensor imaging (DTI) datasets has yielded possible applications to tractography, image registration, and white matter pathology. We are developing several useful and novel diffusion tensor imaging (DTI) analysis algorithms modeled on the principles of fluid mechanics for inclusion within the NA-MIC framework. The goal of this project is to develop these methods, make them compatible with the NA-MIC ITK-based software infrastructure (i.e. Slicer), and promote their dissemination to the scientific community.

See our [[hageman:NAMICFluidMechDTITractography|Project Page]] for more information.

</div>

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

<h1>Approach, Plan</h1>

We have developed and initially validated a DTI tractography method based on Navier-Stokes fluid mechanics. See the papers listed in the reference section for complete details on the method. Our approach for this project week will focus on the following:
* Building the our current CL Slicer module into an interactive GUI in Slicer 3. Our method is currently integrated as a CL Slicer module in a custom build of Slicer 3. The module has the following functionalities:
**reconstruction of the diffusion tensor and computation of common DTI scalar volumes (FA, LI, RGB). In addition, if users prefer using their own tensor reconstruction methods, the module can be run with any arbitrary set of tensor volumes.
**computation of fluid velocity vector field volume
**reconstruction of tracts based on the above fluid velocity volume
** Optimizing initial coding of method in ITK (better use of multithreading)
** Specialized visualization using VTK:
*** Fluid velocity vector field animation
*** Layout for Slicer 3 Plug-in
*** Interactive (real-time) manipulation of sources/sinks (ROIs) on steady-state fluid solution (possible application for intra-operative DTI)
* Working with the interested groups in analyzing control and white matter pathology data. Specifically, we have seen promising results when looking at the flow perturbation around white matter lesions seen in multiple sclerosis or stroke that may suggest a novel method for automatic lesion detection in DTI.
</div>

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

<h1>Progress</h1>
* Command line fluid mechanics tractography module integrated into Slicer 3.
* VTK module for fluid mechanics visualization completed and to be included in next Slicer release.
* Arrangements made to include FM tractography as part of DTI validation effort.
</div>

<br style="clear: both;" />

</div>

===References===
* Hageman NS, Shattuck DW, Narr K, Toga AW (2006). A diffusion tensor imaging tractography method based on Navier-Stokes fluid mechanics. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2006), Arlington, VA, USA, 6-9 April 2006. p. 798-801
* Hageman NS, Toga AW, Narr K, Shattuck DW (2008). A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics. IEEE Trans. in Medicial Imaging, In Submission.
* Hamilton L, Nuechterlein K, Hageman NS, Woods R, Asarnow R, Alger J, Gaser C, Toga AW, Narr K (2008). Mean Diffusivity and Fractional Anisotropy as Indicators of Schizophrenia and Genetic Vulnerability, Neuroimage, In Submission.

2009 Winter Project Week Hageman FMTractography

2009-01-09T17:06:53Z

Nhageman: /* Key Investigators */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:Hageman_cspfig4NAMIC_07-06-22.png|thumb|320px|Corticospinal tracts segmented using our fluid mechanics based tractography method.]]
|[[Image:Hageman_FullBrainSlicerTractography.jpg|thumb|320px|Full brain tracts segmented using multiple fluid sources/sinks.]]
|[[Image:FMModuleScreenshot.png|thumb|320px|Screenshot of Slicer Module for Fluid Mechanics Tractography.]]
|}

__NOTOC__

===Key Investigators===
* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D
* Isomics: Steve Pieper and Alex Yarmarkovich

<div style="margin: 20px;">

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

<h1>Objective</h1>
Computational fluid dynamics is a rich field and its application to the analysis of diffusion tensor imaging (DTI) datasets has yielded possible applications to tractography, image registration, and white matter pathology. We are developing several useful and novel diffusion tensor imaging (DTI) analysis algorithms modeled on the principles of fluid mechanics for inclusion within the NA-MIC framework. The goal of this project is to develop these methods, make them compatible with the NA-MIC ITK-based software infrastructure (i.e. Slicer), and promote their dissemination to the scientific community.

See our [[hageman:NAMICFluidMechDTITractography|Project Page]] for more information.

</div>

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

<h1>Approach, Plan</h1>

We have developed and initially validated a DTI tractography method based on Navier-Stokes fluid mechanics. See the papers listed in the reference section for complete details on the method. Our approach for this project week will focus on the following:
* Building the our current CL Slicer module into an interactive GUI in Slicer 3. Our method is currently integrated as a CL Slicer module in a custom build of Slicer 3. The module has the following functionalities:
**reconstruction of the diffusion tensor and computation of common DTI scalar volumes (FA, LI, RGB). In addition, if users prefer using their own tensor reconstruction methods, the module can be run with any arbitrary set of tensor volumes.
**computation of fluid velocity vector field volume
**reconstruction of tracts based on the above fluid velocity volume
** Optimizing initial coding of method in ITK (better use of multithreading)
** Specialized visualization using VTK:
*** Fluid velocity vector field animation
*** Layout for Slicer 3 Plug-in
*** Interactive (real-time) manipulation of sources/sinks (ROIs) on steady-state fluid solution (possible application for intra-operative DTI)
* Working with the interested groups in analyzing control and white matter pathology data. Specifically, we have seen promising results when looking at the flow perturbation around white matter lesions seen in multiple sclerosis or stroke that may suggest a novel method for automatic lesion detection in DTI.
</div>

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

<h1>Progress</h1>
* Command line fluid mechanics tractography module integrated into Slicer 3.
* vtk module for fluid mechanics visualization completed and to be included in next Slicer release.

</div>

<br style="clear: both;" />

</div>

===References===
* Hageman NS, Shattuck DW, Narr K, Toga AW (2006). A diffusion tensor imaging tractography method based on Navier-Stokes fluid mechanics. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2006), Arlington, VA, USA, 6-9 April 2006. p. 798-801
* Hageman NS, Toga AW, Narr K, Shattuck DW (2008). A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics. IEEE Trans. in Medicial Imaging, In Submission.
* Hamilton L, Nuechterlein K, Hageman NS, Woods R, Asarnow R, Alger J, Gaser C, Toga AW, Narr K (2008). Mean Diffusivity and Fractional Anisotropy as Indicators of Schizophrenia and Genetic Vulnerability, Neuroimage, In Submission.