File:Fletcher NAMIC AHM2010.ppt

2010-01-06T17:42:01Z

Fletcher:

File:Fletcher NAMIC NCBC2008.ppt

2008-08-18T18:29:30Z

Fletcher:

Events:August 2008 NCBC AHM

2008-08-18T18:28:08Z

Fletcher:

=Agenda=
There will be a [http://meetings.nigms.nih.gov/index.cfm?event=home&ID=4095 all hands meeting] for the NCBC program at NIH.

{| border="00" cellpadding="8" cellspacing="0"
|-
| rowspan="2"| * The dates are August 13-14 and the location will be on the NIH campus
* Wednesday - August 13th, 8:30 AM - 6:30 PM
** 8:30 - 8:45 AM Introduction by Dr. Zerhouni, or Dr Berg, Natcher Auditorium
** 8:45 - 10:15 AM NCBC Presentations from PIs ('''Ron''', [[media:NA-MIC 2008.ppt|10 minute overview over NA-MIC]])
** 10:15 - 10:30 AM Big P and Building Bridges Summary (Russ Altman)
** 10:30 - 11:00 AM Break
***PI Meeting with Drs. Zerhouni, Berg, Lindberg, Natcher A
** 11:00 - 12:15 PM Presentations from Jr. Faculty Natcher Auditorium ('''Tom Fletcher''': 10 Minutes - [[media:Fletcher_NAMIC_NCBC2008.ppt|"Statistical Analysis of Anatomy from Medical Images"]])
** 12:15 - 1:30 PM Working Lunch: Working Groups and Building Bridges
** 1:30 - 3:30 PM "Hot Topic" Presentations Natcher Auditorium (30 Mins - '''Ross Whitaker''' - "NAMIC Highlights: From Algorithms and Software to Biomedical Science"): The best science of the center, focus on Biology impact and DBPs. Share the highlights/titles by July 15th.
** 3:30 - 3:45 PM Break
** 3:45 - 5:15 PM "Hot Topic" Presentations continued
** 5:15 - 6:00 PM Discussion of network DBP opportunities and Working Group #3
** 6:30 - --- PM Open Reception at hotel with Industry Host. PIs and Project Team will join at 6:45PM. PI Meeting with Project team, Natcher A
* Thursday - August 14th, 8:30 AM - 12:15 PM
** 8:30 - 9:30 AM Presentation from each Center: Introduction to the science fair program demos and schedule (teaser for the Science Fair, '''Will Schroeder''')
** 9:30 - 11:00 AM Science Fair: [[media:NA-MIC kit NCBC AHM2008 SPujol.ppt |"Three ways to use the NA-MIC kit"]] ('''Sonia Pujol''')
Abstract: The National Alliance for Medical Imaging Computing (NA-MIC) develops a collection of tools and applications to improve the deployment of advanced image analysis methods to the research community. By combining science and technology, the NA-MIC kit fosters leading edge clinical research achievements in a collaborative and open-source environment.
The Science Fair will present the NA-MIC kit through the perspectives of each of our three target audiences: clinical researchers, biomedical engineers and algorithm developers. Attendees will be exposed to potential uses of the NA-MIC kit in the context of 3D visualization to facilitate data interpretation, in the use of advanced image analysis to extract relevant information, and in the development of tailored plug-ins to extend image computing capabilities. Through demonstrations of image processing methods within the 3D Slicer deployment platform, and presentations of NA-MIC pragmatic teaching initiatives to translate techniques into skills, the Science Fair will provide an overview of the benefits of NA-MIC efforts to the research community.
** 11:00 - 12:00 noon Working Groups Report Out, Future Plans, Discussion(s)
** 12:00 - 12:15 PM Wrap-up and adjournment of main program (Conference ends for all but PIs, and Project Team and invited guests)
** 12.15 - 1.15 PM Lunch (Conference ends for all but PIs) DBP discussion: Diabetes, MH, others
** 1.15 - 3:00 PM Moderated Discussions with other NIH Programs: PIs: CaBIG, CTSA, BIRN, NIH Clinical Center, others
| style="background: #ebeced" colspan="2" align="center"| NA-MIC is one of seven National Centers for Biomedical Computing, part of the NIH roadmap initiative.
 See [http://meetings.nigms.nih.gov/index.cfm?event=home&ID=4095 here] for the program of this years' all hands meeting.
|-
| style="background: #ebeced" align="center"| [[Image:NCBC-Logo.jpg|204px]]
|}
 

=NCBC Presentation Materials=
Russ Altman will be giving a 10 minutes overview over the entire NCBC program. He has reqested from each of the NCBCs the following information about accomplishments.
==DBPs==
A short summary of the original and renewal DBPs (this will also be used in the DBP sig breakout session). Basically title and one paragraph description.

1) During the first three years of NA-MIC, Core 3 consisted of four DBPs which were grouped into two thrusts.
*Thrust 1 was directed by Drs. Shenton and Saykin. Thrust 2 was directed by Drs. Potkin and Kennedy. The focus of the research was to utilize neuroimaging tools to evaluate fronto-temporal connectivity abnormalities in schizophrenia, as well as abnormalities in hemispheric connections (i.e., corpus callosum), and abnormalities in the anterior limb of the internal capsule. Improved segmentation techniques, coregistration of structural MRI, DTI-MR, and fMRI, as well as novel processing tools for evaluating white matter fiber tracts and interregional functional connectivity were needed to accomplish these goals, and they were developed in conjunction with Cores 1 and 2.
*Findings from this project, which involve both structural and functional information about brain abnormalities in schizophrenia, were correlated with neurocognitive, clinical, and behavioral data in order to understand further the relationship between brain abnormalities and cognition/behavior in schizophrenia.

2) Starting with the 4th year of NA-MIC, the DBPs were shifted from schizophrenia to lupus, autism, velocardiofacial syndrome (VCSF), and prostate cancer.
*These DBPs now drive the computational research within NA-MIC. Specifically:
** Drs. Jeremy Bockholt and Charles Gasparovi at the MIND Institute and the University of New Mexico are analyzing brain lesions in Neuropsychiatric Systemic Lupus Erythematosis,
** Drs. Heather Hazlett and Joseph Piven at University of North Carolina, Chapel Hill are conducting a longitudinal MRI study of early brain development in Autism,
** Dr. Marek Kubicki at Harvard Medical School is investigating VCSF as a genetic model for schizophrenia, and
** Dr. Gabor Fichtinger at Queens University is developing a robotic percutaneous surgery system for treatment of prostate cancer.

[[Image:NA-MIC-Image-Gallery-2008.png|thumb|250px|[http://www.na-mic.org/pages/Special:PubDB_Gallery?collection=12 The NA-MIC image gallery]]]

==Publications==
1) A few key journal publications that have emerged directly from each center (say the top 5 per center). These should not be presented in a center-specific context but just to show the volume and quality of scientific production. You should be able to get these directly from your progress reports.
* We use our publications database to gather download statistics about our publications. See [http://www.na-mic.org/pages/Special:PubDB_Stats?collectionid=12 here] for an up-to-date view.
*This are the top five papers from our database in terms of number of downloads between September 2007 and July 2008
*# [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=609 Pohl K, Fisher J, Bouix S, Shenton M, McCarley R, Grimson E, Kikinis R, Wells W. Using the logarithm of odds to define a vector space on probabilistic atlases. Med Image Anal. 2007 Oct;11(5):465-77.]
*# [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=996 Hata N, Piper S, Jolesz F, Tempany C, Black P, Morikawa S, Iseki H, Hashizume M, Kikinis R. Application of Open Source Image Guided Therapy Software in MR-guided Therapies. Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 1):491-8]
*# [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=544 Yeo B, Sabuncu M, Desikan R, Fischl B, Golland P. Effects of Registration Regularization and Atlas Sharpness on Segmentation Accuracy. Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 1):683-91]
*# [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=361 Bouix S, Martin-Fernandez M, Ungar L, Nakamura M, Koo M, McCarley R, Shenton M. On evaluating brain tissue classifiers without a ground truth. Neuroimage. 2007 Jul 15;36(4):1207-1224]
*# [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=540 Georgiou T, Michailovich O, Rathi Y, Malcolm J, Tannenbaum A. Distribution Metrics and Image Segmentation. Linear Algebra and its Applications. 2007;425(2-3):663-672]

2) Some statistics of publications: total number in the last year or cumulative. Again, these should be presented in aggregate rather than by center.
* 198 cumulative publications. http://www.na-mic.org/pages/Special:Publications?collection=12
* See also [http://www.na-mic.org/pages/Special:PubDB_Stats?collectionid=12 here] for a geographical distribution of the downloads. This link is sometimes slow.

[[Image:Slicer3-11-2007.jpg|thumb|250px|[[NA-MIC-Kit|Go to the NA-MIC Kit]]]]

==Tools==
A list of tools produced by the center with one or two highlights where you have high volume download or many journal citations.
*[[NA-MIC-Kit|NA-MIC Kit]], which includes [http://www.slicer.org 3D Slicer], a popular visualization package (see [http://slicer.org/pages/Special:Download_Stats here] for un-curated download statistics--it is helpful if you sort by number of downloads to see the full impact).

==Outreach==
*List of conferences/meetings where people in your center have explicitly advertised or demoed the NCBC’s activities.
**MICCAI, RSNA, Human Brain Mapping, IGT Workshops at NIH
*Newsletters, conferences, and other activities promoted by the centers.
**The semi-annual hands-on event called the "NA-MIC Project Week".

==Collaborations==

http://wiki.na-mic.org/Wiki/index.php/NA-MIC_External_Collaborations

==Buiding Bridges Postdoc==
[[Image:Spines01.jpg|thumb|250px|A small fragment of a dendrite (gray) with segmented spines (color).]]
* Who was the bridge built to?
**The National Center for Microscopy and Imaging Research (NCMIR; http://ncmir.ucsd.edu) at the University of California, San Diego. A key emphasis of NCMIR is the application of advanced imaging technologies to the nervous system in health and disease. Affiliated with UCSD’s Center for Research in Biological Systems (CRBS), the NCMIR is a recognized authority in the development of technologies for high throughput multi-scale imaging and analysis of biological systems at the mesoscale, the dimensional range spanning 5 nm3 and 50µm3. Macromolecules, organelles, and multi-component structures like synapses which are encompassed in this dimensional range have traditionally been challenging to study because they fall in the resolution gap between X-ray crystallography at one end and medical imaging at the other.
* What is the general topic of the research?
**Work within the Slicer environment to address multi-scale microscopy imaging data, thereby allowing for the analysis and visualization of cellular data. The project has focused on the importation of data into Slicer and the investigation of algorithms for cellular and sub-cellular data (e.g. see - http://www.na-mic.org/Wiki/index.php/Projects/Slicer3/2007_Project_Week_Support_for_electron_microscopy).

==NA-MIC Description==

NA-MIC is a multi-institutional, interdisciplinary team of computer scientists, software engineers, and medical investigators who develop computational tools for the analysis and visualization of medical image data. The purpose of the center is to provide the infrastructure and environment for the development of computational algorithms and open source technologies, and then oversee the training and dissemination of these tools to the medical research community. This world-class software and development environment serves as a foundation for accelerating the development and deployment of computational tools that are readily accessible to the medical research community. The team combines cutting-edge computer vision research (to create medical imaging analysis algorithms) with state of the art software engineering techniques (based on "extreme" programming techniques in a distributed, open-source environment) to enable computational examination of both basic neuroscience and neurological disorders. In developing this infrastructure resource, the team is significantly expanding upon proven open systems technology and platforms.

The driving biological projects for NA-MIC include the study of autism, lupus, prostate cancer, VCSF, and schizophrenia, but the methods are applicable to many other diseases. The computational tools developed in NA-MIC are used to perform image-analysis at a range of scales, and across a range of modalities including diffusion MRI, quantitative ECG, and metabolic and receptor PET, but potentially including microscopic, genomic, and other image data. It applies to image data from individual patients, and to studies executed across large populations. The data is taken from subjects across a wide range of time scales and ultimately apply to a broad range of diseases in a broad range of organs.

Events:August 2008 NCBC AHM

2008-08-05T14:52:09Z

Fletcher:

=Agenda=
There will be a [http://meetings.nigms.nih.gov/index.cfm?event=home&ID=4095 all hands meeting] for the NCBC program at NIH.

{| border="00" cellpadding="8" cellspacing="0"
|-
| rowspan="2"| * The dates are August 13-14 and the location will be on the NIH campus
* Wednesday - August 13th, 8:30 AM - 6:30 PM
** 8:30 - 8:45 AM Introduction by Dr. Zerhouni, or Dr Berg, Natcher Auditorium
** 8:45 - 10:15 AM NCBC Presentations from PIs ('''Ron''', 10 minutes)
** 10:15 - 10:30 AM Big P and Building Bridges Summary (Russ Altman)
** 10:30 - 11:00 AM Break
***PI Meeting with Drs. Zerhouni, Berg, Lindberg, Natcher A
** 11:00 - 12:15 PM Presentations from Jr. Faculty Natcher Auditorium ('''Tom Fletcher''': 10 Minutes - "Statistical Analysis of Anatomy from Medical Images")
** 12:15 - 1:30 PM Working Lunch: Working Groups and Building Bridges
** 1:30 - 3:30 PM "Hot Topic" Presentations Natcher Auditorium (30 Mins - '''Ross Whitaker''' - "NAMIC Highlights: From Algorithms and Software to Biomedical Science"): The best science of the center, focus on Biology impact and DBPs. Share the highlights/titles by July 15th.
** 3:30 - 3:45 PM Break
** 3:45 - 5:15 PM "Hot Topic" Presentations continued
** 5:15 - 6:00 PM Discussion of network DBP opportunities and Working Group #3
** 6:30 - --- PM Open Reception at hotel with Industry Host. PIs and Project Team will join at 6:45PM. PI Meeting with Project team, Natcher A
* Thursday - August 14th, 8:30 AM - 12:15 PM
** 8:30 - 9:30 AM Presentation from each Center: Introduction to the science fair program demos and schedule (teaser for the Science Fair, '''Will Schroeder''')
** 9:30 - 11:00 AM Science Fair: "Three ways to use the NA-MIC kit" ('''Sonia Pujol''')
Abstract: The National Alliance for Medical Imaging Computing (NA-MIC) develops a collection of tools and applications to improve the deployment of advanced image analysis methods to the research community. By combining science and technology, the NA-MIC kit fosters leading edge clinical research achievements in a collaborative and open-source environment.
The Science Fair will present the NA-MIC kit through the perspectives of each of our three target audiences: clinical researchers, biomedical engineers and algorithm developers. Attendees will be exposed to potential uses of the NA-MIC kit in the context of 3D visualization to facilitate data interpretation, in the use of advanced image analysis to extract relevant information, and in the development of tailored plug-ins to incubate new concepts. Through demonstrations of image processing methods within the 3D Slicer deployment platform, and presentations of NA-MIC pragmatic teaching initiatives to translate techniques into skills, the Science Fair will provide an overview of the potential benefits of NA-MIC efforts to the research community.
** 11:00 - 12:00 noon Working Groups Report Out, Future Plans, Discussion(s)
** 12:00 - 12:15 PM Wrap-up and adjournment of main program (Conference ends for all but PIs, and Project Team and invited guests)
** 12.15 - 1.15 PM Lunch (Conference ends for all but PIs) DBP discussion: Diabetes, MH, others
** 1.15 - 3:00 PM Moderated Discussions with other NIH Programs: PIs: CaBIG, CTSA, BIRN, NIH Clinical Center, others
| style="background: #ebeced" colspan="2" align="center"| NA-MIC is one of the National Centers for Biomedical Computing
 See [http://meetings.nigms.nih.gov/index.cfm?event=home&ID=4095 here] for the program of this years' all hands meeting.
|-
| style="background: #ebeced" align="center"| [[Image:NCBC-Logo.jpg|204px]]
|}
 

=NCBC Presentation Materials=
Russ Altman will be giving a 10 minutes overview over the entire NCBC program. He has reqested from each of the NCBCs the following information about accomplishments.
==DBPs==
A short summary of the original and renewal DBPs (this will also be used in the DBP sig breakout session). Basically title and one paragraph description.

1) During the first three years of NA-MIC, Core 3 consisted of four DBPs which were grouped into two thrusts.
*Thrust 1 was directed by Drs. Shenton and Saykin. Thrust 2 was directed by Drs. Potkin and Kennedy. The focus of the research was to utilize neuroimaging tools to evaluate fronto-temporal connectivity abnormalities in schizophrenia, as well as abnormalities in hemispheric connections (i.e., corpus callosum), and abnormalities in the anterior limb of the internal capsule. Improved segmentation techniques, coregistration of structural MRI, DTI-MR, and fMRI, as well as novel processing tools for evaluating white matter fiber tracts and interregional functional connectivity were needed to accomplish these goals, and they were developed in conjunction with Cores 1 and 2.
*Findings from this project, which involve both structural and functional information about brain abnormalities in schizophrenia, were correlated with neurocognitive, clinical, and behavioral data in order to understand further the relationship between brain abnormalities and cognition/behavior in schizophrenia.

2) Starting with the 4th year of NA-MIC, the DBPs were shifted from schizophrenia to lupus, autism, velocardiofacial syndrome (VCSF), and prostate cancer.
*These DBPs now drive the computational research within NA-MIC. Specifically: Drs. Jeremy Bockholt and Charles Gasparovi at the MIND Institute and the University of New Mexico are analyzing brain lesions in Neuropsychiatric Systemic Lupus Erythematosis, Drs. Heather Hazlett and Joseph Piven at University of North Carolina, Chapel Hill are conducting a longitudinal MRI study of early brain development in Autism, Dr. Marek Kubicki at Harvard Medical School is investigating VCSF as a genetic model for schizophrenia, and Dr. Gabor Fichtinger at Queens University is developing a robotic percutaneous surgery system for treatment of prostate cancer.

[[Image:NA-MIC-Image-Gallery-2008.png|thumb|250px|[http://www.na-mic.org/pages/Special:PubDB_Gallery?collection=12 The NA-MIC image gallery]]]

==Publications==
1) A few key journal publications that have emerged directly from each center (say the top 5 per center). These should not be presented in a center-specific context but just to show the volume and quality of scientific production. You should be able to get these directly from your progress reports.
* We use our publications database to gather download statistics about our publications. See [http://www.na-mic.org/pages/Special:PubDB_Stats?collectionid=12 here] for an up-to-date view.
*This are the top five papers from our database in terms of number of downloads between September 2007 and July 2008
*# http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=609
*# http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=996
*# http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=544
*# http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=361
*# http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=540

2) Some statistics of publications: total number in the last year or cumulative. Again, these should be presented in aggregate rather than by center.
* 198 cumulative publications. http://www.na-mic.org/pages/Special:Publications?collection=12
* See also [http://www.na-mic.org/pages/Special:PubDB_Stats?collectionid=12 here] for a geographical distribution of the downloads. This link is sometimes slow.

[[Image:Slicer3-11-2007.jpg|thumb|250px|[[NA-MIC-Kit|Go to the NA-MIC Kit]]]]

==Tools==
A list of tools produced by the center with one or two highlights where you have high volume download or many journal citations.
*[[NA-MIC-Kit|NA-MIC Kit]], which includes [http://www.slicer.org 3D Slicer], a popular visualization package (see [http://slicer.org/pages/Special:Download_Stats here] for un-curated download statistics--it is helpful if you sort by number of downloads to see the full impact).

==Outreach==
*List of conferences/meetings where people in your center have explicitly advertised or demoed the NCBC’s activities.
**MICCAI, RSNA, Human Brain Mapping, IGT Workshops at NIH
*Newsletters, conferences, and other activities promoted by the centers.
**The semi-annual hands-on event called the "NA-MIC Project Week".

==NA-MIC Description==

NA-MIC is a multi-institutional, interdisciplinary team of computer scientists, software engineers, and medical investigators who develop computational tools for the analysis and visualization of medical image data. The purpose of the center is to provide the infrastructure and environment for the development of computational algorithms and open source technologies, and then oversee the training and dissemination of these tools to the medical research community. This world-class software and development environment serves as a foundation for accelerating the development and deployment of computational tools that are readily accessible to the medical research community. The team combines cutting-edge computer vision research (to create medical imaging analysis algorithms) with state of the art software engineering techniques (based on "extreme" programming techniques in a distributed, open-source environment) to enable computational examination of both basic neuroscience and neurological disorders. In developing this infrastructure resource, the team is significantly expanding upon proven open systems technology and platforms.

The driving biological projects for NA-MIC include the study of autism, lupus, prostate cancer, VCSF, and schizophrenia, but the methods are applicable to many other diseases. The computational tools developed in NA-MIC are used to perform image-analysis at a range of scales, and across a range of modalities including diffusion MRI, quantitative ECG, and metabolic and receptor PET, but potentially including microscopic, genomic, and other image data. It applies to image data from individual patients, and to studies executed across large populations. The data is taken from subjects across a wide range of time scales and ultimately apply to a broad range of diseases in a broad range of organs.

2008 Summer Project Week

2008-05-29T19:06:48Z

Fletcher: /* Diffusion Image Analysis */

Back to [[Engineering:Programming_Events|Programming/Project Events]]

[[Image:ProjectWeek-2008.png|thumb|220px|right|Summer 2008]]

== Logistics ==

'''Dates:''' June 23-27, 2008

'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

'''Registration Fee:''' $260 (this will cover the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 13th, 2008. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139

If you are attending for one day only, the registration fee is not required.

'''Hotel:''' We have a group rate of $239/night (plus tax) for a room with either 1 king or 2 queen beds at the [http://www.hotelatmit.com Hotel at MIT (now called Le Meridien)]. [http://www.starwoodmeeting.com/StarGroupsWeb/booking/reservation?id=0805167317&key=4FD1B 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.

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

==Introduction to NA-MIC Project Week==

NA-MIC Project Week is a hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the [[NA-MIC-Kit|NA-MIC Kit]] calendar. This event is the seventh of the [[Engineering:Programming_Events|'''series''']]. It is held in the summer at MIT (typically the last week of June), and a shorter version is held in Salt Lake City in the winter (typically the second week of January).
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

* NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the [[NA-MIC-Kit|NA-MIC Kit]], and those who can help make it happen.
* This is not an introduction to the components of the [[NA-MIC-Kit|NA-MIC Kit]].
* NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the [[NA-MIC-Kit|NA-MIC Kit]] capabilities, integrate Core 1 algorithms, and refine workflows for Core 3.
* NA-MIC Core 3 (DBP) - bring your data to work on with the [[NA-MIC-Kit|NA-MIC Kit]] and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
* External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.
* Everyone should '''bring a laptop'''. We will have four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.

== 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
** 9:00-9:45am: NA-MIC Software Process
** 10-10:30am [[Project Week 2008 Slicer 3.0 Update|Slicer 3.0 Update]] (Jim Miller, Steve Pieper)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: Non-Linear Registration]]
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9:00-12pm [[Project Week 2008 Special topic breakout: ITK]] (Luis Ibanez)
** noon lunch
** 2:30-3:30pm: [[Project Week 2008 Special topic breakout: XNAT Database]] (Daniel Marcus)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** noon lunch
**2:30-3:30pm [[Project Week 2008 Special topic breakout: GWE]] (Marco Ruiz)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: Project Progress using update [[#Projects|Project Wiki pages]]
** noon lunch boxes and adjourn. (Next one [[AHM_2009| in Utah the week of Jan 5, 2009]])

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list

# [[Engineering:TCON_2008|May 08 and May 15 TCON DBPs ONLY]] at 3pm ET to discuss NA-MIC DBP Projects ONLY.
# [[Engineering:TCON_2008|May 22 TCON#1]] at 3pm ET to discuss NA-MIC Engr Core Projects and Assign/Verify Teams
# [[Engineering:TCON_2008|May 29 TCON#2]] at 3pm ET to discuss NA-MIC ALGORITHMS Core Lead Projects. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 5 TCON#3]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All NIH funded "collaborations with NCBC" leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 12 TCON#4]] at 3pm ET to discuss NA-MIC EXTERNAL Collaborations. All other collaboration leads should call. Project leads should sign up for a slot [[Engineering:TCON_2008|here]]. Projects will be discussed in order of the signups.
# [[Engineering:TCON_2008|June 19 TCON#5]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 12, 2008: [[NA-MIC/Projects/Theme/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 19, 2008: 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...

== A History in Wiki Links ==

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

== Projects ==

===DBP II===
These are projects by the new set of DBPS:
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)
##EPI-DWI Distortion correction (Sylvain Bouix BWH, Tauseef Rehman GATech)
##EPI-DWI Eddy Current distortion correction (Sylvain Bouix BWH, Ran Tao Utah)
##Lobe Parcellation of 3T MR data - need help parametrization (Sylvain Bouix BWH, Priya Srinivasan BWH, Brad Davis Kitware)
##Finsler method (John Melonakos GATech, Marek Kubicki BWH)
##Group Analysis on DTI (Casey Goodlett Utah, Marek Kubicki BWH)
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)
##Add Projects for this DBP here...
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)
##[[DBP2:MIND:RoadmapProject|Finish Roadmap Project]]
##[[DBP2:MIND:LongitudinalRegistrationProject|Longitudinal Registration]]
##[[DBP2:MIND:BeyondLesionsProject|Beyond Lesions]]
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)
##Add Projects for this DBP here...

===Structural Analysis===

===Diffusion Image Analysis===
#[[2008_Summer_Project_Week:EddyCurrentCorrection|Eddy current and head motion correction of DWIs]] (Ran Tao, Utah, Sylvain Bouix, BWH, Xiaodong Tao, GE, Tom Fletcher, Utah)

===Calibration/Validation===

===NA-MIC Kit - Slicer 3===

===External Collaborations===
#[[NA-MIC/Projects/Collaboration/UWA-Perth]] (Adam Wittek)
#[[NA-MIC/Projects/Collaboration/MRSI Module for Slicer]] (Bjoern Menze)
#NIREP: Non-rigid Image Registration Evaluation (Gary Christensen Group)
#Lung Atlas (Gary Christensen Group)
#Non-rigid image registration (Gary Christensen Group)
#[[NA-MIC/Projects/Collaboration/SARP phantom]] (Keith Gunderson)

===Non-Medical Collaborations===

==Attendee List==
# Ron Kikinis, BWH
# Gary Christensen, The University of Iowa
# Jeffrey Hawley, Gary Christensen's student
# Kate Raising, Gary Christensen's student
# Nathan Fritze, Gary Christensen's student
# Paul Song, Gary Christensen's student
# Cheng Zhang, Gary Christensen's student
# Ying Wei, Gary Christensen's student
# Nathan Burnette, The University of Iowa
# Hans Johnson, The University of Iowa
# Vincent Magnotta, The University of Iowa
# Keith Gunderson, The University of Iowa
# Steve Pieper, Isomics, Core 2/6
# Dana C. Peters, BIDMC Harvard Medical
# Jason Taclas, BIDMC Harvard Medical
# Nicole Aucoin, BWH, Core 2
# Will Schroeder, Kitware, Cores 2/4
# Sebastien Barre, Kitware, Core 2
# Julien Jomier, Kitware, Core 2
# Luis Ibanez, Kitware, Core 2
# Curtis Lisle, KnowledgeVis, Core 2
# Katie Hayes, BWH, Core 2
# Randy Gollub, MGH, Core 5
# Clement Vachet, UNC, Core 3
# Casey Goodlett, Utah, Core 1
# Jeffrey Grethe, UCSD, Core 2
# Marco Ruiz, UCSD, Core 2
# Zhen Qian, Rutgers University
# Jinghao Zhou, Rutgers University
# Luca Antiga, Mario Negri Institute
# Adam Wittek, The University of Western Australia
# Grand Joldes, The University of Western Australia
# Jamie Berger, The University of Western Australia
# Serdar Balci, MIT, Core 1
# Bryce Kim, MIT, Core1
# Tina Kapur, BWH, Core 6
# Carling Cheung, Robarts Research Institute / The University of Western Ontario
# Danielle Pace, Robarts Research Institute / The University of Western Ontario
# Sean Megason, Dept of Systems Biology, Harvard Medical School
# Alex Gouaillard, Dept of Systems Biology, Harvard Medical School
# Kishore Mosaliganti, Dept of Systems Biology, Harvard Medical School
# Arnaud Gelas, Dept of Systems Biology, Harvard Medical School
# Sonia Pujol, Surgical Planning Laboratory, BWH
# Bjoern Menze, (then) Surgical Planning Laboratory, BWH
# Alex Yarmarkovich, Isomics, Core 2
# Sylvain Bouix, BWH, Core 3
# Priya Srinivasan, BWH, Core 3
# Chris Churas, UCSD, Core 2
# John Melonakos, Georgia Tech, Core 1
# Yi Gao, Georgia Tech, Core 1
# Tauseef Rehman, Georgia Tech, Core 1
# Clare Poynton, MIT, Core 1
# H. Jeremy Bockholt, MRN Lupus DBP Core 3
# Mark Scully, MRN Lupus DBP Core 3
# Gabor Fichtinger, Queen's, Core 2
# David Gobbi, Queen's, Core 2
# Purang Abolmaesumi, Queen's, Core 2
# Siddharth Vikal, Queen's, Core 2
# Daniel Blezek, Mayo
# Csaba Csoma, JHU, Core 2
# Ran Tao, University of Utah, Core 1
# Jim Miller, GE Research, Core 2
# Viswanath Avasarala, GE Research, NAC

==Pictures==

File:NAMIC-AHM2008-Utah1.ppt

2008-01-10T14:16:59Z

Fletcher:

AHM 2008

2008-01-10T14:16:15Z

Fletcher: /* Agenda */

__NOTOC__
== Introduction ==

{| border="00" cellpadding="8" cellspacing="0"
|-
| rowspan="2"| '''This is the home page for the 2008 NA-MIC all hands meeting (AHM).''' NA-MIC participants meet for a AHM once a year. The purpose of the AHM is to coordinate, discuss plans and report to NIH officers and the external advisory board (EAB). The external advisory board meets with the NA-MIC leadership immediately after the AHM. In parallel, NA-MIC is organizing a project week. These events, with the exception of the EAB meeting, are open to collaborators and potential collaborators.

For more information about the project weeks in general, click [[Engineering:Programming_Events|'''here''']].

For information about the January 2008 project week, see below or click [[2008_Winter_Project_Week|'''here''']].

For information about Utah as a travel destination click [http://www.utah.com '''here'''].
| style="background: #ebeced" colspan="2" align="center"| [[Image:SLC.jpg|center|350px|View of the City]]
|-
| style="background: #ebeced"| SLC
| style="background: #ebeced"|The 2008 AHM, EAB and Project Week will be held in Salt Lake City, UT, January 7-11 2008.
|}
 

We have three wireless access points at the AHM.

Two of them are located in the capital ballroom. One is named capital-ballroom, the other is named capital-ballroom2. If one access point doesn't let you connect it is probably overloaded. In that case, please try connecting to the other one.

The wireless in the amethyst ballroom is named linksys.

None of these access points require a password to connect.

== Agenda ==

{| border="1" cellpadding="5"
|- style="background:#ebeced; color:black" align="left"
| style="width:4%" | '''Time'''
| style="width:12%" | '''Monday, January 7'''
| style="width:12%" | '''Tuesday, January 8'''
| style="width:12%" | '''Wednesday, January 9'''
| style="width:32%" | '''Thursday, January 10 '''
| style="width:12%" | '''Friday, January 11'''
|-
| style="background:#ffffdd; color:black"|
| style="background:#b4d597; color:#522200"| '''[[2008_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
| style="background:#b4d597; color:#522200"| '''[[2008_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
| style="background:#b4d597; color:#522200"| '''[[2008_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
| style="background:#fff6a6; color:#522200"| '''AHM''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol A-B], [[2008_EAB|'''EAB''']] in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Olympus B]
'''[[2008_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Olympus A]
| style="background:#b4d597; color:#522200"|'''[[2008_Winter_Project_Week|Project Activities]] ''' in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol B-C]
|-
| style="background:#ffffdd; color:black"|'''7:30-'''
| style="background:#ebeced; color:black"|
| style="background:#b4d597; color:black"| Breakfast
| style="background:#b4d597; color:black"| Breakfast
| style="background:#fff6a6; color:black"| Breakfast
| style="background:#b4d597; color:black"| Breakfast
|-
| style="background:#ffffdd; color:black"|'''8:00-10:00'''
| style="background:#ebeced; color:black"|'''9:30''' Core 1 and 2 PI closed session in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Capitol A]
| style="background:#b4d597; color:black"|Project Work [[2008 Winter Project Week Plug-ins for Slicer3|Plug-ins for Slicer3]] in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
| style="background:#b4d597; color:black"|Project Work '''8:00-9:00''' [[2008 Winter Project Week IGT|IGT Breakout Session]] [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
 
9am: [[2008 Winter Project Week Tractography|Tractography Breakout Session]] in [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 2]
| style="background:#fff6a6; color:black"| 
'''8:00''' [[AHM 2008 Introduction|Introduction]], Ron Kikinis 

'''Core 1 and 2 Presentations''' 
'''8:05''' [[Media:NAMIC-AHM2008-Utah1.ppt | Utah 1]], Ross Whitaker 
'''8:20''' [[Media:Utah-Gerig-EAB.ppt‎ | Utah 2]], Guido Gerig 
'''8:30''': [[Media:MIT_NAMIC_AHM2008.ppt‎ | MIT]], Polina Golland 
'''8:45''': [[Media:20080110-AHM-GeorgiaTech.zip|Georgia Tech]], Allen Tannenbaum 
'''9:00''': [[Media:2008 UNC Core1 NAMIC AHM.ppt | UNC]], Martin Styner 
'''9:10''': MGH/WUSTL, Dan Marcus 
'''9:25''': Kitware, Will Schroeder 
'''9:40''': [[Media:GE Research AHM 2008.ZIP | GE Research]], Jim Miller
| style="background:#b4d597; color:black"|Project Work
|-
| style="background:#ffffdd; color:black"|'''10:00-10:30'''
| style="background:#ebeced; color:black"| Core 1 and 2 PI closed session
| style="background:#b4d597; color:black"| Coffee
| style="background:#b4d597; color:black"| Coffee
| style="background:#fff6a6; color:black"| Coffee
| style="background:#b4d597; color:black"| Coffee
|-
| style="background:#ffffdd; color:black"|'''10:30-12:00'''
| style="background:#ebeced; color:black"| Core 1 and 2 PI closed session
| style="background:#b4d597; color:black"|Project Work
| style="background:#b4d597; color:black"|Project Work 
[[2008 Winter Project Week Tractography|Tractography Breakout Session contd]]
| style="background:#fff6a6; color:black"|
'''10:30''': [[media:2008 NA-MIC AHM Isomics.ppt | Isomics]], Steve Pieper 
'''10:45''': [[media:NA-MIC_2008AHM_UCSD.ppt | UCSD]], Mark Ellisman 
'''11:00''': UCLA, Arthur Toga 
'''11:15''': Outreach: Training & [[media:2008 NA-MIC AHM Dissemination.ppt|Dissemination]], Randy Gollub 
'''11:25''': Invited speaker: Mike Sherman, Stanford NCBC Simbios, SimTK Architect
| style="background:#b4d597; color:black"|Project Work
|-
| style="background:#ffffdd; color:black"|'''12:00-1:00'''
| style="background:#b4d597; color:black"| Lunch
| style="background:#b4d597; color:black"| Lunch [[DBP Engineering Resource|DPB Engineers Lunch meeting]]
| style="background:#b4d597; color:black"| Lunch [[AHM 2008 fMRI|Birds of a Feather: fMRI]]
| style="background:#fff6a6; color:black"| Lunch
| style="background:#b4d597; color:black"| Adjourn
|-
| style="background:#ffffdd; color:black"|'''1:00-3:00'''
| style="background:#b4d597; color:black"|Introduce Projects and Participants
| style="background:#b4d597; color:black"|Breakout: [[2008 Winter Project Week Geometry and Topology processing of Meshes|Geometry and Topology processing of Meshes]] [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amthyst 1]
| style="background:#b4d597; color:black"|Project Work [[2008 Winter Project Week Tractography|Tractography Breakout Session contd]]
| style="background:#fff6a6; color:black"|
'''DBP results''' 
'''1:00''': [[Media:DBP2-Prostate-AHM2008.pdf | Queens/JHU]], David Gobbi 
'''1:15''':UNC, Heather Cody Hazlett 
'''1:30''':[[Media:NA-MIC_Kubicki.ppt | Harvard]], Marek Kubicki 
'''1:45''':MIND/UNM, Jeremy Bockholt 

'''NCBC Collaborations''' 
'''2:00''': [[Image:NA-MIC_Cleary_RF_Ablation_Georgetown.pdf | Georgetown, Kevin Cleary]] 
'''2:15''': [[Media:External-Wyatt-WFUSM.ppt‎|Wake Forest/VT, Chris Wyatt]] 
'''2:30''': [[Media:NA-MIC Mesh Collaboration - 2008.ppt| UIowa, Nicole Grosland,Vincent Magnotta]] 
| style="background:#ebeced; color:black"|
|-
| style="background:#ffffdd; color:black"|'''3:30-4:00'''
| style="background:#b4d597; color:black"| Coffee
| style="background:#b4d597; color:black"| Coffee
| style="background:#b4d597; color:black"| Coffee
| style="background:#fff6a6; color:black"| Coffee
| style="background:#ebeced; color:black"|
|-
| style="background:#ffffdd; color:black"|'''3:00-5:00'''
| style="background:#b4d597; color:black"|'''3:00-4:00''' Slicer Update [[Media:2008 NA-MIC AHM Slicer3.ppt | Slides]] 
'''4:00-5:00''' Breakout: [[2008 Winter Project Week EM Segmenter User Group|EM Segmenter User Group]] [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
| style="background:#b4d597; color:black"|Project Work [[2008_Winter_Project_Week_Image_Registration_Update| Registration Breakout]] [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
| style="background:#b4d597; color:black"|Project Work '''3:00-4:00''' [[2008 Winter Project Week Batchmake Update|Batchmake Update]] [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Amethyst 1]
[[2008 Winter Project Week Tractography|Tractography Breakout Session contd]] 
| style="background:#fff6a6; color:black"|[[2008 EAB|EAB]] [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Olympus B] '''3:00-4:00''' Discussion with NA-MIC Leadership '''4:00-5:00''' Closed Session
| style="background:#ebeced; color:black"|
|-
| style="background:#ffffdd; color:black"|'''05:00-07:00'''
| style="background:#b4d597; color:black"|
| style="background:#b4d597; color:black"|
| style="background:#b4d597; color:black"|'''5:00''' Optional: [[2008-SCI-tour|Tour]] of the new SCI building
| style="background:#fff6a6; color:black"|'''6:00''' Optional: [http://www.skisaltlake.com/murphys.htm Beer at Murphy's] (like last year)
| style="background:#ebeced; color:black"|
|}

Please note that there will be a Core 1&2 Site PI Retreat on the morning of Monday, January 7th. This is a closed session for Core 1&2 Site PIs, with no delegates. The topic is the competitive renewal.

== Dates. Venue. Registration ==

'''Dates:'''
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 10th'''.
* Project Activities will be held rest of the week between '''Monday, January 7th and Friday, January 11th'''.

'''Venue:''' The venue for the meeting is [http://www.marriott.com/hotels/travel/slccc-salt-lake-city-marriott-city-center/ Marriot City Center, Salt Lake City, Utah] Mariott City Center, Salt Lake City, Utah. [http://marriott.com/property/meetingsandevents/floorplans/slccc (Floorplan)]. To reserve rooms at the meeting rate of $129/night, please either call the hotel at 1-801-961-8700 or 1-866-961-8700 (toll free) and mention that you are attending the NAMIC meeting or book online by using the code SCISCIA. Please note that we do need attendees to use this hotel in order to not incur additional charges for the use of conference rooms.

<big> '''Registration:''' We are charging a registration fee to all participants. The fee covers the costs of the facilities and food provided. In order to keep the fee low, we need to get a sufficient number of hotel nights by our participants. See above for more on this. Please click [http://www.sci.utah.edu/namic2008/registration.html '''here'''] for online registration. This registration must be completed by Friday, December 14, 2007. </big>

== Attendees ==

Please note that unlike past events, registration will not be done on the wiki. Instead you need to follow [http://www.sci.utah.edu/namic2008/registration.html this registration link] to complete your online registration. The organizers will periodically publish the list of registered attendees in the space below. Attendees should '''NOT''' add their names in this section.

This is the list of attendees who have registered as of January 5, 2008

===AHM===
# Michael J. Ackerman, Ph.D. National Library of Medicine
# Everette Burdette Acoustic MedSystems, Inc.
# German Cavelier NIHNIMH
# Kevin Cleary Georgetown University collaborator
# Zohara Cohen National Institutes of Health
# Jack Collins SAIC-Frederick, Inc.
# Gabor Fichtinger Queens University
# Chris Johnson External Advisory Board EAB member
# Danial Lashkari MIT MIT
# Mikhail Milchenko Washington University at St Louis 2
# Sandy Napel Stanford EAB member
# Godfrey Pearlson Yale EAB member
# Fred Prior External Advisory Board EAB member
# Mike Sherman Stanford Invited Speaker
# Arthur Toga Laboratory of Neuro Imaging, UCLA
# Chris Wyatt Virginia Tech Collaborator
# Terry S. Yoo National Library of Medicine

===AHM and Project Event===
# Douglas Alan Harvard University IIC Collaborator
# Luca Antiga Mario Negri Institute
# Kevin Archie Washington University School of Medicine
# Nicole Aucoin Brigham and Women's Hospital 2
# Stephen Aylward Kitware, Inc.
# Serdar Balci MIT
# Sebastien Barre Kitware, Inc.
# Jack Blevins Acoustic MedSystems, Inc.
# Daniel Blezek Mayo Clinic External
# H Jeremy Bockholt The MIND Research Network MIND DBP2
# Sylvain Bouix Brigham and Womens Hospital Psychiatry Neuroimaging Lab Core 3
# Francois Budin Brigham and Womens Hospital
# Patrick Cheng Georgetown University collaborator
# Kiyoyuki Chinzei AIST, Japan
# Nikos Chrisochoides College of William and Mary
# Csaba Csoma Johns Hopkins University
# Brad Davis Kitware, Inc.
# Preston Tom Fletcher SCI Institute
# Andreas Freudling Brigham and Women's Hospital Leadership Core
# Yi Gao Georgia Tech
# Guido Gerig SCI Institute
# David Gobbi Queens University DBP2
# Polina Golland MIT Core 1
# Randy Gollub MGH Department of Psychiatry Core 5
# Casey Goodlett SCI Institute
# Alexandre Gouaillard Caltech
# Sylvain Gouttard SCI Institute
# Benjamin Grauer Brigham and Women's Hospital Leadership Core
# Jeffrey Grethe UCSD 2
# Nicole Grosland The University of Iowa, CCAD
# Nathan Hageman UCLA
# Michael Halle Brigham and Women's Hospital Leadership Core
# Nobuhiko Hata Brigham and Women's Hospital Leadership Core
# Nobuhiko Hata Brigham and Women's Hospital
# Kathryn Hayes Brigham and Womens Hospital 2 - Engineering
# Heather Cody Hazlett University of North Carolina DBP Core2
# Bill Hoffman Kitware, Inc.
# Jaesung Hong Kyushu University
# Luis Ibanez Kitware, Inc.
# Mustafa Okan Irfanoglu OSU
# Firdaus Janoos ohio-state univ
# Julien Jomier Kitware, Inc.
# Usman Khan Brigham and Womens Hospital
# Ron Kikinis Brigham and Womens Hospital Leadership Core
# Marek Kubicki Brigham and Womens Hospital
# Curtis Lisle KnowledgeVis, LLC 2
# Haiying Liu Brigham and Womens Hospital
# William Lorensen External Advisory Board EAB
# Raghu Machiraju The Ohio State University
# Vincent Magnotta The University of Iowa, CCAD
# Daniel Marcus Washington University Core 2
# Doug Markant Brigham and Women's Hospital Leadership Core
# Katie Mastrogiacomo SPL, Brigham and Women's Hospital Leadership Core
# Sean Megason Caltech
# John Melonakos Georgia Tech
# James V Miller GE Global Research
# Vandana Mohan Georgia Inst of Technology 1
# Kishore Mosaliganti The Ohio State University
# Tri Ngo MIT
# Ipek Oguz UNC 2
# Steve Pieper Isomics, Inc. 2, 6
# Carlo Pierpaoli NIH
# Wendy Plesniak Brigham and Women's Hospital Leadership Core
# Kilian Pohl Brigham and Women's Hospital 1
# Marcel Prastawa SCI Institute
# Sonia Pujol Brigham and Women's Hospital Leadership Core
# Katharina Quintus Brigham and Women's Hospital Leadership Core
# Yogesh Rathi Brigham and Womens Hospital
# Mert Sabuncu MIT
# Will Schroeder Kitware, Inc.
# Mark Scully The MIND Research Network
# Li Shen Indiana University
# Kiran Shivanna The University of Iowa, CCAD
# Martin Styner UNC Chapel Hill 1
# Padma Sundaram Brigham and Womens Hospital Brigham and Womens
# Xiaodong Tao GE
# Kinh Tieu Brigham and Women's Hospital
# Junichi Tokuda Brigham and Women's Hospital Leadership Core
# Clement Vachet UNC Chapel Hill 3
# Koen Van Leemput MIT
# Sandy Wells Brigham and Womens Hospital
# Carl-Fredrik Westin Brigham and Womens Hospital NAC
# Nathan Wilson Cardiovascular Simulation, Inc.
# Alexander Yarmarkovich Isomics, Inc. Engineering Core 2
# Anastasia Yendiki MGH
# Boon Thye Yeo MIT
# Tim Yin Stony Brook University

This is the list of attendees who have registered as of January 5, 2008. Please note that unlike past events, registration will not be done on the wiki. Instead you need to follow [http://www.sci.utah.edu/namic2008/registration.html this registration link] to complete your online registration. The organizers will periodically publish the list of registered attendees in the space above. Attendees should '''NOT''' add their names in this section.

2008 Winter Project Week Tractography

2008-01-09T20:48:08Z

Fletcher:

== Tractography Validation Beadeker ==

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

== Algorithm specific presentations ==

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

== Discussion, future planning ==

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

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

2007-12-09T23:12:36Z

Fletcher:

Projects:DTIProcessingTools

2007-12-09T23:08:27Z

Fletcher:

Projects:DTIVolumetricWhiteMatterConnectivity

2007-12-09T23:07:30Z

Fletcher:

Back to [[NA-MIC_Collaborations|NA-MIC_Collaborations]], [[Algorithm:Utah|Utah Algorithms]]

= DTI Volumetric White Matter Connectivity =

We have developed a PDE-based approach to white matter connectivity from DTI that is founded on the principal of minimal paths through the tensor volume. Our method computes a volumetric representation of a white matter tract given two endpoint regions. We have also developed statistical methods for quantifying the full tensor data along these pathways, which should be useful in clinical studies using DT-MRI. This work has been accepted to IPMI 2007.

{|
|[[Image:FiberTracts-top.jpg|thumb|256px|Five extracted fiber tracts (top view)]]
|[[Image:FiberTracts-angle.jpg|thumb|256px|Five extracted fiber tracts (side angle view)]]
|}

''Effecient GPU implementation:'' We have recently implemented a fast solver for the volumetric white matter connectivity using graphics hardware, i.e., the Graphics Processing Unit (GPU). This method takes advantage of the massively parallel nature of modern GPUs and runs 50-100 times faster than a standard implementation on the CPU. The fast solver allows interactive visualization of white matter pathways. We have developed a user interface in which a user can select two endpoint regions for the white matter tract of interest, which is typically computed and displayed within 1-3 seconds. This work has been submitted to VIS 2007.

{|
|[[Image:GPU-tract.jpg|thumb|320px|A screen shot from the interactive white matter connectivity solver. Shown are two selected endpoint regions and the resulting white matter pathway.]]
|}

= Key Investigators =
Tom Fletcher, Ran Tao, Won-Ki Jeong, Ross Whitaker

= Publications =

* PT Fletcher, R Tao, W-K Jeong, RT Whitaker, A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI, IPMI 2007, pp. 346-358.

[http://www.na-mic.org/Special:Publications?text=Projects%3ADTIVolumetricWhiteMatterConnectivity&submit=Search&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&sponsors=checked&searchbytag=checked| NA-MIC Publications Database]

2007-06-21T20:26:08Z

Fletcher:

File:Ptv.jpg

2007-06-21T20:25:23Z

Fletcher:

Projects/Diffusion/2007 Project Week DTI Registration

2007-06-21T20:12:41Z

Fletcher:

2007 Programming/Project Week MIT

2007-05-24T14:53:47Z

Fletcher: /* Attendee List */

Back to [[Engineering:Programming_Events|Programming/Project Events]]
[[Image:ProjectWeek-2007.png|thumb|450px|right|Summer 2007]]
== Logistics ==

'''Dates:''' June 25-29, 2007

'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

'''Registration Fee:''' $200 (this will cover the cost of breakfast and lunch for the week). Due by Tuesday, June 19, 2007. Please make checks out to "Massachusetts Institute of Technology" and mail to:
Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409b, Cambridge, MA 02139

If you are attending for one day only, the registration fee is not required.

'''Hotel:''' There is no official hotel for the meeting. Here is some information about 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.

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

===Introduction to NA-MIC Project Week===

This is a week of hands on activity -- programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC calendar. A full week of hands on activities is held in the summer at MIT (typically the last week of June), and for half a week in Salt Lake City in the winter (typically the second week of January).
The main goal of these events if to move forward the deliverables of NA-MIC. NA-MIC participants and their collaborators are welcome to attend.

* NA-MIC Members: Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
* This is not an introduction to the components of the NA-MIC Kit.
* NA-MIC Core 1 (Algorithms) - bring your algorithms and code to work on in the company of Core 2 engineers and Core 3 scientists.
* NA-MIC Core 2 (Engineering) - bring your code for infrastructure and applications to extend the NA-MIC Kit capabiliities, integrate Core 1 algorithms, and refine worflows for Core 3.
* NA-MIC Core 3 (DBP) - bring your data to work on with the NA-MIC Kit and get assistance and provide feedback to Core 1 scientists and Core 2 engineers.
* External Collaborators - if you are working on a project that uses the [[NA-MIC-Kit|NA-MIC kit]], and want to participate to get help from NA-MIC Engineering, please send an email to Tina Kapur (tkapur at bwh.harvard.edu). Please note that the event is open to people outside NA-MIC, subject to availability.
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.

=== Draft Agenda===
Please note that this agenda is a draft and will be finalized by June 15th.

* Monday June 25
** noon-1pm lunch
** 1-3:30pm Introduce Projects using templated wiki pages (all Project Leads)
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
** 9-945am: NA-MIC Software Process (Bill Hoffman - TBC)
** 10-10:30am Slicer 3.0 Update(Jim Miller, Steve Pieper)
** 11-12pm: [[Special topic breakout: IGT for Prostate]]
** noon lunch
** 1-2pm: [[Special topic breakout: KWWidgets]]
** 2-3pm: [[Special topic breakout: Non-Linear Registration]]
** 3-4pm: [[Special topic breakout: Atlases]]
** 4-5pm: [[Special topic breakout: DWI/DTI]]
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** noon lunch
** 1-2pm: Special topic breakout: [[NA-MIC:2007 Plan for Long-Lead Time Items| Plan for Long Lead Time Items]]
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** noon lunch
** 3:30-5pm Special topic breakout: TBD
** 5:30pm adjourn for day
* Friday June 29
** 8:30am breakfast
** 10am-noon: Project Progress using the templated wiki pages
** noon lunch boxes and adjourn

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_2007#2007-05-03|May 3, 2007: Kickoff TCON#1 to discuss Engr Core Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-10|May 10, 2007: TCON#2 to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-05-17|May 17, 2007: TCON#3 to discuss outstanding projects and teams from previous week]]
# May 17, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# May 31, 2007: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)
# By 3pm ET on June 21, 2007: Complete the templated wiki page for your project. THe final version of this template will be circulated by May 25th.
# [[Engineering:TCON_2007#2005-06-21|June 21, 2007: TCON#4 Final Call before showtime...]]
# 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...

== Projects ==

===DBP II===
These are projects by the new set of DBPS:
*[[DBP2:MIND | Longitudinal Classification of White Matter Lesions in Lupus]] (MIND/UNM)
*[[DBP2:JHU | Segmentation and Registration Tools for Robotic Prostate Interventions]] (JHU/Queen's)
*[[DBP2:UNC |Longitudinal MRI study of early brain development in neuropsychiatric disorder: UNC Autism Study]] (UNC)
*[[DBP2:Harvard|Velocardiofacial Syndrome (VCFS) as a genetic model for schizophrenia]] (Harvard)

===Structural Analysis===
*EMSegmentation Validation (Brad Davis, Sylvain Bouix)
*vtkITK wrapper for rule based segmentation (John Melonakos, Brad Davis, Marek Kubicki)
** Application of the Slicer2 module on DBP data
** Conversion to Slicer3

===Diffusion Image Analysis===
* [[Algorithm:UNC:DTI#Population_Analysis | DTI population analysis]] (Casey Goodlett)
* Slicer3 Whole brain Seeding platform: data representation and pipeline execution (Raul San Jose, Lauren O'Donnell, Alex Y.)
* Slicer3 Tractography editor (Lauren O'Donnell, Raul San Jose, Alex Y.)

===NA-MIC Kit===
* Slicer3
** [[2007_Project_Week_MIT_QDEC_Slicer3_Integration | QDEC integration into Slicer3]] (Nicole Aucoin BWH, Kevin Teich MGH, Nick Schmansky MGH, Doug Greve MGH, Gheorghe Postelnicu MGH, Steve Pieper Isomics)
** [[2007_Project_Week_MIT_Display_Optimization | Display Optimization]] (Raimundo Sierra, David Gobbi, Steve Pieper)
** [[2007_Project_Week_MIT_MRML_Scenes_for_the_Execution_Model]], including transforms (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
** Support for Unstructured Grids (Steve, Nicole, Alex, Curt)
** Python support in Slicer3 (Luca, Steve, Dan)
** CPack, Ctest infrastructure improvements (Andy, Katie, Steve)
** Drafting Human Interface and Slicer Style Guidelines (Wendy)
** Slicer Matlab Pipeline for scalars and tensors (Katharina, Sylvain, Steve)
* Slicer2

===External Collaborations===
* Meshing
** Adding VTK interactive wwidgets to Slicer3 (Will, Vince, Kiran, Curt)
** Migrate Iowa Neural Net code to pure ITK (Vince, Stephen)
*IGT
** [[Tracker Integration]] (Noby, Haiying, Katie Hayes BWH)
** [[Collaboration/MGH/Radiation Therapy Radiation Therapy Planning]] (Greg Sharp MGH, Tina Kapur BWH, Sandy Wells BWH, Steve Pieper Isomics, Katie Hayes BWH)
** [[Collaboration/JHU/Brachytherapy needle positioning robot integration|Brachytherapy needle positioning robot integration]] (Csaba Csoma, Peter Kazanzides JHU, David Gobbi Queen's, Katie Hayes BWH)
** [[Collaboration/BWH/RadVision and Tracker Integration|RadVision and Tracker Integration]] (Jack Blevins, Noby)
* Registration
** [[Collaboration/UIowa/Non_Rigid_Registration|Implementing Non-rigid Image Registration and Evaluation Project (NIREP) software using NA-MIC Kit]] (Gary Christensen UIowa, Stephen Aylward, Kitware, Sandy Wells BWH)
** [[Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit|Developing Electronic Atlas Software using NA-MIC Kit]] (Gary Christensen UIowa, Jeff Grethe)
** [[Collaboration/UIowa/Developing a GUI for non-rigid image registration programs using NA-MIC Kit|Developing a GUI for non-rigid image registration programs using NA-MIC Kit]] (Gary Christensen UIowa, Yumin Kitware)
* [[Collaboration/VMTK |vmtk (vmtk.sourceforge.net) integration within Slicer3]] (Luca Antiga, MNI, Dan Blezek(GE))
* [[Collaboration/NWU/Radiology Workstation| A Translation Station]](Skip, Alex, Vlad, Pat, Alex, Steve)
* [[Collaboration/WFU/NonHuman Primate Neuroimaging| Applying EMSegmenter to NonHuman Primate Neuroimaging]](Chris Wyatt VT, Kilian Pohl BWH)
* [[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure|3D+t Cells Lineage:GoFigure]] (Alex G, Yumin)

===Non-Medical Collaborations===
* AstroMed (Michael Halle, Douglas Alan)

==Attendee List==
#Kilian Pohl, BWH, Core 1
#John Melonakos, Georgia Tech, Core 1, (Hotel at MIT request)
#Tauseef Rehman, Georgia Tech, Core 1
#Casey Goodlett, UNC, Core 1, (Hotel at MIT request)
#W. Bryan Smith, UCSD/NCMIR, Core 2
#Jim Miller, GE Core 2, Booked at the Hotel At MIT
#Steve Pieper, Isomics, Core 2
#Katie Hayes, BWH, Core 2
#Dan Blezek, GE Core 2, Booked at the Hotel At MIT
#Tina Kapur, BWH, Core 6
#Ron Kikinis, Core 7, PI
#Peter Kazanzides, JHU, Collaborator
#Wendy Plesniak, BWH, Collaborator
#Luca Antiga, Mario Negri Institute, Collaborator
#Sylvain Bouix, BWH, Core 3
#Marek Kubicki, BWH, Core 3
#Chris Wyatt, Virginia Tech, Collaborator
#Nicole Aucoin, BWH, Core 2
#Will Schroeder, Kitware, Core 2
#Yumin Yuan, Kitware, Core 2
#Brad Davis, Kitware, Core 2
#Stephen Aylward, Kitware, Collaborator
#Luis Ibanez, Kitware, Core 2
#Bill Hoffman, Kitware, Core 2
#Raimundo Sierra, BWH, Core 2
#Clare Tempany, BWH Collaborator (Tuesday, June 26th only)
#Noby Hata, BWH Collaborator (Monday, June 25th only)
#Haiying Liu, BWH Collaborator
#Alex Yarmarkovich, Isomics, Core 2
#Vincent Magnotta, University of Iowa, Collaborator (Hotel at MIT request)
#Hans Johnson, University of Iowa, Collaborator
#Gary E. Christensen, University of Iowa, Collaborator
#Joo Hyun (Paul) Song, University of Iowa, Gary's student
#Xiujuan Geng, University of Iowa, Gary's student
#Jake Nickel, University of Iowa, Gary's student
#Nick Kiguta, University of Iowa, Gary's student
#Kunlin Cao, University of Iowa, Gary's student
#James Harris, University of Iowa, Gary's student
#Kai Ding, University of Iowa, Gary's student
#Jeff Hawley, University of Iowa, Gary's student
#Skip Talbot, Northwestern University, Collaborator (Hotel at MIT request)
#Alex Kogan, Northwestern University, Collaborator (Hotel at MIT request)
#Vladimir Kleper, Northwestern University, Collaborator (Hotel at MIT request)
#Pat Mongkolwat, Northwestern University, Collaborator (Hotel at MIT request)
#Csaba Csoma, Johns Hopkins University, Collaborator (Hotel at MIT request)
#David Gobbi, Queen's University, Collaborator (Hotel at MIT request)
#H. Jeremy Bockholt, The MIND Institute, DBP2:MIND PI
#Mark Scully, The MIND Institute, DBP2:MIND software engineer
#Sumner Williams, The MIND Institute, Magnotta/Johnson/Bockholt BRAINS grant software engineer
#Greg Sharp, MGH, Collaborator
#Lauren O'Donnell, BWH
#Raul San Jose, BWH
#Katharina Quintus, BWH, Core 3
#Marc Niethammer, BWH. Core 3
#Kevin Teich, MGH
#Michael Halle, BWH/IIC
#James Ross, GE
#Kiran Shivanna, University of Iowa, Collaborator (Hotel at MIT request)
#Douglas Alan, Harvard IIC
#Heather Cody Hazlett, UNC Core 3 (only part of week) (Hotel @ MIT request)
#Clement Vachet, UNC Core 3 (CS programmer) - full week (Hotel @ MIT request)
#Rachel G. Smith, UNC Core 3 (image lab manager) - tentative (may not be full week) (Hotel @ MIT request)
#Ran Tao, Utah, Core 1

Projects:FiberTractStatistics

2007-04-19T22:04:50Z

Fletcher:

'''Objective:''' We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.

'''Progress:''' Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.

''References:''
* Fletcher, P.T., Tao, R., Jeong, W.-K., Whitaker, R.T., "A Volumetric Approach to Quantifying Region-to-Region White Matter Connectivity in Diffusion Tensor MRI," to appear Information Processing in Medical Imaging (IPMI) 2007.
* Corouge, I., Fletcher, P.T., Joshi, S., Gilmore, J.H., and Gerig, G., "Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis," Medical Image Analysis 10 (2006), 786--798.
* Corouge, I., Fletcher, P.T., Joshi, S., Gilmore J.H., and Gerig, G., Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis, Lecture Notes in Computer Science LNCS, James S. Duncan and Guido Gerig, editors, Springer Verlag, Vol. 3749, Oct. 2005, pp. 131 -- 138
* C. Goodlett, I. Corouge, M. Jomier, and G. Gerig, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .

'''Key Investigators:'''

* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
* Utah: Tom Fletcher, Ross Whitaker

'''Links:'''

* [[Progress_Report:Diffusion_Tensor_Statistics|Diffusion Tensor Statistics Progress Report]]

{|
|[[Image:genuFAp.jpg|thumb|320px|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.]]
|[[Image:genuFA.jpg|thumb|320px|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.]]
|}

File:GenuFA.jpg

2007-04-19T22:04:12Z

Fletcher:

File:GenuFAp.jpg

2007-04-19T22:03:54Z

Fletcher:

Projects:FiberTractStatistics

2007-04-19T21:54:29Z

Fletcher:

Projects:AutomatedShapeModelConstruction

2007-04-19T21:51:32Z

Fletcher:

Back to [[NA-MIC_Collaborations|NA-MIC_Collaborations]]

'''Objective:''' We are developing a new method for automatically constructing shape models, including defining boundary correspondences on shapes in a population. This method can be directly applied to segmentations of brain structures from structural MRI.

'''Progress:''' We have implemented a software tool to automatically construct shape models from an input of several binary segmentations. This method finds boundary correspondences by creating the most efficient probability distribution for the population of input shapes. The shape models output by our method can then be used to compare differences in brain structure shape between healthy controls and patients with neuropsychiatric disorders. We are investigating the power of this method in statistical group comparisons.

This method is currently being applied to studying shape changes in the hippocampus and caudate between normal and schizophrenic groups in collaboration with Harvard. We have also extended the method from single figure anatomical objects to a formulation of the multi-object correspondence optimization, and have applied it to a proof-of-concept application to the analysis of brain structure complexes from a longitudinal study of pediatric autism that is underway at UNC Chapel Hill.

''References:''
* J. Cates, P.T. Fletcher, M. Styner, M. Shenton, R. Whitaker. Shape Modeling and Analysis with Entropy-Based Particle Systems. IPMI 2007, accepted.
* J. Cates, P.T. Fletcher, R. Whitaker. Entropy-Based Particle Systems for Shape Corresopndence. Mathematical Foundations of Computational Anatomy Workshop, MICCAI 2006. pp. 90-99 Oct 2006.

'''Key Investigators:'''

* Utah: Joshua Cates, Miriah Meyer, Tom Fletcher, Ross Whitaker
* Harvard PNL: Sylvain Bouix, Marc Niethammer, Doug Markant, Adam Cohen, Mark Dreusicke, Jim Levitt, Martha Shenton
* UNC: Martin Styner, Heather Cody Hazlett, Joe Piven

'''Links:'''

[[Algorithm:Utah|Utah Algorithms Page]]

{|
|[[Image:Lcomb-grayscale.png|thumbnail|Figure 1]]
|[[Image:Rcomb-grayscale.png|thumbnail|Figure 2]]
|[[Image:meanviews.png|thumbnail|Figure 3]]
|}
Figure 1,2 illustrates results of hypothesis testing for group differences from the control population for the left/right hippocampus and the left/right caudate. Raw and FDR-corrected p-values are given. Areas of significant group differences ($p <= 0.05$) are shown as dark regions. Areas with insignificant group differences ($p > 0.05$) are shown as light regions. Our results correlate with with other published hypothesis testing results on this data.

Figure 3 shows the raw p-values from hypothesis testing for group differences as color-maps on mean shapes of the autism group (top row) and the normal control group (bottom row).