NAMIC Wiki - User contributions [en]

2010 Winter Project Week HARDI RSH

2010-01-08T17:25:27Z

Lbloy:

__NOTOC__
<gallery>
Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]]
Image:PW 2010W_HardiRsh_VolumesModule.png|Screen shot of visualization module
</gallery>

==Key Investigators==
* UPenn: Luke Bloy, Ragini Verma
* BWH: Carl-Fredrik Westin

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

<h3>Objective</h3>
We would like to provide support for high angular resolution diffusion imaging (HARDI) data models which make use of the symmetric real spherical harmonic functions (RSH) as a basis for functions on the sphere.
</div>

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

<h3>Approach, Plan</h3>
First consensus must be reached on the exact form of the RSH basis to be used. This will provide a basis for future development.

The functionality we would like to provide is the following:
# MRML representations for images of RSH coefficients
# Visualization of images of RSH coefficients
# Routines for estimating the orientation distribution function (ODF) (Descoteaux2007)
# Routines for estimating the fiber orientation distribution (FOD) (Tournier2007) using both filtered and constrained spherical deconvolution.

</div>

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

<h3>Progress</h3>

We have implemented the RSH basis and RSH coefficients as ITK based C++ classes, and written ITK image filters to perform the
model estimation. Slicer modules need to be written to perform the integrated these filters into the Slicer framework.

MRML nodes have been written for RSH volumes. These nodes were based (blindly) off of the DiffusionTensor MRML nodes. There is a mathematics class
which computes scalar maps based off of the RSH coefficients, as well as glpyher which currently only supports sphere sources. Support for line glyph source, to show only the principle diffusion directions would be very beneficial since rendering all the points on the sphere source is very resource intensive.

Visualization is currently being achieved by an extension to the Volumes module in slicer. The display widget nodes to facilitate this were again based on the Diffusion Widget classes.

</div>
</div>

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

==References==
*Maxime Descoteaux, Elaine Angelino, Shaun Fitzgibbons, and Rachid Deriche, “Regularized, fast, and robust analytical q-ball imaging,” Magnetic Resonance in Medicine, vol. 58, no. 3, pp. 497–510, 2007.
*J-Donald Tournier, Fernando Calamante, and Alan Connelly, “Robust determination of the fibre orientation distribution in diffusion mri: Non-negativity constrained super-resolved spherical deconvolution,” NeuroImage, vol. 35, no. 4, pp. 1459–1472, May 2007.

</div>

2010 Winter Project Week HARDI RSH

2010-01-06T16:38:16Z

Lbloy:

__NOTOC__
<gallery>
Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]]
Image:PW 2010W_HardiRsh_glyph.png|Example glyphs
Image:PW 2010W_HardiRsh_VolumesModule.png|Screen shot of visualization module
</gallery>

==Key Investigators==
* UPenn: Luke Bloy, Ragini Verma
* BWH: Carl-Fredrik Westin

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

<h3>Objective</h3>
We would like to provide support for high angular resolution diffusion imaging (HARDI) data models which make use of the symmetric real spherical harmonic functions (RSH) as a basis for functions on the sphere.
</div>

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

<h3>Approach, Plan</h3>
First consensus must be reached on the exact form of the RSH basis to be used. This will provide a basis for future development.

The functionality we would like to provide is the following:
# MRML representations for images of RSH coefficients
# Visualization of images of RSH coefficients
# Routines for estimating the orientation distribution function (ODF) (Descoteaux2007)
# Routines for estimating the fiber orientation distribution (FOD) (Tournier2007) using both filtered and constrained spherical deconvolution.

</div>

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

<h3>Progress</h3>

We have implemented the RSH basis and RSH coefficients as ITK based C++ classes, and written ITK image filters to perform the
model estimation. Slicer modules need to be written to perform the integrated these filters into the Slicer framework.

MRML nodes have been written for RSH volumes. These nodes were based (blindly) off of the DiffusionTensor MRML nodes. There is a mathematics class
which computes scalar maps based off of the RSH coefficients, as well as glpyher which currently only supports sphere sources. Support for line glyph source, to show only the principle diffusion directions would be very beneficial since rendering all the points on the sphere source is very resource intensive.

Visualization is currently being achieved by an extension to the Volumes module in slicer. The display widget nodes to facilitate this were again based on the Diffusion Widget classes.

</div>
</div>

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

==References==
*Maxime Descoteaux, Elaine Angelino, Shaun Fitzgibbons, and Rachid Deriche, “Regularized, fast, and robust analytical q-ball imaging,” Magnetic Resonance in Medicine, vol. 58, no. 3, pp. 497–510, 2007.
*J-Donald Tournier, Fernando Calamante, and Alan Connelly, “Robust determination of the fibre orientation distribution in diffusion mri: Non-negativity constrained super-resolved spherical deconvolution,” NeuroImage, vol. 35, no. 4, pp. 1459–1472, May 2007.

</div>

File:PW 2010W HardiRsh VolumesModule.png

2010-01-06T16:35:24Z

Lbloy:

File:PW 2010W HardiRsh glyph.png

2010-01-06T16:27:18Z

Lbloy:

2010 Winter Project Week HARDI RSH

2009-12-01T16:22:57Z

Lbloy: HARDI RSH

__NOTOC__
<gallery>
Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* UPenn: Luke Bloy, Ragini Verma
* BWH: Carl-Fredrik Westin

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

<h3>Objective</h3>
We would like to provide support for high angular resolution diffusion imaging (HARDI) data models which make use of the symmetric real spherical harmonic functions (RSH) as a basis for functions on the sphere.
</div>

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

<h3>Approach, Plan</h3>
First consensus must be reached on the exact form of the RSH basis to be used. This will provide a basis for future development.

The functionality we would like to provide is the following:
# MRML representations for images of RSH coefficients
# Visualization of images of RSH coefficients
# Routines for estimating the orientation distribution function (ODF) (Descoteaux2007)
# Routines for estimating the fiber orientation distribution (FOD) (Tournier2007) using both filtered and constrained spherical deconvolution.

</div>

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

<h3>Progress</h3>

We have implemented the RSH basis and RSH coefficients as ITK based C++ classes, and written ITK image filters to perform the
model estimation. Slicer modules need to be written to perform the integrated these filters into the Slicer framework.

MRML nodes have been written for RSH volumes. These nodes were based (blindly) off of the DiffusionTensor MRML nodes. There is a mathematics class
which computes scalar maps based off of the RSH coefficients, as well as glpyher which currently only supports sphere sources. Support for line glyph source, to show only the principle diffusion directions would be very beneficial since rendering all the points on the sphere source is very resource intensive.

Visualization is currently being achieved by an extension to the Volumes module in slicer. The display widget nodes to facilitate this were again based on the Diffusion Widget classes.

</div>
</div>

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

==References==
*Maxime Descoteaux, Elaine Angelino, Shaun Fitzgibbons, and Rachid Deriche, “Regularized, fast, and robust analytical q-ball imaging,” Magnetic Resonance in Medicine, vol. 58, no. 3, pp. 497–510, 2007.
*J-Donald Tournier, Fernando Calamante, and Alan Connelly, “Robust determination of the fibre orientation distribution in diffusion mri: Non-negativity constrained super-resolved spherical deconvolution,” NeuroImage, vol. 35, no. 4, pp. 1459–1472, May 2007.

</div>

2010 Winter Project Week

2009-12-01T15:50:36Z

Lbloy: /* Diffusion */

Back to [[Project Events]], [[AHM_2010]], [[Events]]

__NOTOC__

==Background==

From January 4-8, 2010, the tenth project week for hands-on research and development activity in Image-Guided Therapy and Neuroscience applications will be hosted in Salt Lake City, Utah. Participant engange in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

== Dates.Venue.Registration ==

Please [[AHM_2010#Dates._Venue._Registration| click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2010#Agenda|click here for the agenda for AHM 2010 and Project Week]].

==Projects==

=== Segmentation ===
#[[2010_Winter_Project_Week_The_Vascular_Modeling_Toolkit_in_3D_Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Steve Pieper)

=== Registration ===
#[[2010_Winter_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library Project]] (Dominik Meier, Casey Goodlett, Ron Kikinis)

=== IGT ===
# [[2010_Winter_Project_Week_Fast_Imaging_Library_%2B_Siemens_EPI]] (Scott Hoge, Nick Todd, Dennis Parker)

=== Radiotherapy ===

=== Analysis ===

=== Informatics ===

=== Diffusion ===
#[[ 2010_Winter_Project_Week_HARDI_RSH|Integration of Real Spherical Harmonic basis for HARDI models ]] (Luke Bloy, C-F Westin)

=== Python ===

=== NA-MIC Kit Internals ===
#Testing for Extensions (Steve, Andre, Jim, Julien Jomier)
#[[2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration|Integration of SPECTRE Java module into 3D Slicer]] (Nicole Aucoin, Aaron Carass, Min Chen)

=== Execution Model ===

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
# Starting Thursday, October 15th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 15: Engineering Infrastructure Projects
#*October 22: Funded External Collaboration Projects
#*October 29: Funded External Collaboration Projects
#*November 5: DPB Projects
#*November 19: DPB Projects
#*December 3: Other/new collaborations
#*December 10: Finalize Engineering Projects
#*December 17: Loose Ends
#By December 17, 2010: [[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 December 17, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
## 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...

2010 Winter Project Week

2009-12-01T15:49:43Z

Lbloy: /* Diffusion */

Back to [[Project Events]], [[AHM_2010]], [[Events]]

__NOTOC__

==Background==

From January 4-8, 2010, the tenth project week for hands-on research and development activity in Image-Guided Therapy and Neuroscience applications will be hosted in Salt Lake City, Utah. Participant engange in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

== Dates.Venue.Registration ==

Please [[AHM_2010#Dates._Venue._Registration| click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2010#Agenda|click here for the agenda for AHM 2010 and Project Week]].

==Projects==

=== Segmentation ===
#[[2010_Winter_Project_Week_The_Vascular_Modeling_Toolkit_in_3D_Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Steve Pieper)

=== Registration ===
#[[2010_Winter_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library Project]] (Dominik Meier, Casey Goodlett, Ron Kikinis)

=== IGT ===
# [[2010_Winter_Project_Week_Fast_Imaging_Library_%2B_Siemens_EPI]] (Scott Hoge, Nick Todd, Dennis Parker)

=== Radiotherapy ===

=== Analysis ===

=== Informatics ===

=== Diffusion ===
[[ 2010_Winter_Project_Week_HARDI_RSH|Integration of Real Spherical Harmonic basis for HARDI models ]] (Luke Bloy, C-F Westin)

=== Python ===

=== NA-MIC Kit Internals ===
#Testing for Extensions (Steve, Andre, Jim, Julien Jomier)
#[[2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration|Integration of SPECTRE Java module into 3D Slicer]] (Nicole Aucoin, Aaron Carass, Min Chen)

=== Execution Model ===

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
# Starting Thursday, October 15th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 15: Engineering Infrastructure Projects
#*October 22: Funded External Collaboration Projects
#*October 29: Funded External Collaboration Projects
#*November 5: DPB Projects
#*November 19: DPB Projects
#*December 3: Other/new collaborations
#*December 10: Finalize Engineering Projects
#*December 17: Loose Ends
#By December 17, 2010: [[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 December 17, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
## 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...