NAMIC Wiki - User contributions [en]

2010 Summer Project Week HandN Cancer

2010-06-25T12:51:06Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
File:HN_CBCT.png|Sample Image Dataset.
Image:RegistrationRigidHN.png|Sample Image Registration Output.
</gallery>

==Key Investigators==
* Politecnico di Milano / MIT / MGH: Marta Peroni
* MIT: Polina Golland
* MGH: Greg Sharp

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

<h3>Objective</h3>
The project aims at allowing plan adaptation throughout the treatment course by means of CBCT. This imaging technique is at its early stage in radio– and proton-therapy application and it is not yet considered a reliable tool for planning.
We would like to use Deformable registration algorithms and automatic segmentation for:
* dose adaptation on the basis of a displacement field obtained by image co-registration, which could nevetheless lead to non consistent plans both from physics and technology point of view (i.e. are not deliverable).
* organ shape prediction both intra- and across patients
</div>

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

<h3>Approach, Plan</h3>
One crucial step of this approach is the rigid alignment prior to deformable registration. For CT/CBCT co-registration, this is even more difficult given the presence of immobilization devices (e.g. thermoplastic masks) and the different image quality.

We tested out both Versor and Quaternions (currently in slicer) and the plan for the week is to gain a better understanding of both in terms of:
* stopping conditions (i.e. no stopping condition for quaternions?)
* computational velocity
* improvement to reduct influence of metal artifacts and different image quality on the final output

The plan includes the implementation of possible solution that address this problem.

A side problem includes the removal of the immobilization devices + tube artifacts from CBCT images. At the moment we proceed with a combination of registration and erode/dilate morphological operations given a contour on a previous image, but we would be happy to discuss about this :) (NB: maybe smt similar to the skull stripping algorithm would help us?)

</div>

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

<h3>Progress</h3>

* developed monitor algorithm for registration
* gained a better understanding of the methods
* fixed affine/rigid registration
* tests on segmentation of the body contour of a CBCT with BRAINSfit are indicating we might be able to get rid of all the structures external to the patient

</div>
</div>

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

</div>

2010 Summer Project Week HandN Cancer

2010-06-21T17:12:51Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
File:HN_CBCT.png|Sample Image Dataset.
Image:RegistrationRigidHN.png|Sample Image Registration Output.
</gallery>

==Key Investigators==
* Politecnico di Milano / MIT / MGH: Marta Peroni
* MIT: Polina Golland
* MGH: Greg Sharp

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

<h3>Objective</h3>
The project aims at allowing plan adaptation throughout the treatment course by means of CBCT. This imaging technique is at its early stage in radio– and proton-therapy application and it is not yet considered a reliable tool for planning.
We would like to use Deformable registration algorithms and automatic segmentation for:
* dose adaptation on the basis of a displacement field obtained by image co-registration, which could nevetheless lead to non consistent plans both from physics and technology point of view (i.e. are not deliverable).
* organ shape prediction both intra- and across patients
</div>

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

<h3>Approach, Plan</h3>
One crucial step of this approach is the rigid alignment prior to deformable registration. For CT/CBCT co-registration, this is even more difficult given the presence of immobilization devices (e.g. thermoplastic masks) and the different image quality.

We tested out both Versor and Quaternions (currently in slicer) and the plan for the week is to gain a better understanding of both in terms of:
* stopping conditions (i.e. no stopping condition for quaternions?)
* computational velocity
* improvement to reduct influence of metal artifacts and different image quality on the final output

The plan includes the implementation of possible solution that address this problem.

A side problem includes the removal of the immobilization devices + tube artifacts from CBCT images. At the moment we proceed with a combination of registration and erode/dilate morphological operations given a contour on a previous image, but we would be happy to discuss about this :) (NB: maybe smt similar to the skull stripping algorithm would help us?)

</div>

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

<h3>Progress</h3>
will be filled by the end of the week

</div>
</div>

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

</div>

2010 Summer Project Week HandN Cancer

2010-06-15T22:46:53Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:HNCBCT.jpg|Sample Image Dataset.
Image:RegistrationRigidHN.png|Sample Image Registration Output.
</gallery>

==Key Investigators==
* Politecnico di Milano / MIT / MGH: Marta Peroni
* MIT: Polina Golland
* MGH: Greg Sharp

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

<h3>Objective</h3>
The project aims at allowing plan adaptation throughout the treatment course by means of CBCT. This imaging technique is at its early stage in radio– and proton-therapy application and it is not yet considered a reliable tool for planning.
We would like to use Deformable registration algorithms and automatic segmentation for:
* dose adaptation on the basis of a displacement field obtained by image co-registration, which could nevetheless lead to non consistent plans both from physics and technology point of view (i.e. are not deliverable).
* organ shape prediction both intra- and across patients
</div>

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

<h3>Approach, Plan</h3>
One crucial step of this approach is the rigid alignment prior to deformable registration. For CT/CBCT co-registration, this is even more difficult given the presence of immobilization devices (e.g. thermoplastic masks) and the different image quality.
We tested out both Versor and Quaternions (currently in slicer) and the plan for the week is to gain a better understanding of both in terms of:
- stopping conditions (i.e. no stopping condition for quaternions?)
- computational velocity
- improvement to reduct influence of metal artifacts and different image quality on the final output
The plan includes the implementation of possible solution that address this problem.
A side problem includes the removal of the immobilization devices + tube artifacts from CBCT images. At the moment we proceed with a combination of registration and erode/dilate morphological operations given a contour on a previous image, but we would be happy to discuss about this :) (NB: maybe smt similar to the skull stripping algorithm would help us?)

</div>

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

<h3>Progress</h3>
will be filled by the end of the week

</div>
</div>

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

</div>

File:RegistrationRigidHN.png

2010-06-15T22:45:36Z

MartaPeroni: Example of registration output (CT/CT from 2 different patients)

Example of registration output (CT/CT from 2 different patients)

File:HN CBCT.png

2010-06-15T22:11:08Z

MartaPeroni: uploaded a new version of "File:HN CBCT.png"

CBCT original image and masked one

2010 Summer Project Week HandN Cancer

2010-06-15T22:08:53Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:[[File:HN_CBCT.jpg]]|Sample Image Dataset.
Image:HN_rigid.jpg|Sample Image Registration Output.
</gallery>

==Key Investigators==
* Politecnico di Milano / MIT / MGH: Marta Peroni
* MIT: Polina Golland
* MGH: Greg Sharp

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

<h3>Objective</h3>
The project aims at allowing plan adaptation throughout the treatment course by means of CBCT. This imaging technique is at its early stage in radio– and proton-therapy application and it is not yet considered a reliable tool for planning.
We would like to use Deformable registration algorithms and automatic segmentation for:
* dose adaptation on the basis of a displacement field obtained by image co-registration, which could nevetheless lead to non consistent plans both from physics and technology point of view (i.e. are not deliverable).
* organ shape prediction both intra- and across patients
</div>

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

<h3>Approach, Plan</h3>
One crucial step of this approach is the rigid alignment prior to deformable registration. For CT/CBCT co-registration, this is even more difficult given the presence of immobilization devices (e.g. thermoplastic masks) and the different image quality.
We tested out both Versor and Quaternions (currently in slicer) and the plan for the week is to gain a better understanding of both in terms of:
- stopping conditions (i.e. no stopping condition for quaternions?)
- computational velocity
- improvement to reduct influence of metal artifacts and different image quality on the final output
The plan includes the implementation of possible solution that address this problem.
A side problem includes the removal of the immobilization devices + tube artifacts from CBCT images. At the moment we proceed with a combination of registration and erode/dilate morphological operations given a contour on a previous image, but we would be happy to discuss about this :) (NB: maybe smt similar to the skull stripping algorithm would help us?)

</div>

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

<h3>Progress</h3>
will be filled by the end of the week

</div>
</div>

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

</div>

File:HN CBCT.png

2010-06-15T22:08:17Z

MartaPeroni: CBCT original image and masked one

CBCT original image and masked one

2010 Summer Project Week HandN Cancer

2010-06-15T22:01:28Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:HN_CBCT.jpg|Sample Image Dataset.
Image:HN_rigid.jpg|Sample Image Registration Output.
</gallery>

==Key Investigators==
* Politecnico di Milano / MIT / MGH: Marta Peroni
* MIT: Polina Golland
* MGH: Greg Sharp

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

<h3>Objective</h3>
The project aims at allowing plan adaptation throughout the treatment course by means of CBCT. This imaging technique is at its early stage in radio– and proton-therapy application and it is not yet considered a reliable tool for planning.
We would like to use Deformable registration algorithms and automatic segmentation for:
* dose adaptation on the basis of a displacement field obtained by image co-registration, which could nevetheless lead to non consistent plans both from physics and technology point of view (i.e. are not deliverable).
* organ shape prediction both intra- and across patients
</div>

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

<h3>Approach, Plan</h3>
One crucial step of this approach is the rigid alignment prior to deformable registration. For CT/CBCT co-registration, this is even more difficult given the presence of immobilization devices (e.g. thermoplastic masks) and the different image quality.
We tested out both Versor and Quaternions (currently in slicer) and the plan for the week is to gain a better understanding of both in terms of:
- stopping conditions (i.e. no stopping condition for quaternions?)
- computational velocity
- improvement to reduct influence of metal artifacts and different image quality on the final output
The plan includes the implementation of possible solution that address this problem.
A side problem includes the removal of the immobilization devices + tube artifacts from CBCT images. At the moment we proceed with a combination of registration and erode/dilate morphological operations given a contour on a previous image, but we would be happy to discuss about this :) (NB: maybe smt similar to the skull stripping algorithm would help us?)

</div>

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

<h3>Progress</h3>
will be filled by the end of the week

</div>
</div>

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

</div>

2010 Summer Project Week HandN Cancer

2010-05-11T23:42:47Z

MartaPeroni: Created page with '__NOTOC__ <gallery> Image:PW-MIT2010.png|Projects List Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus…'

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
</gallery>

==Key Investigators==
* Politecnico di Milano / MIT : Marta Peroni
* MIT: Polina Golland
* MGH: Greg Sharp

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

<h3>Objective</h3>
The project aims at allowing plan adaptation throughout the treatment course by means of CBCT. This imaging technique is at its early stage in radio– and proton-therapy application and it is not yet considered a reliable tool for planning.
We would like to use Deformable registration algorithms and automatic segmentation for:
* dose adaptation on the basis of a displacement field obtained by image co-registration, which could nevetheless lead to non consistent plans both from physics and technology point of view (i.e. are not deliverable).
* organ shape prediction both intra- and across patients
</div>

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

<h3>Approach, Plan</h3>

</div>

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

<h3>Progress</h3>

</div>
</div>

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

==Delivery Mechanism==

==References==

</div>

2010 Summer Project Week

2010-05-11T23:34:35Z

MartaPeroni: /* Radiotherapy */

__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]]

== TENTATIVE Agenda==

'''PLEASE NOTE THAT THIS IS A TENTATIVE AGENDA. IT WILL BE CONFIRMED IN MAY 2010.
'''
=== 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 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)
**1-5pm: Breakout Session: Prostate Interventions (Junichi Tokuda)
**3-4pm: Breakout Session: VTK Widgets (Nicole, Kilian, JC)
**3-5pm: Breakout Session: QA Training (Luis Ibanesz)
** 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: GWE (Marco Ruiz)
** 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, Fill in Dates]]

==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/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, ?)

=== 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]] (Greg Sharp, Nadya Shusharina)

=== IGT ===
* Liver Ablation (Ziv Yaniv, Haiying Liu)

=== Radiotherapy ===
*[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp)
*[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)

=== Analysis ===
*[[Microscopy Image Analysis]] (Arnaud Gelas)
*Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
*Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)

=== Informatics ===

=== Diffusion ===

=== Python ===

=== Slicer Internals ===
*Module Inventory (Steve, Jim)
*Viewer Manager Factory (Alex Y., Kilian, Steve, Nicole)

=== Execution Model ===

===Other NA-MIC Kit Internals===
*VTKWidgets (JC, Nicole)
*Superbuild (Dave Partika)

== 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].

2009 Summer Project Week TrigeminalNerve

2009-06-26T15:00:58Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:Trigeminal_1.png|Overlay between warped atlas (red) and patient MRI (green)
Image:Trigeminal_2.png|Comparison between patient CT (gray), patient MRI (green) and warped atlas (red)
Image:trigeminalUpdate2.jpg|result 1
Image:trigeminalUpdate3.jpg|result 2
</gallery>

==Key Investigators==
* PoliMI: Marta Peroni
* UMG: Maria Francesca Spadea
* MGH: Greg Sharp

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

<h3>Objective</h3>
We are tuning and testing multimodal image registration in [http://www.plastimatch.org plastimatch] to allow accurate localization of the trigeminal nerve. The final objective is to register an [http://www.bic.mni.mcgill.ca/brainweb/ atlas] to patient CT, in order to avoid 3T MRI. The registration would allow the physician to identify the trigeminal nerve on the atlas and plan the Cyberknife treatment accordingly.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to crop and "adjust" the patient CT histogram and to crop the atlas to obtain a more robust result. The output of Bspline deformable registration is than compared to the patient 3T MRI (whenever possible in the same modality - T1). The MRIs are acquired generally with CISS sequence.

Our plan for the project week is:
* solve offset issues and parameter handling between rigid and non-rigid stage
* do we really need to "adjust" CT histogram?
* investigate why the cropping is necessary for the registration to produce an output "acceptable"

</div>

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

<h3>Progress as on 06/26</h3>
* full pipeline implemented (coarse alignment + rigid + affine + deformable)
* we need to cut-off the CT histogram or re-implement MI
* cropping the CT to the same region of the atlas is necessary
* new ideas: validation / correction of registration by mean of corresponding points
* still needs work: rigid stage needs to be optimized (or maybe not included?)

</div>
</div>

<div style="width: 970%; float: left;">

==References==
* Klein A, Andersson J, Ardekani BA et al., Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration., Neuroimage. 2009 Jul 1;46(3):786-802. Epub 2009 Jan 13.
* Chakravarty MM, Sadikot AF, Germann J, Bertrand G, Collins DL., Towards a validation of atlas warping techniques., Med Image Anal. 2008 Dec;12(6):713-26. Epub 2008 May 13.
* Borchers JD 3rd, Yang HJ, Sakamoto GT, Howes GA, Gupta G, Chang SD, Adler JR Jr., Cyberknife stereotactic radiosurgical rhizotomy for trigeminal neuralgia: anatomic and morphological considerations., Neurosurgery. 2009 Feb;64(2 Suppl):A91-5.
* Antypas C, Pantelis E., Performance evaluation of a CyberKnife G4 image-guided robotic stereotactic radiosurgery system. Phys Med Biol. 2008 Sep 7;53(17):4697-718. Epub 2008 Aug 11.

</div>

2009 Summer Project Week TrigeminalNerve

2009-06-26T14:52:40Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:Trigeminal_1.png|Overlay between warped atlas (red) and patient MRI (green)
Image:Trigeminal_2.png|Comparison between patient CT (gray), patient MRI (green) and warped atlas (red)
Image:trigeminalUpdate2.jpg|result 1
Image:trigeminalUpdate3.jpg|result 2
</gallery>

==Key Investigators==
* PoliMI: Marta Peroni
* UMG: Maria Francesca Spadea
* MGH: Greg Sharp

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

<h3>Objective</h3>
We are tuning and testing multimodal image registration in [http://www.plastimatch.org plastimatch] to allow accurate localization of the trigeminal nerve. The final objective is to register an [http://www.bic.mni.mcgill.ca/brainweb/ atlas] to patient CT, in order to avoid 3T MRI. The registration would allow the physician to identify the trigeminal nerve on the atlas and plan the Cyberknife treatment accordingly.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to crop and "adjust" the patient CT histogram and to crop the atlas to obtain a more robust result. The output of Bspline deformable registration is than compared to the patient 3T MRI (whenever possible in the same modality - T1). The MRIs are acquired generally with CISS sequence.

Our plan for the project week is:
* solve offset issues and parameter handling between rigid and non-rigid stage
* do we really need to "adjust" CT histogram?
* investigate why the cropping is necessary for the registration to produce an output "acceptable"

</div>

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

<h3>Progress as on 06/26</h3>
* 06/21: cropping only CT to match atlas size seems to be ok for registration
* full pipeline implemented (coarse alignment + rigid + affine + deformable)
* we need to cut-off the CT histogram or re-implement MI
* cropping the CT to the same region of the atlas is necessary, further tests are needed to check if more cropping is required
* new ideas: validation / correction of registration by mean of corresponding points
* still needs work: rigid stage needs to be optimized (or maybe not included?)

</div>
</div>

<div style="width: 970%; float: left;">

==References==
* Klein A, Andersson J, Ardekani BA et al., Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration., Neuroimage. 2009 Jul 1;46(3):786-802. Epub 2009 Jan 13.
* Chakravarty MM, Sadikot AF, Germann J, Bertrand G, Collins DL., Towards a validation of atlas warping techniques., Med Image Anal. 2008 Dec;12(6):713-26. Epub 2008 May 13.
* Borchers JD 3rd, Yang HJ, Sakamoto GT, Howes GA, Gupta G, Chang SD, Adler JR Jr., Cyberknife stereotactic radiosurgical rhizotomy for trigeminal neuralgia: anatomic and morphological considerations., Neurosurgery. 2009 Feb;64(2 Suppl):A91-5.
* Antypas C, Pantelis E., Performance evaluation of a CyberKnife G4 image-guided robotic stereotactic radiosurgery system. Phys Med Biol. 2008 Sep 7;53(17):4697-718. Epub 2008 Aug 11.

</div>

File:TrigeminalUpdate3.jpg

2009-06-26T14:52:11Z

MartaPeroni:

2009 Summer Project Week TrigeminalNerve

2009-06-26T14:49:42Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:Trigeminal_1.png|Overlay between warped atlas (red) and patient MRI (green)
Image:Trigeminal_2.png|Comparison between patient CT (gray), patient MRI (green) and warped atlas (red)
Image:trigeminalUpdate2.jpg|result 2
</gallery>

==Key Investigators==
* PoliMI: Marta Peroni
* UMG: Maria Francesca Spadea
* MGH: Greg Sharp

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

<h3>Objective</h3>
We are tuning and testing multimodal image registration in [http://www.plastimatch.org plastimatch] to allow accurate localization of the trigeminal nerve. The final objective is to register an [http://www.bic.mni.mcgill.ca/brainweb/ atlas] to patient CT, in order to avoid 3T MRI. The registration would allow the physician to identify the trigeminal nerve on the atlas and plan the Cyberknife treatment accordingly.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to crop and "adjust" the patient CT histogram and to crop the atlas to obtain a more robust result. The output of Bspline deformable registration is than compared to the patient 3T MRI (whenever possible in the same modality - T1). The MRIs are acquired generally with CISS sequence.

Our plan for the project week is:
* solve offset issues and parameter handling between rigid and non-rigid stage
* do we really need to "adjust" CT histogram?
* investigate why the cropping is necessary for the registration to produce an output "acceptable"

</div>

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

<h3>Progress as on 06/26</h3>
* 06/21: cropping only CT to match atlas size seems to be ok for registration
* full pipeline implemented (coarse alignment + rigid + affine + deformable)
* we need to cut-off the CT histogram or re-implement MI
* cropping the CT to the same region of the atlas is necessary, further tests are needed to check if more cropping is required
* new ideas: validation / correction of registration by mean of corresponding points
* still needs work: rigid stage needs to be optimized (or maybe not included?)

</div>
</div>

<div style="width: 970%; float: left;">

==References==
* Klein A, Andersson J, Ardekani BA et al., Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration., Neuroimage. 2009 Jul 1;46(3):786-802. Epub 2009 Jan 13.
* Chakravarty MM, Sadikot AF, Germann J, Bertrand G, Collins DL., Towards a validation of atlas warping techniques., Med Image Anal. 2008 Dec;12(6):713-26. Epub 2008 May 13.
* Borchers JD 3rd, Yang HJ, Sakamoto GT, Howes GA, Gupta G, Chang SD, Adler JR Jr., Cyberknife stereotactic radiosurgical rhizotomy for trigeminal neuralgia: anatomic and morphological considerations., Neurosurgery. 2009 Feb;64(2 Suppl):A91-5.
* Antypas C, Pantelis E., Performance evaluation of a CyberKnife G4 image-guided robotic stereotactic radiosurgery system. Phys Med Biol. 2008 Sep 7;53(17):4697-718. Epub 2008 Aug 11.

</div>

2009 Summer Project Week TrigeminalNerve

2009-06-26T14:49:07Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:Trigeminal_1.png|Overlay between warped atlas (red) and patient MRI (green)
Image:Trigeminal_2.png|Comparison between patient CT (gray), patient MRI (green) and warped atlas (red)

Image:trigeminalUpdate.jpg|result 1
Image:trigeminalUpdate2.jpg|result 2
</gallery>

==Key Investigators==
* PoliMI: Marta Peroni
* UMG: Maria Francesca Spadea
* MGH: Greg Sharp

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

<h3>Objective</h3>
We are tuning and testing multimodal image registration in [http://www.plastimatch.org plastimatch] to allow accurate localization of the trigeminal nerve. The final objective is to register an [http://www.bic.mni.mcgill.ca/brainweb/ atlas] to patient CT, in order to avoid 3T MRI. The registration would allow the physician to identify the trigeminal nerve on the atlas and plan the Cyberknife treatment accordingly.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to crop and "adjust" the patient CT histogram and to crop the atlas to obtain a more robust result. The output of Bspline deformable registration is than compared to the patient 3T MRI (whenever possible in the same modality - T1). The MRIs are acquired generally with CISS sequence.

Our plan for the project week is:
* solve offset issues and parameter handling between rigid and non-rigid stage
* do we really need to "adjust" CT histogram?
* investigate why the cropping is necessary for the registration to produce an output "acceptable"

</div>

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

<h3>Progress as on 06/26</h3>
* 06/21: cropping only CT to match atlas size seems to be ok for registration
* full pipeline implemented (coarse alignment + rigid + affine + deformable)
* we need to cut-off the CT histogram or re-implement MI
* cropping the CT to the same region of the atlas is necessary, further tests are needed to check if more cropping is required
* new ideas: validation / correction of registration by mean of corresponding points
* still needs work: rigid stage needs to be optimized (or maybe not included?)

</div>
</div>

<div style="width: 970%; float: left;">

==References==
* Klein A, Andersson J, Ardekani BA et al., Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration., Neuroimage. 2009 Jul 1;46(3):786-802. Epub 2009 Jan 13.
* Chakravarty MM, Sadikot AF, Germann J, Bertrand G, Collins DL., Towards a validation of atlas warping techniques., Med Image Anal. 2008 Dec;12(6):713-26. Epub 2008 May 13.
* Borchers JD 3rd, Yang HJ, Sakamoto GT, Howes GA, Gupta G, Chang SD, Adler JR Jr., Cyberknife stereotactic radiosurgical rhizotomy for trigeminal neuralgia: anatomic and morphological considerations., Neurosurgery. 2009 Feb;64(2 Suppl):A91-5.
* Antypas C, Pantelis E., Performance evaluation of a CyberKnife G4 image-guided robotic stereotactic radiosurgery system. Phys Med Biol. 2008 Sep 7;53(17):4697-718. Epub 2008 Aug 11.

</div>

2009 Summer Project Week TrigeminalNerve

2009-06-26T14:48:49Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:Trigeminal_1.png|Overlay between warped atlas (red) and patient MRI (green)
Image:Trigeminal_2.png|Comparison between patient CT (gray), patient MRI (green) and warped atlas (red)

</gallery>

==Key Investigators==
* PoliMI: Marta Peroni
* UMG: Maria Francesca Spadea
* MGH: Greg Sharp

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

<h3>Objective</h3>
We are tuning and testing multimodal image registration in [http://www.plastimatch.org plastimatch] to allow accurate localization of the trigeminal nerve. The final objective is to register an [http://www.bic.mni.mcgill.ca/brainweb/ atlas] to patient CT, in order to avoid 3T MRI. The registration would allow the physician to identify the trigeminal nerve on the atlas and plan the Cyberknife treatment accordingly.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to crop and "adjust" the patient CT histogram and to crop the atlas to obtain a more robust result. The output of Bspline deformable registration is than compared to the patient 3T MRI (whenever possible in the same modality - T1). The MRIs are acquired generally with CISS sequence.

Our plan for the project week is:
* solve offset issues and parameter handling between rigid and non-rigid stage
* do we really need to "adjust" CT histogram?
* investigate why the cropping is necessary for the registration to produce an output "acceptable"

</div>

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

<h3>Progress as on 06/26</h3>
* 06/21: cropping only CT to match atlas size seems to be ok for registration
* full pipeline implemented (coarse alignment + rigid + affine + deformable)
* we need to cut-off the CT histogram or re-implement MI
* cropping the CT to the same region of the atlas is necessary, further tests are needed to check if more cropping is required
* new ideas: validation / correction of registration by mean of corresponding points
* still needs work: rigid stage needs to be optimized (or maybe not included?)

Image:trigeminalUpdate.jpg|result 1
Image:trigeminalUpdate2.jpg|result 2

</div>
</div>

<div style="width: 970%; float: left;">

==References==
* Klein A, Andersson J, Ardekani BA et al., Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration., Neuroimage. 2009 Jul 1;46(3):786-802. Epub 2009 Jan 13.
* Chakravarty MM, Sadikot AF, Germann J, Bertrand G, Collins DL., Towards a validation of atlas warping techniques., Med Image Anal. 2008 Dec;12(6):713-26. Epub 2008 May 13.
* Borchers JD 3rd, Yang HJ, Sakamoto GT, Howes GA, Gupta G, Chang SD, Adler JR Jr., Cyberknife stereotactic radiosurgical rhizotomy for trigeminal neuralgia: anatomic and morphological considerations., Neurosurgery. 2009 Feb;64(2 Suppl):A91-5.
* Antypas C, Pantelis E., Performance evaluation of a CyberKnife G4 image-guided robotic stereotactic radiosurgery system. Phys Med Biol. 2008 Sep 7;53(17):4697-718. Epub 2008 Aug 11.

</div>

File:TrigeminalUpdate.png

2009-06-26T14:48:15Z

MartaPeroni:

2009 Summer Project Week TrigeminalNerve

2009-06-26T14:47:51Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:Trigeminal_1.png|Overlay between warped atlas (red) and patient MRI (green)
Image:Trigeminal_2.png|Comparison between patient CT (gray), patient MRI (green) and warped atlas (red)
Image:trigeminalUpdate2.jpg|result 1
</gallery>

==Key Investigators==
* PoliMI: Marta Peroni
* UMG: Maria Francesca Spadea
* MGH: Greg Sharp

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

<h3>Objective</h3>
We are tuning and testing multimodal image registration in [http://www.plastimatch.org plastimatch] to allow accurate localization of the trigeminal nerve. The final objective is to register an [http://www.bic.mni.mcgill.ca/brainweb/ atlas] to patient CT, in order to avoid 3T MRI. The registration would allow the physician to identify the trigeminal nerve on the atlas and plan the Cyberknife treatment accordingly.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to crop and "adjust" the patient CT histogram and to crop the atlas to obtain a more robust result. The output of Bspline deformable registration is than compared to the patient 3T MRI (whenever possible in the same modality - T1). The MRIs are acquired generally with CISS sequence.

Our plan for the project week is:
* solve offset issues and parameter handling between rigid and non-rigid stage
* do we really need to "adjust" CT histogram?
* investigate why the cropping is necessary for the registration to produce an output "acceptable"

</div>

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

<h3>Progress as on 06/26</h3>
* 06/21: cropping only CT to match atlas size seems to be ok for registration
* full pipeline implemented (coarse alignment + rigid + affine + deformable)
* we need to cut-off the CT histogram or re-implement MI
* cropping the CT to the same region of the atlas is necessary, further tests are needed to check if more cropping is required
* new ideas: validation / correction of registration by mean of corresponding points
* still needs work: rigid stage needs to be optimized (or maybe not included?)

</div>
</div>

<div style="width: 970%; float: left;">

==References==
* Klein A, Andersson J, Ardekani BA et al., Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration., Neuroimage. 2009 Jul 1;46(3):786-802. Epub 2009 Jan 13.
* Chakravarty MM, Sadikot AF, Germann J, Bertrand G, Collins DL., Towards a validation of atlas warping techniques., Med Image Anal. 2008 Dec;12(6):713-26. Epub 2008 May 13.
* Borchers JD 3rd, Yang HJ, Sakamoto GT, Howes GA, Gupta G, Chang SD, Adler JR Jr., Cyberknife stereotactic radiosurgical rhizotomy for trigeminal neuralgia: anatomic and morphological considerations., Neurosurgery. 2009 Feb;64(2 Suppl):A91-5.
* Antypas C, Pantelis E., Performance evaluation of a CyberKnife G4 image-guided robotic stereotactic radiosurgery system. Phys Med Biol. 2008 Sep 7;53(17):4697-718. Epub 2008 Aug 11.

</div>

File:TrigeminalUpdate2.jpg

2009-06-26T14:47:31Z

MartaPeroni:

2009 Summer Project Week TrigeminalNerve

2009-06-26T14:46:57Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:Trigeminal_1.png|Overlay between warped atlas (red) and patient MRI (green)
Image:Trigeminal_2.png|Comparison between patient CT (gray), patient MRI (green) and warped atlas (red)
Image:trigeminalUpdate.png|result 1
</gallery>

==Key Investigators==
* PoliMI: Marta Peroni
* UMG: Maria Francesca Spadea
* MGH: Greg Sharp

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

<h3>Objective</h3>
We are tuning and testing multimodal image registration in [http://www.plastimatch.org plastimatch] to allow accurate localization of the trigeminal nerve. The final objective is to register an [http://www.bic.mni.mcgill.ca/brainweb/ atlas] to patient CT, in order to avoid 3T MRI. The registration would allow the physician to identify the trigeminal nerve on the atlas and plan the Cyberknife treatment accordingly.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to crop and "adjust" the patient CT histogram and to crop the atlas to obtain a more robust result. The output of Bspline deformable registration is than compared to the patient 3T MRI (whenever possible in the same modality - T1). The MRIs are acquired generally with CISS sequence.

Our plan for the project week is:
* solve offset issues and parameter handling between rigid and non-rigid stage
* do we really need to "adjust" CT histogram?
* investigate why the cropping is necessary for the registration to produce an output "acceptable"

</div>

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

<h3>Progress as on 06/26</h3>
* 06/21: cropping only CT to match atlas size seems to be ok for registration
* full pipeline implemented (coarse alignment + rigid + affine + deformable)
* we need to cut-off the CT histogram or re-implement MI
* cropping the CT to the same region of the atlas is necessary, further tests are needed to check if more cropping is required
* new ideas: validation / correction of registration by mean of corresponding points
* still needs work: rigid stage needs to be optimized (or maybe not included?)

</div>
</div>

<div style="width: 970%; float: left;">

==References==
* Klein A, Andersson J, Ardekani BA et al., Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration., Neuroimage. 2009 Jul 1;46(3):786-802. Epub 2009 Jan 13.
* Chakravarty MM, Sadikot AF, Germann J, Bertrand G, Collins DL., Towards a validation of atlas warping techniques., Med Image Anal. 2008 Dec;12(6):713-26. Epub 2008 May 13.
* Borchers JD 3rd, Yang HJ, Sakamoto GT, Howes GA, Gupta G, Chang SD, Adler JR Jr., Cyberknife stereotactic radiosurgical rhizotomy for trigeminal neuralgia: anatomic and morphological considerations., Neurosurgery. 2009 Feb;64(2 Suppl):A91-5.
* Antypas C, Pantelis E., Performance evaluation of a CyberKnife G4 image-guided robotic stereotactic radiosurgery system. Phys Med Biol. 2008 Sep 7;53(17):4697-718. Epub 2008 Aug 11.

</div>

2009 Summer Project Week TrigeminalNerve

2009-06-26T14:46:24Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:Trigeminal_1.png|Overlay between warped atlas (red) and patient MRI (green)
Image:Trigeminal_2.png|Comparison between patient CT (gray), patient MRI (green) and warped atlas (red)

</gallery>

==Key Investigators==
* PoliMI: Marta Peroni
* UMG: Maria Francesca Spadea
* MGH: Greg Sharp

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

<h3>Objective</h3>
We are tuning and testing multimodal image registration in [http://www.plastimatch.org plastimatch] to allow accurate localization of the trigeminal nerve. The final objective is to register an [http://www.bic.mni.mcgill.ca/brainweb/ atlas] to patient CT, in order to avoid 3T MRI. The registration would allow the physician to identify the trigeminal nerve on the atlas and plan the Cyberknife treatment accordingly.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to crop and "adjust" the patient CT histogram and to crop the atlas to obtain a more robust result. The output of Bspline deformable registration is than compared to the patient 3T MRI (whenever possible in the same modality - T1). The MRIs are acquired generally with CISS sequence.

Our plan for the project week is:
* solve offset issues and parameter handling between rigid and non-rigid stage
* do we really need to "adjust" CT histogram?
* investigate why the cropping is necessary for the registration to produce an output "acceptable"

</div>

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

<h3>Progress as on 06/26</h3>
* 06/21: cropping only CT to match atlas size seems to be ok for registration
* full pipeline implemented (coarse alignment + rigid + affine + deformable)
* we need to cut-off the CT histogram or re-implement MI
* cropping the CT to the same region of the atlas is necessary, further tests are needed to check if more cropping is required
* new ideas: validation / correction of registration by mean of corresponding points
* still needs work: rigid stage needs to be optimized (or maybe not included?)

Image:trigeminalUpdate.png | result 1

</div>
</div>

<div style="width: 970%; float: left;">

==References==
* Klein A, Andersson J, Ardekani BA et al., Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration., Neuroimage. 2009 Jul 1;46(3):786-802. Epub 2009 Jan 13.
* Chakravarty MM, Sadikot AF, Germann J, Bertrand G, Collins DL., Towards a validation of atlas warping techniques., Med Image Anal. 2008 Dec;12(6):713-26. Epub 2008 May 13.
* Borchers JD 3rd, Yang HJ, Sakamoto GT, Howes GA, Gupta G, Chang SD, Adler JR Jr., Cyberknife stereotactic radiosurgical rhizotomy for trigeminal neuralgia: anatomic and morphological considerations., Neurosurgery. 2009 Feb;64(2 Suppl):A91-5.
* Antypas C, Pantelis E., Performance evaluation of a CyberKnife G4 image-guided robotic stereotactic radiosurgery system. Phys Med Biol. 2008 Sep 7;53(17):4697-718. Epub 2008 Aug 11.

</div>

2009 Summer Project Week TrigeminalNerve

2009-06-26T14:46:08Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:Trigeminal_1.png|Overlay between warped atlas (red) and patient MRI (green)
Image:Trigeminal_2.png|Comparison between patient CT (gray), patient MRI (green) and warped atlas (red)

</gallery>

==Key Investigators==
* PoliMI: Marta Peroni
* UMG: Maria Francesca Spadea
* MGH: Greg Sharp

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

<h3>Objective</h3>
We are tuning and testing multimodal image registration in [http://www.plastimatch.org plastimatch] to allow accurate localization of the trigeminal nerve. The final objective is to register an [http://www.bic.mni.mcgill.ca/brainweb/ atlas] to patient CT, in order to avoid 3T MRI. The registration would allow the physician to identify the trigeminal nerve on the atlas and plan the Cyberknife treatment accordingly.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to crop and "adjust" the patient CT histogram and to crop the atlas to obtain a more robust result. The output of Bspline deformable registration is than compared to the patient 3T MRI (whenever possible in the same modality - T1). The MRIs are acquired generally with CISS sequence.

Our plan for the project week is:
* solve offset issues and parameter handling between rigid and non-rigid stage
* do we really need to "adjust" CT histogram?
* investigate why the cropping is necessary for the registration to produce an output "acceptable"

</div>

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

<h3>Progress as on 06/26</h3>
* 06/21: cropping only CT to match atlas size seems to be ok for registration
* full pipeline implemented (coarse alignment + rigid + affine + deformable)
* we need to cut-off the CT histogram or re-implement MI
* cropping the CT to the same region of the atlas is necessary, further tests are needed to check if more cropping is required
* new ideas: validation / correction of registration by mean of corresponding points
* still needs work: rigid stage needs to be optimized (or maybe not included?)

Image:TrigeminalUpdate.png | result 1

</div>
</div>

<div style="width: 970%; float: left;">

==References==
* Klein A, Andersson J, Ardekani BA et al., Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration., Neuroimage. 2009 Jul 1;46(3):786-802. Epub 2009 Jan 13.
* Chakravarty MM, Sadikot AF, Germann J, Bertrand G, Collins DL., Towards a validation of atlas warping techniques., Med Image Anal. 2008 Dec;12(6):713-26. Epub 2008 May 13.
* Borchers JD 3rd, Yang HJ, Sakamoto GT, Howes GA, Gupta G, Chang SD, Adler JR Jr., Cyberknife stereotactic radiosurgical rhizotomy for trigeminal neuralgia: anatomic and morphological considerations., Neurosurgery. 2009 Feb;64(2 Suppl):A91-5.
* Antypas C, Pantelis E., Performance evaluation of a CyberKnife G4 image-guided robotic stereotactic radiosurgery system. Phys Med Biol. 2008 Sep 7;53(17):4697-718. Epub 2008 Aug 11.

</div>

2009 Summer Project Week TrigeminalNerve

2009-06-26T11:44:26Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:Trigeminal_1.png|Overlay between warped atlas (red) and patient MRI (green)
Image:Trigeminal_2.png|Comparison between patient CT (gray), patient MRI (green) and warped atlas (red)
</gallery>

==Key Investigators==
* PoliMI: Marta Peroni
* UMG: Maria Francesca Spadea
* MGH: Greg Sharp

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

<h3>Objective</h3>
We are tuning and testing multimodal image registration in [http://www.plastimatch.org plastimatch] to allow accurate localization of the trigeminal nerve. The final objective is to register an [http://www.bic.mni.mcgill.ca/brainweb/ atlas] to patient CT, in order to avoid 3T MRI. The registration would allow the physician to identify the trigeminal nerve on the atlas and plan the Cyberknife treatment accordingly.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to crop and "adjust" the patient CT histogram and to crop the atlas to obtain a more robust result. The output of Bspline deformable registration is than compared to the patient 3T MRI (whenever possible in the same modality - T1). The MRIs are acquired generally with CISS sequence.

Our plan for the project week is:
* solve offset issues and parameter handling between rigid and non-rigid stage
* do we really need to "adjust" CT histogram?
* investigate why the cropping is necessary for the registration to produce an output "acceptable"

</div>

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

<h3>Progress as on 06/26</h3>
* 06/21: cropping only CT to match atlas size seems to be ok for registration
* full pipeline implemented (coarse alignment + rigid + affine + deformable)
* we need to cut-off the CT histogram or re-implement MI
* cropping the CT to the same region of the atlas is necessary, further tests are needed to check if more cropping is required
* new ideas: validation / correction of registration by mean of corresponding points
* still needs work: rigid stage needs to be optimized (or maybe not included?)

</div>
</div>

<div style="width: 970%; float: left;">

==References==
* Klein A, Andersson J, Ardekani BA et al., Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration., Neuroimage. 2009 Jul 1;46(3):786-802. Epub 2009 Jan 13.
* Chakravarty MM, Sadikot AF, Germann J, Bertrand G, Collins DL., Towards a validation of atlas warping techniques., Med Image Anal. 2008 Dec;12(6):713-26. Epub 2008 May 13.
* Borchers JD 3rd, Yang HJ, Sakamoto GT, Howes GA, Gupta G, Chang SD, Adler JR Jr., Cyberknife stereotactic radiosurgical rhizotomy for trigeminal neuralgia: anatomic and morphological considerations., Neurosurgery. 2009 Feb;64(2 Suppl):A91-5.
* Antypas C, Pantelis E., Performance evaluation of a CyberKnife G4 image-guided robotic stereotactic radiosurgery system. Phys Med Biol. 2008 Sep 7;53(17):4697-718. Epub 2008 Aug 11.

</div>

2009 Summer Project Week TrigeminalNerve

2009-06-26T11:42:46Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:Trigeminal_1.png|Overlay between warped atlas (red) and patient MRI (green)
Image:Trigeminal_2.png|Comparison between patient CT (gray), patient MRI (green) and warped atlas (red)
</gallery>

==Key Investigators==
* PoliMI: Marta Peroni
* UMG: Maria Francesca Spadea
* MGH: Greg Sharp

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

<h3>Objective</h3>
We are tuning and testing multimodal image registration in [http://www.plastimatch.org plastimatch] to allow accurate localization of the trigeminal nerve. The final objective is to register an [http://www.bic.mni.mcgill.ca/brainweb/ atlas] to patient CT, in order to avoid 3T MRI. The registration would allow the physician to identify the trigeminal nerve on the atlas and plan the Cyberknife treatment accordingly.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to crop and "adjust" the patient CT histogram and to crop the atlas to obtain a more robust result. The output of Bspline deformable registration is than compared to the patient 3T MRI (whenever possible in the same modality - T1). The MRIs are acquired generally with CISS sequence.

Our plan for the project week is:
* solve offset issues and parameter handling between rigid and non-rigid stage
* do we really need to "adjust" CT histogram?
* investigate why the cropping is necessary for the registration to produce an output "acceptable"

</div>

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

<h3>Progress</h3>
* 06/21: cropping only CT to match atlas size seems to be ok for registration
* full pipeline implemented (coarse alignment + rigid + affine + deformable)
* we need to cut-off the CT histogram or re-implement MI
* cropping the CT to the same region of the atlas is necessary, further tests are needed to check if more cropping is required
* new ideas: validation / correction of registration by mean of corresponding points
* still needs work: rigid stage needs to be optimized (or maybe not included?)

</div>
</div>

<div style="width: 970%; float: left;">

==References==
* Klein A, Andersson J, Ardekani BA et al., Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration., Neuroimage. 2009 Jul 1;46(3):786-802. Epub 2009 Jan 13.
* Chakravarty MM, Sadikot AF, Germann J, Bertrand G, Collins DL., Towards a validation of atlas warping techniques., Med Image Anal. 2008 Dec;12(6):713-26. Epub 2008 May 13.
* Borchers JD 3rd, Yang HJ, Sakamoto GT, Howes GA, Gupta G, Chang SD, Adler JR Jr., Cyberknife stereotactic radiosurgical rhizotomy for trigeminal neuralgia: anatomic and morphological considerations., Neurosurgery. 2009 Feb;64(2 Suppl):A91-5.
* Antypas C, Pantelis E., Performance evaluation of a CyberKnife G4 image-guided robotic stereotactic radiosurgery system. Phys Med Biol. 2008 Sep 7;53(17):4697-718. Epub 2008 Aug 11.

</div>

2009 Summer Project Week TrigeminalNerve

2009-06-22T17:37:41Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:Trigeminal_1.png|Overlay between warped atlas (red) and patient MRI (green)
Image:Trigeminal_2.png|Comparison between patient CT (gray), patient MRI (green) and warped atlas (red)
</gallery>

==Key Investigators==
* PoliMI: Marta Peroni
* UMG: Maria Francesca Spadea
* MGH: Greg Sharp

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

<h3>Objective</h3>
We are tuning and testing multimodal image registration in [http://www.plastimatch.org plastimatch] to allow accurate localization of the trigeminal nerve. The final objective is to register an [http://www.bic.mni.mcgill.ca/brainweb/ atlas] to patient CT, in order to avoid 3T MRI. The registration would allow the physician to identify the trigeminal nerve on the atlas and plan the Cyberknife treatment accordingly.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to crop and "adjust" the patient CT histogram and to crop the atlas to obtain a more robust result. The output of Bspline deformable registration is than compared to the patient 3T MRI (whenever possible in the same modality - T1). The MRIs are acquired generally with CISS sequence.

Our plan for the project week is:
* solve offset issues and parameter handling between rigid and non-rigid stage
* do we really need to "adjust" CT histogram?
* investigate why the cropping is necessary for the registration to produce an output "acceptable"

</div>

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

<h3>Progress</h3>
* 06/21: cropping only CT to match atlas size seems to be ok for registration

</div>
</div>

<div style="width: 970%; float: left;">

==References==
* Klein A, Andersson J, Ardekani BA et al., Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration., Neuroimage. 2009 Jul 1;46(3):786-802. Epub 2009 Jan 13.
* Chakravarty MM, Sadikot AF, Germann J, Bertrand G, Collins DL., Towards a validation of atlas warping techniques., Med Image Anal. 2008 Dec;12(6):713-26. Epub 2008 May 13.
* Borchers JD 3rd, Yang HJ, Sakamoto GT, Howes GA, Gupta G, Chang SD, Adler JR Jr., Cyberknife stereotactic radiosurgical rhizotomy for trigeminal neuralgia: anatomic and morphological considerations., Neurosurgery. 2009 Feb;64(2 Suppl):A91-5.
* Antypas C, Pantelis E., Performance evaluation of a CyberKnife G4 image-guided robotic stereotactic radiosurgery system. Phys Med Biol. 2008 Sep 7;53(17):4697-718. Epub 2008 Aug 11.

</div>

2009 Summer Project Week TrigeminalNerve

2009-06-22T17:05:02Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:Trigeminal_1.png|Overlay between warped atlas (red) and patient MRI (green)
Image:Trigeminal_2.png|Comparison between patient CT (gray), patient MRI (green) and warped atlas (red)
</gallery>

==Key Investigators==
* PoliMI: Marta Peroni
* UMG: Maria Francesca Spadea
* MGH: Greg Sharp

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

<h3>Objective</h3>
We are tuning and testing multimodal image registration in [http://www.plastimatch.org plastimatch] to allow accurate localization of the trigeminal nerve. The final objective is to register an [http://www.bic.mni.mcgill.ca/brainweb/ atlas] to patient CT, in order to avoid 3T MRI. The registration would allow the physician to identify the trigeminal nerve on the atlas and plan the Cyberknife treatment accordingly.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to crop and "adjust" the patient CT histogram and to crop the atlas to obtain a more robust result. The output of Bspline deformable registration is than compared to the patient 3T MRI (whenever possible in the same modality - T1). The MRIs are acquired generally with CISS sequence.

Our plan for the project week is:
* solve issues with parameter handling between rigid and non-rigid stage
* do we really need to "adjust" CT histogram?
* investigate why the cropping is necessary for the registration to produce an output "acceptable"

</div>

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

<h3>Progress</h3>
* 06/21: cropping only CT to match atlas size seems to be ok for registration

</div>
</div>

<div style="width: 970%; float: left;">

==References==
* Klein A, Andersson J, Ardekani BA et al., Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration., Neuroimage. 2009 Jul 1;46(3):786-802. Epub 2009 Jan 13.
* Chakravarty MM, Sadikot AF, Germann J, Bertrand G, Collins DL., Towards a validation of atlas warping techniques., Med Image Anal. 2008 Dec;12(6):713-26. Epub 2008 May 13.
* Borchers JD 3rd, Yang HJ, Sakamoto GT, Howes GA, Gupta G, Chang SD, Adler JR Jr., Cyberknife stereotactic radiosurgical rhizotomy for trigeminal neuralgia: anatomic and morphological considerations., Neurosurgery. 2009 Feb;64(2 Suppl):A91-5.
* Antypas C, Pantelis E., Performance evaluation of a CyberKnife G4 image-guided robotic stereotactic radiosurgery system. Phys Med Biol. 2008 Sep 7;53(17):4697-718. Epub 2008 Aug 11.

</div>

2009 Summer Project Week TrigeminalNerve

2009-06-22T17:04:08Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:Trigeminal_1.png|Overlay between warped atlas (red) and patient MRI (green)
Image:Trigeminal_2.png|Comparison between patient CT (gray), patient MRI (green) and warped atlas (red)
</gallery>

==Key Investigators==
* PoliMI: Marta Peroni
* UMG: Maria Francesca Spadea
* MGH: Greg Sharp

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

<h3>Objective</h3>
We are tuning and testing multimodal image registration in [http://www.plastimatch.org plastimatch] to allow accurate localization of the trigeminal nerve. The final objective is to register an [http://www.bic.mni.mcgill.ca/brainweb/ atlas] to patient CT, in order to avoid 3T MRI. The registration would allow the physician to identify the trigeminal nerve on the atlas and plan the Cyberknife treatment accordingly.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to crop and "adjust" the patient CT histogram and to crop the atlas to obtain a more robust result. The output of Bspline deformable registration is than compared to the patient 3T MRI (whenever possible in the same modality - T1). The MRIs are acquired generally with CISS sequence.

Our plan for the project week is:
* solve issues with parameter handling between rigid and non-rigid stage
* why do we need to "adjust" CT histogram?
* investigate why the cropping is necessary for the registration to produce an output "acceptable"

</div>

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

<h3>Progress</h3>
* 06/21: cropping only CT to match atlas size seems to be ok for registration

</div>
</div>

<div style="width: 970%; float: left;">

==References==
* Klein A, Andersson J, Ardekani BA et al., Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration., Neuroimage. 2009 Jul 1;46(3):786-802. Epub 2009 Jan 13.
* Chakravarty MM, Sadikot AF, Germann J, Bertrand G, Collins DL., Towards a validation of atlas warping techniques., Med Image Anal. 2008 Dec;12(6):713-26. Epub 2008 May 13.
* Borchers JD 3rd, Yang HJ, Sakamoto GT, Howes GA, Gupta G, Chang SD, Adler JR Jr., Cyberknife stereotactic radiosurgical rhizotomy for trigeminal neuralgia: anatomic and morphological considerations., Neurosurgery. 2009 Feb;64(2 Suppl):A91-5.
* Antypas C, Pantelis E., Performance evaluation of a CyberKnife G4 image-guided robotic stereotactic radiosurgery system. Phys Med Biol. 2008 Sep 7;53(17):4697-718. Epub 2008 Aug 11.

</div>

2009 Summer Project Week TrigeminalNerve

2009-06-22T15:12:26Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:Trigeminal_1.png|Overlay between warped atlas (red) and patient MRI (green)
Image:Trigeminal_2.png|Comparison between patient CT (gray), patient MRI (green) and warped atlas (red)
</gallery>

==Key Investigators==
* PoliMI: Marta Peroni
* UMG: Maria Francesca Spadea
* MGH: Greg Sharp

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

<h3>Objective</h3>
We are tuning and testing multimodal image registration in [http://www.plastimatch.org plastimatch] to allow accurate localization of the trigeminal nerve. The final objective is to register an [http://www.bic.mni.mcgill.ca/brainweb/ atlas] to patient CT, in order to avoid 3T MRI. The registration would allow the physician to identify the trigeminal nerve on the atlas and plan the Cyberknife treatment accordingly.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to crop and "threshold" the CT and to crop the atlas to obtain a more robust result. The output of Bspline deformable registration is than compared to the patient 3T MRI (whenever possible in the same modality - T1). The MRIs are acquired generally with CISS sequence.

Our plan for the project week is:
* solve issues with parameter handling between rigid and non-rigid stage
* why do we need to "adjuct" CT histogram?
* investigate why the cropping is necessary for the registration to produce an output "acceptable"

</div>

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

<h3>Progress</h3>
* 06/21: cropping only CT to match atlas size seems to be ok for registration

</div>
</div>

<div style="width: 970%; float: left;">

==References==
* Klein A, Andersson J, Ardekani BA et al., Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration., Neuroimage. 2009 Jul 1;46(3):786-802. Epub 2009 Jan 13.
* Chakravarty MM, Sadikot AF, Germann J, Bertrand G, Collins DL., Towards a validation of atlas warping techniques., Med Image Anal. 2008 Dec;12(6):713-26. Epub 2008 May 13.
* Borchers JD 3rd, Yang HJ, Sakamoto GT, Howes GA, Gupta G, Chang SD, Adler JR Jr., Cyberknife stereotactic radiosurgical rhizotomy for trigeminal neuralgia: anatomic and morphological considerations., Neurosurgery. 2009 Feb;64(2 Suppl):A91-5.
* Antypas C, Pantelis E., Performance evaluation of a CyberKnife G4 image-guided robotic stereotactic radiosurgery system. Phys Med Biol. 2008 Sep 7;53(17):4697-718. Epub 2008 Aug 11.

</div>

2009 Summer Project Week TrigeminalNerve

2009-06-22T15:11:37Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:Trigeminal_1.png|Overlay between warped atlas (red) and patient MRI (green)
Image:Trigeminal_2.png|Comparison between patient CT (gray), patient MRI (green) and warped atlas (red)
</gallery>

==Key Investigators==
* PoliMI: Marta Peroni
* UMG: Maria Francesca Spadea
* MGH: Greg Sharp

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

<h3>Objective</h3>
We are tuning and testing multimodal image registration in [http://www.plastimatch.org plastimatch] to allow accurate localization of the trigeminal nerve. The final objective is to register an atlas [http://www.bic.mni.mcgill.ca/brainweb/] to patient CT, in order to avoid 3T MRI. The registration would allow the physician to identify the trigeminal nerve on the atlas and plan the Cyberknife treatment accordingly.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to crop and "threshold" the CT and to crop the atlas to obtain a more robust result. The output of Bspline deformable registration is than compared to the patient 3T MRI (whenever possible in the same modality - T1). The MRIs are acquired generally with CISS sequence.

Our plan for the project week is:
* solve issues with parameter handling between rigid and non-rigid stage
* why do we need to "adjuct" CT histogram?
* investigate why the cropping is necessary for the registration to produce an output "acceptable"

</div>

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

<h3>Progress</h3>
* 06/21: cropping only CT to match atlas size seems to be ok for registration

</div>
</div>

<div style="width: 970%; float: left;">

==References==
* Klein A, Andersson J, Ardekani BA et al., Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration., Neuroimage. 2009 Jul 1;46(3):786-802. Epub 2009 Jan 13.
* Chakravarty MM, Sadikot AF, Germann J, Bertrand G, Collins DL., Towards a validation of atlas warping techniques., Med Image Anal. 2008 Dec;12(6):713-26. Epub 2008 May 13.
* Borchers JD 3rd, Yang HJ, Sakamoto GT, Howes GA, Gupta G, Chang SD, Adler JR Jr., Cyberknife stereotactic radiosurgical rhizotomy for trigeminal neuralgia: anatomic and morphological considerations., Neurosurgery. 2009 Feb;64(2 Suppl):A91-5.
* Antypas C, Pantelis E., Performance evaluation of a CyberKnife G4 image-guided robotic stereotactic radiosurgery system. Phys Med Biol. 2008 Sep 7;53(17):4697-718. Epub 2008 Aug 11.

</div>

2009 Summer Project Week TrigeminalNerve

2009-06-22T15:10:39Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:Trigeminal_1.png|Overlay between warped atlas (red) and patient MRI (green)
Image:Trigeminal_2.png|Comparison between patient CT (gray), patient MRI (green) and warped atlas (red)
</gallery>

==Key Investigators==
* PoliMI: Marta Peroni
* UMG: Maria Francesca Spadea
* MGH: Greg Sharp

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

<h3>Objective</h3>
We are tuning and testing multimodal image registration in [http://www.plastimatch.org plastimatch] to allow accurate localization of the trigeminal nerve. The final objective is to register an atlas to patient CT, in order to avoid 3T MRI. The registration would allow the physician to identify the trigeminal nerve on the atlas and plan the Cyberknife treatment accordingly.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to crop and "threshold" the CT and to crop the atlas to obtain a more robust result. The output of Bspline deformable registration is than compared to the patient 3T MRI (whenever possible in the same modality - T1). The MRIs are acquired generally with CISS sequence.

Our plan for the project week is:
* solve issues with parameter handling between rigid and non-rigid stage
* why do we need to "adjuct" CT histogram?
* investigate why the cropping is necessary for the registration to produce an output "acceptable"

</div>

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

<h3>Progress</h3>
* 06/21: cropping only CT to match atlas size seems to be ok for registration

</div>
</div>

<div style="width: 970%; float: left;">

==References==
* Klein A, Andersson J, Ardekani BA et al., Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration., Neuroimage. 2009 Jul 1;46(3):786-802. Epub 2009 Jan 13.
* Chakravarty MM, Sadikot AF, Germann J, Bertrand G, Collins DL., Towards a validation of atlas warping techniques., Med Image Anal. 2008 Dec;12(6):713-26. Epub 2008 May 13.
* Borchers JD 3rd, Yang HJ, Sakamoto GT, Howes GA, Gupta G, Chang SD, Adler JR Jr., Cyberknife stereotactic radiosurgical rhizotomy for trigeminal neuralgia: anatomic and morphological considerations., Neurosurgery. 2009 Feb;64(2 Suppl):A91-5.
* Antypas C, Pantelis E., Performance evaluation of a CyberKnife G4 image-guided robotic stereotactic radiosurgery system. Phys Med Biol. 2008 Sep 7;53(17):4697-718. Epub 2008 Aug 11.

</div>

2009 Summer Project Week TrigeminalNerve

2009-06-22T15:09:30Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
Image:Trigeminal_1.png|Overlay between warped atlas (red) and patient MRI (green)
Image:Trigeminal_2.png|Comparison between patient CT (gray), patient MRI (green) and warped atlas (red)
</gallery>

==Key Investigators==
* PoliMI: Marta Peroni
* UMG: Maria Francesca Spadea
* MGH: Greg Sharp

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

<h3>Objective</h3>
We are tuning and testing multimodal image registration in [http://www.plastimatch.org plastimatch] to allow accurate localization of the trigeminal nerve. The final objective is to register an atlas to patient CT, in order to avoid 3T MRI. The registration would allow the physician to identify the trigeminal nerve on the atlas and plan the Cyberknife treatment accordingly.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to crop and "threshold" the CT and to crop the atlas to obtain a more robust result. The output of Bspline deformable registration is than compared to the patient 3T MRI (whenever possible in the same modality - T1). The MRIs are acquired generally with CISS sequence.

Our plan for the project week is:
* solve issues with parameter handling between rigid and non-rigid stage
* why do we need to "adjuct" CT histogram?
* investigate why the cropping is necessary for the registration to produce an output "acceptable"

</div>

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

<h3>Progress</h3>
COME BACK SOON FOR MORE DETAILS...

</div>
</div>

<div style="width: 970%; float: left;">

==References==
* Klein A, Andersson J, Ardekani BA et al., Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration., Neuroimage. 2009 Jul 1;46(3):786-802. Epub 2009 Jan 13.
* Chakravarty MM, Sadikot AF, Germann J, Bertrand G, Collins DL., Towards a validation of atlas warping techniques., Med Image Anal. 2008 Dec;12(6):713-26. Epub 2008 May 13.
* Borchers JD 3rd, Yang HJ, Sakamoto GT, Howes GA, Gupta G, Chang SD, Adler JR Jr., Cyberknife stereotactic radiosurgical rhizotomy for trigeminal neuralgia: anatomic and morphological considerations., Neurosurgery. 2009 Feb;64(2 Suppl):A91-5.
* Antypas C, Pantelis E., Performance evaluation of a CyberKnife G4 image-guided robotic stereotactic radiosurgery system. Phys Med Biol. 2008 Sep 7;53(17):4697-718. Epub 2008 Aug 11.

</div>

2009 Summer Project Week TrigeminalNerve

2009-06-22T12:42:43Z

MartaPeroni:

File:Trigeminal 2.png

2009-06-22T12:41:03Z

MartaPeroni:

File:Trigeminal 1.png

2009-06-22T12:35:42Z

MartaPeroni: Screenshot of overlay between warped atlas and original MRI of a patient with trigeminal neuralgia

Screenshot of overlay between warped atlas and original MRI of a patient with trigeminal neuralgia

2009 Summer Project Week TrigeminalNerve

2009-06-16T16:58:55Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
Image:fig2.png|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.

</gallery>

==Key Investigators==
* PoliMI: Marta Peroni
* UMG: Maria Francesca Spadea
* MGH: Greg Sharp

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

<h3>Objective</h3>
We are tuning and testing multimodal image registration in [http://www.plastimatch.org plastimatch] to allow accurate localization of the trigeminal nerve. The final objective is to register an atlas to patient CT, in order to avoid 3T MRI. The registration would allow the physician to identify the trigeminal nerve on the atlas and plan the Cyberknife treatment accordingly.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to crop and "threshold" the CT and to crop the atlas to obtain a more robust result. The output of Bspline deformable registration is than compared to the patient 3T MRI (whenever possible in the same modality - T1). The MRIs are acquired generally with CISS sequence.

Our plan for the project week is:
* solve issues with parameter handling between rigid and non-rigid stage
* investigate why the cropping is necessary for the registration to produce an output "acceptable" (TO BE DEFINED)
* investigate the thresholding

</div>

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

<h3>Progress</h3>
COME BACK SOON FOR MORE DETAILS...

</div>
</div>

<div style="width: 970%; float: left;">

==References==
*WILL BE ADDED SOON

</div>

2009 Summer Project Week TrigeminalNerve

2009-06-16T16:58:37Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
Image:fig2.png|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.

</gallery>

==Key Investigators==
* PoliMI: Marta Peroni
* UMG: Maria Francesca Spadea
* MGH: Greg Sharp

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

<h3>Objective</h3>
We are tuning and testing multimodal image registration in [http://www.plastimatch.org link plastimatch] to allow accurate localization of the trigeminal nerve. The final objective is to register an atlas to patient CT, in order to avoid 3T MRI. The registration would allow the physician to identify the trigeminal nerve on the atlas and plan the Cyberknife treatment accordingly.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to crop and "threshold" the CT and to crop the atlas to obtain a more robust result. The output of Bspline deformable registration is than compared to the patient 3T MRI (whenever possible in the same modality - T1). The MRIs are acquired generally with CISS sequence.

Our plan for the project week is:
* solve issues with parameter handling between rigid and non-rigid stage
* investigate why the cropping is necessary for the registration to produce an output "acceptable" (TO BE DEFINED)
* investigate the thresholding

</div>

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

<h3>Progress</h3>
COME BACK SOON FOR MORE DETAILS...

</div>
</div>

<div style="width: 970%; float: left;">

==References==
*WILL BE ADDED SOON

</div>

2009 Summer Project Week TrigeminalNerve

2009-06-16T16:39:52Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.

</gallery>

==Key Investigators==
* PoliMI: Marta Peroni
* UMG: Maria Francesca Spadea
* MGH: Greg Sharp

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

<h3>Objective</h3>
We are tuning and testing multimodal image registration in <a href="http://www.plastimatch.org">plastimatch </a> to allow accurate localization of the trigeminal nerve. The final objective is to register an atlas to patient CT, in order to avoid 3T MRI. The registration would allow the physician to identify the trigeminal nerve on the atlas and plan the Cyberknife treatment accordingly.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to crop and "threshold" the CT and to crop the atlas to obtain a more robust result. The output of Bspline deformable registration is than compared to the patient 3T MRI (whenever possible in the same modality - T1). The MRIs are acquired generally with CISS sequence.

Our plan for the project week is:
* solve issues with parameter handling between rigid and non-rigid stage
* investigate why the cropping is necessary for the registration to produce an output "acceptable" (TO BE DEFINED)
* investigate the thresholding

</div>

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

<h3>Progress</h3>
COME BACK SOON FOR MORE DETAILS...

</div>
</div>

<div style="width: 970%; float: left;">

==References==
*WILL BE ADDED SOON

</div>

2009 Summer Project Week TrigeminalNerve

2009-06-11T18:47:13Z

MartaPeroni:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
</gallery>

==Key Investigators==
* PoliMI: Marta Peroni
* UMG: Maria Francesca Spadea
* MGH: Greg Sharp

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

<h3>Objective</h3>
We are tuning and testing multimodal image registration in <a href="www.plastimatch.org">plastimatch </a> to allow accurate localization of the trigeminal nerve. The final objective is to register an atlas to patient CT, in order to avoid 3T MRI. The registration would allow the physician to identify the trigeminal nerve on the atlas and plan the Cyberknife treatment accordingly.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to crop and "threshold" the CT and to crop the atlas to obtain a more robust result. The output of Bspline deformable registration is than compared to the patient 3T MRI (whenever possible in the same modality - T1). The MRIs are acquired generally with CISS sequence.

Our plan for the project week is:
* solve issues with parameter handling between rigid and non-rigid stage
* investigate why the cropping is necessary for the registration to produce an output "acceptable" (TO BE DEFINED)
* investigate the thresholding

</div>

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

<h3>Progress</h3>
COME BACK SOON FOR MORE DETAILS...

</div>
</div>

<div style="width: 970%; float: left;">

==References==
*WILL BE ADDED SOON

</div>

2009 Summer Project Week TrigeminalNerve

2009-06-11T18:46:04Z

MartaPeroni: Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png|Project Week Main Page Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus ...'

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
</gallery>

==Instructions for Use of this Template==
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name>
#Copy the entire text of this page into the page created above
#Link the created page into the list of projects for the project event
#Delete this section from the created page
#Send an email to tkapur at bwh.harvard.edu if you are stuck

==Key Investigators==
* PoliMI: Marta Peroni
* UMG: Maria Francesca Spadea
* MGH: Greg Sharp

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

<h3>Objective</h3>
We are tuning and testing multimodal image registration in <a href="www.plastimatch.org">plastimatch </a> to allow accurate localization of the trigeminal nerve. The final objective is to register an atlas to patient CT, in order to avoid 3T MRI. The registration would allow the physician to identify the trigeminal nerve on the atlas and plan the Cyberknife treatment accordingly.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to crop and "threshold" the CT and to crop the atlas to obtain a more robust result. The output of Bspline deformable registration is than compared to the patient 3T MRI (whenever possible in the same modality - T1). The MRIs are acquired generally with CISS sequence.

Our plan for the project week is:
* solve issues with parameter handling between rigid and non-rigid stage
* investigate why the cropping is necessary for the registration to produce an output "acceptable" (TO BE DEFINED)
* investigate the thresholding

</div>

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

<h3>Progress</h3>
COME BACK SOON FOR MORE DETAILS...

</div>
</div>

<div style="width: 970%; float: left;">

==References==
*WILL BE ADDED SOON

</div>

2009 Summer Project Week

2009-06-11T18:36:55Z

MartaPeroni:

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-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
** 9-11am [[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_Prostate_Robotics |Prostate Robotics]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_Lupus_Lesion_Segmentation |Lupus Lesion Segmentation]] (Jeremy Bockholt MRN)
#[[Summer2009:VCFS| Pipeline development for VCFS]] (Marek Kubicki BWH)
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]] (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_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 to UCLA]] (Haiying Liu BWH)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Demo|Demo Brainlab-BioImage Suite-Slicer in BWH OR]] (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_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim UNC)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Andrey Fedorov BWH)
# [[EMSegment|EM Segment]] (Sylvain Jaume 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_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)

===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].

==Attendee List==
If you plan to attend, please add your name here.

#Ron Kikinis, BWH (NA-MIC, NAC, NCIGT)
#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) (Attending Tuesday-Friday)
#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 (Attending: Monday/Tuesday/Wednesday)
#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
#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)
#Dana Peters, Beth Israel Deaconess
#Sun Woo Lee, BWH
# Melanie Grebe, Siemens Corporate Research
# Megumi Nakao, BWH/NAIST
# Moti Freiman, The Hebrew Univ. of Jerusalem
#Jack Blevins, Acoustic Med Systems
#Michael Halle, BWH
#Amanda Peters, Harvard SEAS
#Joe Stam, NVIDIA (Wednesday, Thursday)
#Petter Risholm, BWH (NCIGT)
#Kimberly Powell, NVIDIA (Wednesday)
#Padma Akella, BWH (NCIGT)
#Clif Burdette, Acousticmed (Mon, Tue, Wed)

== 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

2009-05-11T16:18:31Z

MartaPeroni:

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) ([[NA-MIC/Projects/Theme/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]]
** 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: TBD
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: Tutorial Contest Winner Announcement and Project Progress using update [[#Projects|Project Wiki pages]]
*** 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.

#Prostate Robotics (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#4D Imaging - currently used for Lung Perfusion (Junichi, Dan Blezek?, Steve, Alex G?)
#Liver Ablation in Slicer (Haiying, Georgetown?)
#SLicer3 and Brainlab - introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)
#Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)
#gpu based registration acceleration (James Balter, Greg Sharp, Alark Joshi?, Aditya K., Yogesh Rathi?, Jimi Malcolm, Sandy Wells, Tina Kapur)
#Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)
#Xnat user interface improvements for NA-MIC (Dan M, Tina, Florin, Ron, Wendy)
#xnat and DICOMRT (Greg Sharp, Dan M) - might be done?
#Xnat user clinic - combine with data clinic
#xnat programmer clinic
#Grid Wizard+xnat clinic (Clement)
#?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, Ipek)
#Demo Brainlab/Slicer in BWH OR (Haiying, Nathan Hageman)
#Skull Stripping (Xiadong)

IGT Projects:
#port 4d gated ultrasound code to Slicer - (Danielle)
#integration of stereo video into Slicer (Mehdi)
#multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data (Diego, sylvain jaume, nicholas, noby)
#neuroendoscope workflow presentation (sebastien barre)
#slicer integration of mri compatible prostate biopsy robot(sid, queens)
#breakout session on Dynamic Patient Models (James Balter)
#gpu acceleration of 2d-3d registration (james balter, greg sharp, sandy wells, noby hata, terry peters proxy)

NA-MIC Engineering Projects
# DICOM Validation and Cleanup Tool (Luis, Sid, Steve, Greg)
# Using ITK in python (Steve, Demian, Jim)
# VTK 3d Widgets in Slicer3 (Nicole, Will/Karthik)
# Update to Slicer3 Colors module (Nicole)
# EM Segmenter (Sylvain, Nicolas)
# Plug-in 3D Viewer based on XIP (Lining)
# IAFE Mesh Modules - improvements and testing (Curt, Steve, Vince)
# Informatics workflow Design (Wen, Steve, Dan M, Dan B)

== 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...

==Attendee List==
If you plan to attend, please add your name here.

#Ron Kikinis, BWH
#Ferenc Jolesz, BWH
#Clare Tempany, BWH
#Tina Kapur, BWH
#Steve Pieper, Isomics Inc
#Jim Miller, GE Research
#Xiaodong Tao, GE Research
#Bill Lorensen, EAB
#Randy Gollub, MGH
#Nicole Aucoin, BWH
#Dan Marcus, WUSTL
#Junichi Tokuda, BWH
#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
#Haiying Liu BWH
#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
#Harish Doddi, Stanford University
#Saikat Pal, Stanford University
#Scott Hoge, BWH
#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

== 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]]