NAMIC Wiki - User contributions [en]

File:Utah1-AHM2014.pptx

2014-01-09T14:31:53Z

Whitaker: uploaded a new version of "File:Utah1-AHM2014.pptx"

AHM 2014 alg core presentations

2014-01-09T06:05:04Z

Whitaker: /* Alg core presentations */

== Alg core presentations ==

* [[media:Utah1-AHM2014.pptx‎ | Utah 1, Ross Whitaker ]]
* [[media:NAMIC-AHM-MIT-2014.pptx | MIT, Polina Golland]]
* Utah 2, Guido Gerig
* [[media:UNC_AHM2014.pptx‎ | UNC, Martin Styner ]]
* Stony Brook, Allen Tannenbaum

File:Utah1-AHM2014.pptx

2014-01-09T05:50:14Z

Whitaker:

AHM 2014 alg core presentations

2014-01-09T05:47:56Z

Whitaker: /* Alg core presentations */

== Alg core presentations ==

* * [[media:Utah1_AHM2014.pptx‎ | Utah 1, Ross Whitaker ]]
* [[media:NAMIC-AHM-MIT-2014.pptx | MIT, Polina Golland]]
* Utah 2, Guido Gerig
* [[media:UNC_AHM2014.pptx‎ | UNC, Martin Styner ]]
* Stony Brook, Allen Tannenbaum

AHM 2014

2014-01-02T19:50:53Z

Whitaker: /* Agenda */

Back to [[Events]]
[[image:PW-SLC2014.png|300px]]

Dates: January 6-10, 2014.

Location: Salt Lake City, UT.

== Introduction ==
{| border="00" cellpadding="8" cellspacing="0"
|-
| rowspan="2" align="left" | '''This is the home page for the 2014 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 2014 project week, see below.

For information about Utah as a travel destination click [http://www.utah.com '''here'''].
| style="background: #ebeced" align="center"| [[Image:SLC.jpg|center|350px|View of the City]]
|-
| style="background: #ebeced"|The 2014 AHM, EAB and Project Week will be held '''January 6-10, 2014''', in '''Salt Lake City''', Utah.
|}
== Dates, Venue, Registration ==
{|
|align="left" style="width:60%"|
'''Dates:'''
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 9th'''.
* Project Activities will be held rest of the week between '''Monday, January 6th and Friday, January 10th'''.

'''Registration:''' Please click [http://www.sci.utah.edu/namic2014.html '''here'''] to register online before '''January 2'''. All participants must pay a registration fee ('''$250''' for AHM only, and '''$550''' for AHM+Project Week), which covers our catering and facilities costs.
After December 25 registration prices will increase by $100. Last call registrations after January 1st will be increased by $200.

'''Venue:''' The venue for the meeting is the Marriott City Center, Salt Lake City, Utah. The room rate for the meeting is 149 USD per night, and the code is "NA-MIC 2014 Conference." You can book online, by clicking [http://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=NA-MIC%202014%20Conference^SLCCC%60NACNACA%60149%60USD%60false%601/5/14%601/10/14%6012/06/13&app=resvlink&stop_mobi=yes here.] PLEASE NOTE THAT THE DEADLINE FOR BOOKING ROOMS AT THESE RATES IS DECEMBER 13th.

== Agenda==
{| border="1" cellpadding="5"
|- style="background:#eeeeee; font-size:125%; color:#0063B6" align="center"
| style="width:5%"| '''Time'''
| style="width:15%" | '''Monday, January 6'''
| style="width:15%" | '''Tuesday, January 7'''
| style="width:15%" | '''Wednesday, January 8'''
| style="width:35%" | '''Thursday, January 9 '''
| style="width:15%" | '''Friday, January 10'''
|-
| style="background:#eeeeee; color:black"|
| style="background:#ffffff; color:#522200"| '''[[2014_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2014_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2014_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#F2E5D3; color:#522200"| '''AHM and [http://wiki.na-mic.org/Wiki/index.php/2014_EAB EAB]''' ''(Olympus B)'' [[2014_Winter_Project_Week|Project Activities]] ''(Amethyst 1 & 2)''
| style="background:#dbf3ff; color:#522200"|'''[[2014_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#F2E5D3; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
| 
|9-10am: [[2014 Winter Project Week DICOM Breakout|Breakout Session:DICOM]] (Steve Pieper) ''(Amethyst 1)'' 
|9-10am: [[2014 Winter Project Week QIICR Breakout|Breakout Session:QIICR]] (Andrey Fedorov) ''(Amethyst 1)'' 
| '''8-8:05am:''' Welcome (Ron Kikinis) 
'''8:05-8:15am:''' [[2014 How about the Future|How about the future?]] (Ron Kikinis) 
'''8:15-9:15am:''' [[AHM_2014_alg_core_presentations | Algorithms Core: Update and Future Plans]] '''9:20-9:55am:''' Invited Speaker: Prof. Wiro Niessen, Erasmus MC. "Quantitative Imaging Biomarkers and Imaging Genetics in Neurodegenerative Disease" 
| style="background:#dbf3ff; color:#522200"|[[2014_Winter_Project_Week|9am: Project Presentations]] ''(Olympus B)''
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#F2E5D3; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
|
| Algorithms PI meeting ''(Olympus A)''
| [[2014 Winter Project Week DTI Tools Breakout|Breakout Session: DTI Tools]] (Martin Styner) ''(Amethyst 2)'' 
| DBP Update and Future Plans '''10:30-10:55am:''' TBI (Jack Van Horn, [[Media:NAMIC_AHM_2014_van_horn.pdf‎|Slides]]) '''10:55-11:20am:''' Huntington's Disease (Hans Johnson, [[Media:20140110_IowaDBPProgress.pdf|Slides]]) '''11:20-11:45am:''' Head and Neck Cancer (Greg Sharp, [[Media:NAMIC-AHM-2014-01-Sharp.pdf|Slides]]) '''11:45-12:10pm:''' Atrial Fibrillation (Rob MacLeod, [[Media:DBP-AF-AHM2014.pdf|Slides]]) '''
|
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)'' 
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)'' 
| style="background:#F2E5D3; color:black"| Lunch ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn ''(Olympus A)''
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''l
| style="background:#dbf3ff; color:#522200"|[[2014_Winter_Project_Week|Project Presentations]] ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"|[[2014_SLC_Training_Workshop|Slicer Training Workshop (Sonia Pujol)]] ''(Amethyst 1)'' 
|'''DBP Team Meetings''' ''(Amethyst 1)'' '''1-2pm:''' [[DBP MGH Head and Neck Cancer 2014]] '''2-3pm:''' [[DBP Utah Atrial Fibrillation 2014]]
|
'''1:15-1:30pm:''' Collaboration R01: Quantification Of 3d Bony Changes In Temporomandibular Joint Osteoarthritis (Lucia Cevidanes, University of Michigan) 
'''1:30-2:15pm:''' [[AHM2014-Engineering_Updates | Engineering Core: Updates and Future Plans]] '''2:15-2:45pm:''' [[Media:AHM2014_TrainingCore_SoniaPujol.pdf | Outreach ]] (Sonia Pujol, Steve Pieper) 
|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#F2E5D3; color:black"| Coffee ''(General area)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''3:00-5:00'''
|
|3:15-4pm: Breakout Session: [[AHM2014-SubjectHierarchy|Subject Hierarchy]] ''(Amethyst 2)'' 4:15-5pm: [[AHM2014-Simple-ITK|SimpleITK Breakout Session]] ''(Amethyst 1)''
|'''DBP Team Meetings''' ''(Amethyst 1)'' '''3-4pm:''' [[DBP UCLA Traumatic Brain Injury 2014]] '''4-5pm:''' [[DBP Iowa Huntington's Disease 2014]]
|'''3-4pm''': [[2014_EAB|EAB meeting]] (Core, Site, and DBP PIs to join) ''(Olympus B)'' '''4-5pm:''' EAB closed session ''(Olympus B)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''05:00-07:00'''
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#F2E5D3; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)
| style="background:#ffffff; color:black"|
|}

[http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Floorplan]

'''General Announcements:'''

**Will be added here

*Murphy's Reception is all set for Thursday, January 9th. The price per person is the same as last year $35. Please see Donna at the registration table to pre-pay for dinner.

==Registered Attendees==

<big>'''NOTE:'''</big> The registered attendee list will be posted here by the organizers. '''DO NOT''' add your name to this list yourself. To register, please click [http://www.sci.utah.edu/namic2014-registration.html here].

# Ackerman , Michael , National Library of Medicine
# Aucoin , Nicole , BWH
# Aylward , Stephen , Kitware
# Bengali , Salma , SCI Institute
# Binder , Polina , MIT
# Boen , Vinicius , The University of Michigan
# Bronson , Jonathan , SCI Institute
# Budin , Francois , UNC
# Cates , Joshua , SCI Institute
# Cevidanes , Lucia , The University of Michigan
# Clogenson , Marine , EPFL
# COOK , JAMES , Duke University
# Diedrich , Karl , AZE Technology, Inc.
# Evans , John , MGH
# Fedorov , Andriy ,
# Fillion-Robin , Jean-Christophe , Kitware
# Fishbaugh , James , SCI Institute
# Gao , Yi , UAB
# Girault , Alexis , University of North Carolina at Chapel Hill
# Golland , Polina , MIT CSAIL
# Harmouche , Rola , Brigham and Womens Hospital
# Jain , Saurabh , Johns Hopkins University
# Johnson , Chris , EAB Chair
# Johnson , Hans , University of Iowa
# Kalpathy-Cramer , Jayashree , MGH
# Kikinis , Ron , SPL, BWH, Harvard
# Kim , Eun Young , University of Iowa
# King , Franklin , Queens University
# Kochis , Donna , Kitware
# Kolesov , Ivan , Stony Brook University
# Lasso , Andras , Queens University
# Lorensen , William , William Lorensen
# Lowekamp , Bradley ,
# MacLeod , Rob , SCI Institute
# McCormick , Matthew , Kitware, Inc
# Alireza , Mehrtash BWH
# Miller , James , GE Research
# Nardelli , Pietro , Brigham and Womens Hospital
# Pace , Danielle , MIT
# Pieper , Steve , Steve Pieper
# Pinter , Csaba , Queens University
# Prastawa , Marcel , General Electric
# Pujol , Sonia , Sonia Pujol
# Ross , James , Brigham and Womens Hospital
# San Jose , Raul , Brigham and Womens Hospital
# Savadjiev , Peter , Brigham and Womens Hospital
# Sharma , Anuja , SCI Institute
# Sharp , Gregory , MGH
# Shusharina , Nadya , Massachusetts General Hospital
# Sridharan , Ramesh , MIT
# Styner , Martin , University of North Carolina
# Tannenbaum , Allen , Stony Brook University
# Toews , Matthew , BWH, Harvard Medical School
# Tokuda , Junichi ,
# Ulrich , Ethan , University of Iowa
# Vast , Erwin ,
# Wang , Bo , SCI Institute
# Wang , Kevin , Princess Margaret Cancer Centre
# Welch , David , University of Iowa
# Whitaker , Ross , SCI Institute
# Yamada , Atsushi , Shiga University of Medical Science
# Yarmarkovich , Alexander , Isomics
# Yoo , Terry , National Library of Medicine
# Zhu , Liangjia , Stony Brook University

AHM 2014

2014-01-02T19:49:56Z

Whitaker: /* Agenda */

Back to [[Events]]
[[image:PW-SLC2014.png|300px]]

Dates: January 6-10, 2014.

Location: Salt Lake City, UT.

== Introduction ==
{| border="00" cellpadding="8" cellspacing="0"
|-
| rowspan="2" align="left" | '''This is the home page for the 2014 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 2014 project week, see below.

For information about Utah as a travel destination click [http://www.utah.com '''here'''].
| style="background: #ebeced" align="center"| [[Image:SLC.jpg|center|350px|View of the City]]
|-
| style="background: #ebeced"|The 2014 AHM, EAB and Project Week will be held '''January 6-10, 2014''', in '''Salt Lake City''', Utah.
|}
== Dates, Venue, Registration ==
{|
|align="left" style="width:60%"|
'''Dates:'''
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 9th'''.
* Project Activities will be held rest of the week between '''Monday, January 6th and Friday, January 10th'''.

'''Registration:''' Please click [http://www.sci.utah.edu/namic2014.html '''here'''] to register online before '''January 2'''. All participants must pay a registration fee ('''$250''' for AHM only, and '''$550''' for AHM+Project Week), which covers our catering and facilities costs.
After December 25 registration prices will increase by $100. Last call registrations after January 1st will be increased by $200.

'''Venue:''' The venue for the meeting is the Marriott City Center, Salt Lake City, Utah. The room rate for the meeting is 149 USD per night, and the code is "NA-MIC 2014 Conference." You can book online, by clicking [http://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=NA-MIC%202014%20Conference^SLCCC%60NACNACA%60149%60USD%60false%601/5/14%601/10/14%6012/06/13&app=resvlink&stop_mobi=yes here.] PLEASE NOTE THAT THE DEADLINE FOR BOOKING ROOMS AT THESE RATES IS DECEMBER 13th.

== Agenda==
{| border="1" cellpadding="5"
|- style="background:#eeeeee; font-size:125%; color:#0063B6" align="center"
| style="width:5%"| '''Time'''
| style="width:15%" | '''Monday, January 6'''
| style="width:15%" | '''Tuesday, January 7'''
| style="width:15%" | '''Wednesday, January 8'''
| style="width:35%" | '''Thursday, January 9 '''
| style="width:15%" | '''Friday, January 10'''
|-
| style="background:#eeeeee; color:black"|
| style="background:#ffffff; color:#522200"| '''[[2014_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2014_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2014_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#F2E5D3; color:#522200"| '''AHM and [http://wiki.na-mic.org/Wiki/index.php/2014_EAB EAB]''' ''(Olympus B)'' [[2014_Winter_Project_Week|Project Activities]] ''(Amethyst 1 & 2)''
| style="background:#dbf3ff; color:#522200"|'''[[2014_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#F2E5D3; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
| 
|9-10am: [[2014 Winter Project Week DICOM Breakout|Breakout Session:DICOM]] (Steve Pieper) ''(Amethyst 1)'' 
|9-10am: [[2014 Winter Project Week QIICR Breakout|Breakout Session:QIICR]] (Andrey Fedorov) ''(Amethyst 1)'' 
| '''8-8:05am:''' Welcome (Ron Kikinis) 
'''8:05-8:15am:''' [[2014 How about the Future|How about the future?]] (Ron Kikinis) 
'''8:15-9:15am:''' [[AHM_2014_alg_core_presentations | Algorithms Core: Update and Future Plans]] '''9:20-9:55am:''' Invited Speaker: Prof. Wiro Niessen, Erasmus MC. "Quantitative Imaging Biomarkers and Imaging Genetics in Neurodegenerative Disease" 
| style="background:#dbf3ff; color:#522200"|[[2014_Winter_Project_Week|9am: Project Presentations]] ''(Olympus B)''
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#F2E5D3; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
|
| Algorithms PI meeting ''(Amethyst 1)'' 
| [[2014 Winter Project Week DTI Tools Breakout|Breakout Session: DTI Tools]] (Martin Styner) ''(Amethyst 2)'' 
| DBP Update and Future Plans '''10:30-10:55am:''' TBI (Jack Van Horn, [[Media:NAMIC_AHM_2014_van_horn.pdf‎|Slides]]) '''10:55-11:20am:''' Huntington's Disease (Hans Johnson, [[Media:20140110_IowaDBPProgress.pdf|Slides]]) '''11:20-11:45am:''' Head and Neck Cancer (Greg Sharp, [[Media:NAMIC-AHM-2014-01-Sharp.pdf|Slides]]) '''11:45-12:10pm:''' Atrial Fibrillation (Rob MacLeod, [[Media:DBP-AF-AHM2014.pdf|Slides]]) '''
|
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)'' 
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)'' 
| style="background:#F2E5D3; color:black"| Lunch ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn ''(Olympus A)''
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''l
| style="background:#dbf3ff; color:#522200"|[[2014_Winter_Project_Week|Project Presentations]] ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"|[[2014_SLC_Training_Workshop|Slicer Training Workshop (Sonia Pujol)]] ''(Amethyst 1)'' 
|'''DBP Team Meetings''' ''(Amethyst 1)'' '''1-2pm:''' [[DBP MGH Head and Neck Cancer 2014]] '''2-3pm:''' [[DBP Utah Atrial Fibrillation 2014]]
|
'''1:15-1:30pm:''' Collaboration R01: Quantification Of 3d Bony Changes In Temporomandibular Joint Osteoarthritis (Lucia Cevidanes, University of Michigan) 
'''1:30-2:15pm:''' [[AHM2014-Engineering_Updates | Engineering Core: Updates and Future Plans]] '''2:15-2:45pm:''' [[Media:AHM2014_TrainingCore_SoniaPujol.pdf | Outreach ]] (Sonia Pujol, Steve Pieper) 
|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#F2E5D3; color:black"| Coffee ''(General area)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''3:00-5:00'''
|
|3:15-4pm: Breakout Session: [[AHM2014-SubjectHierarchy|Subject Hierarchy]] ''(Amethyst 2)'' 4:15-5pm: [[AHM2014-Simple-ITK|SimpleITK Breakout Session]] ''(Amethyst 1)''
|'''DBP Team Meetings''' ''(Amethyst 1)'' '''3-4pm:''' [[DBP UCLA Traumatic Brain Injury 2014]] '''4-5pm:''' [[DBP Iowa Huntington's Disease 2014]]
|'''3-4pm''': [[2014_EAB|EAB meeting]] (Core, Site, and DBP PIs to join) ''(Olympus B)'' '''4-5pm:''' EAB closed session ''(Olympus B)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''05:00-07:00'''
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#F2E5D3; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)
| style="background:#ffffff; color:black"|
|}

[http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Floorplan]

'''General Announcements:'''

**Will be added here

*Murphy's Reception is all set for Thursday, January 9th. The price per person is the same as last year $35. Please see Donna at the registration table to pre-pay for dinner.

==Registered Attendees==

<big>'''NOTE:'''</big> The registered attendee list will be posted here by the organizers. '''DO NOT''' add your name to this list yourself. To register, please click [http://www.sci.utah.edu/namic2014-registration.html here].

# Ackerman , Michael , National Library of Medicine
# Aucoin , Nicole , BWH
# Aylward , Stephen , Kitware
# Bengali , Salma , SCI Institute
# Binder , Polina , MIT
# Boen , Vinicius , The University of Michigan
# Bronson , Jonathan , SCI Institute
# Budin , Francois , UNC
# Cates , Joshua , SCI Institute
# Cevidanes , Lucia , The University of Michigan
# Clogenson , Marine , EPFL
# COOK , JAMES , Duke University
# Diedrich , Karl , AZE Technology, Inc.
# Evans , John , MGH
# Fedorov , Andriy ,
# Fillion-Robin , Jean-Christophe , Kitware
# Fishbaugh , James , SCI Institute
# Gao , Yi , UAB
# Girault , Alexis , University of North Carolina at Chapel Hill
# Golland , Polina , MIT CSAIL
# Harmouche , Rola , Brigham and Womens Hospital
# Jain , Saurabh , Johns Hopkins University
# Johnson , Chris , EAB Chair
# Johnson , Hans , University of Iowa
# Kalpathy-Cramer , Jayashree , MGH
# Kikinis , Ron , SPL, BWH, Harvard
# Kim , Eun Young , University of Iowa
# King , Franklin , Queens University
# Kochis , Donna , Kitware
# Kolesov , Ivan , Stony Brook University
# Lasso , Andras , Queens University
# Lorensen , William , William Lorensen
# Lowekamp , Bradley ,
# MacLeod , Rob , SCI Institute
# McCormick , Matthew , Kitware, Inc
# Alireza , Mehrtash BWH
# Miller , James , GE Research
# Nardelli , Pietro , Brigham and Womens Hospital
# Pace , Danielle , MIT
# Pieper , Steve , Steve Pieper
# Pinter , Csaba , Queens University
# Prastawa , Marcel , General Electric
# Pujol , Sonia , Sonia Pujol
# Ross , James , Brigham and Womens Hospital
# San Jose , Raul , Brigham and Womens Hospital
# Savadjiev , Peter , Brigham and Womens Hospital
# Sharma , Anuja , SCI Institute
# Sharp , Gregory , MGH
# Shusharina , Nadya , Massachusetts General Hospital
# Sridharan , Ramesh , MIT
# Styner , Martin , University of North Carolina
# Tannenbaum , Allen , Stony Brook University
# Toews , Matthew , BWH, Harvard Medical School
# Tokuda , Junichi ,
# Ulrich , Ethan , University of Iowa
# Vast , Erwin ,
# Wang , Bo , SCI Institute
# Wang , Kevin , Princess Margaret Cancer Centre
# Welch , David , University of Iowa
# Whitaker , Ross , SCI Institute
# Yamada , Atsushi , Shiga University of Medical Science
# Yarmarkovich , Alexander , Isomics
# Yoo , Terry , National Library of Medicine
# Zhu , Liangjia , Stony Brook University

AHM 2014

2014-01-02T19:47:31Z

Whitaker: /* Agenda */

Back to [[Events]]
[[image:PW-SLC2014.png|300px]]

Dates: January 6-10, 2014.

Location: Salt Lake City, UT.

== Introduction ==
{| border="00" cellpadding="8" cellspacing="0"
|-
| rowspan="2" align="left" | '''This is the home page for the 2014 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 2014 project week, see below.

For information about Utah as a travel destination click [http://www.utah.com '''here'''].
| style="background: #ebeced" align="center"| [[Image:SLC.jpg|center|350px|View of the City]]
|-
| style="background: #ebeced"|The 2014 AHM, EAB and Project Week will be held '''January 6-10, 2014''', in '''Salt Lake City''', Utah.
|}
== Dates, Venue, Registration ==
{|
|align="left" style="width:60%"|
'''Dates:'''
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 9th'''.
* Project Activities will be held rest of the week between '''Monday, January 6th and Friday, January 10th'''.

'''Registration:''' Please click [http://www.sci.utah.edu/namic2014.html '''here'''] to register online before '''January 2'''. All participants must pay a registration fee ('''$250''' for AHM only, and '''$550''' for AHM+Project Week), which covers our catering and facilities costs.
After December 25 registration prices will increase by $100. Last call registrations after January 1st will be increased by $200.

'''Venue:''' The venue for the meeting is the Marriott City Center, Salt Lake City, Utah. The room rate for the meeting is 149 USD per night, and the code is "NA-MIC 2014 Conference." You can book online, by clicking [http://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=NA-MIC%202014%20Conference^SLCCC%60NACNACA%60149%60USD%60false%601/5/14%601/10/14%6012/06/13&app=resvlink&stop_mobi=yes here.] PLEASE NOTE THAT THE DEADLINE FOR BOOKING ROOMS AT THESE RATES IS DECEMBER 13th.

== Agenda==
{| border="1" cellpadding="5"
|- style="background:#eeeeee; font-size:125%; color:#0063B6" align="center"
| style="width:5%"| '''Time'''
| style="width:15%" | '''Monday, January 6'''
| style="width:15%" | '''Tuesday, January 7'''
| style="width:15%" | '''Wednesday, January 8'''
| style="width:35%" | '''Thursday, January 9 '''
| style="width:15%" | '''Friday, January 10'''
|-
| style="background:#eeeeee; color:black"|
| style="background:#ffffff; color:#522200"| '''[[2014_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2014_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"| '''[[2014_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
| style="background:#F2E5D3; color:#522200"| '''AHM and [http://wiki.na-mic.org/Wiki/index.php/2014_EAB EAB]''' ''(Olympus B)'' [[2014_Winter_Project_Week|Project Activities]] ''(Amethyst 1 & 2)''
| style="background:#dbf3ff; color:#522200"|'''[[2014_Winter_Project_Week|Project Activities]] ''' ''(Olympus B)''
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#F2E5D3; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
| 
|9-10am: [[2014 Winter Project Week DICOM Breakout|Breakout Session:DICOM]] (Steve Pieper) ''(Amethyst 1)'' 
|9-10am: [[2014 Winter Project Week QIICR Breakout|Breakout Session:QIICR]] (Andrey Fedorov) ''(Amethyst 1)'' 
| '''8-8:05am:''' Welcome (Ron Kikinis) 
'''8:05-8:15am:''' [[2014 How about the Future|How about the future?]] (Ron Kikinis) 
'''8:15-9:15am:''' [[AHM_2014_alg_core_presentations | Algorithms Core: Update and Future Plans]] '''9:20-9:55am:''' Invited Speaker: Prof. Wiro Niessen, Erasmus MC. "Quantitative Imaging Biomarkers and Imaging Genetics in Neurodegenerative Disease" 
| style="background:#dbf3ff; color:#522200"|[[2014_Winter_Project_Week|9am: Project Presentations]] ''(Olympus B)''
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#F2E5D3; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
|
| Algorithms PI meeting
| [[2014 Winter Project Week DTI Tools Breakout|Breakout Session: DTI Tools]] (Martin Styner) ''(Amethyst 2)'' 
| DBP Update and Future Plans '''10:30-10:55am:''' TBI (Jack Van Horn, [[Media:NAMIC_AHM_2014_van_horn.pdf‎|Slides]]) '''10:55-11:20am:''' Huntington's Disease (Hans Johnson, [[Media:20140110_IowaDBPProgress.pdf|Slides]]) '''11:20-11:45am:''' Head and Neck Cancer (Greg Sharp, [[Media:NAMIC-AHM-2014-01-Sharp.pdf|Slides]]) '''11:45-12:10pm:''' Atrial Fibrillation (Rob MacLeod, [[Media:DBP-AF-AHM2014.pdf|Slides]]) '''
|
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)'' 
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)'' 
| style="background:#F2E5D3; color:black"| Lunch ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn ''(Olympus A)''
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''l
| style="background:#dbf3ff; color:#522200"|[[2014_Winter_Project_Week|Project Presentations]] ''(Olympus B)''
| style="background:#dbf3ff; color:#522200"|[[2014_SLC_Training_Workshop|Slicer Training Workshop (Sonia Pujol)]] ''(Amethyst 1)'' 
|'''DBP Team Meetings''' ''(Amethyst 1)'' '''1-2pm:''' [[DBP MGH Head and Neck Cancer 2014]] '''2-3pm:''' [[DBP Utah Atrial Fibrillation 2014]]
|
'''1:15-1:30pm:''' Collaboration R01: Quantification Of 3d Bony Changes In Temporomandibular Joint Osteoarthritis (Lucia Cevidanes, University of Michigan) 
'''1:30-2:15pm:''' [[AHM2014-Engineering_Updates | Engineering Core: Updates and Future Plans]] '''2:15-2:45pm:''' [[Media:AHM2014_TrainingCore_SoniaPujol.pdf | Outreach ]] (Sonia Pujol, Steve Pieper) 
|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#F2E5D3; color:black"| Coffee ''(General area)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''3:00-5:00'''
|
|3:15-4pm: Breakout Session: [[AHM2014-SubjectHierarchy|Subject Hierarchy]] ''(Amethyst 2)'' 4:15-5pm: [[AHM2014-Simple-ITK|SimpleITK Breakout Session]] ''(Amethyst 1)''
|'''DBP Team Meetings''' ''(Amethyst 1)'' '''3-4pm:''' [[DBP UCLA Traumatic Brain Injury 2014]] '''4-5pm:''' [[DBP Iowa Huntington's Disease 2014]]
|'''3-4pm''': [[2014_EAB|EAB meeting]] (Core, Site, and DBP PIs to join) ''(Olympus B)'' '''4-5pm:''' EAB closed session ''(Olympus B)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''05:00-07:00'''
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#F2E5D3; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)
| style="background:#ffffff; color:black"|
|}

[http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ Floorplan]

'''General Announcements:'''

**Will be added here

*Murphy's Reception is all set for Thursday, January 9th. The price per person is the same as last year $35. Please see Donna at the registration table to pre-pay for dinner.

==Registered Attendees==

<big>'''NOTE:'''</big> The registered attendee list will be posted here by the organizers. '''DO NOT''' add your name to this list yourself. To register, please click [http://www.sci.utah.edu/namic2014-registration.html here].

# Ackerman , Michael , National Library of Medicine
# Aucoin , Nicole , BWH
# Aylward , Stephen , Kitware
# Bengali , Salma , SCI Institute
# Binder , Polina , MIT
# Boen , Vinicius , The University of Michigan
# Bronson , Jonathan , SCI Institute
# Budin , Francois , UNC
# Cates , Joshua , SCI Institute
# Cevidanes , Lucia , The University of Michigan
# Clogenson , Marine , EPFL
# COOK , JAMES , Duke University
# Diedrich , Karl , AZE Technology, Inc.
# Evans , John , MGH
# Fedorov , Andriy ,
# Fillion-Robin , Jean-Christophe , Kitware
# Fishbaugh , James , SCI Institute
# Gao , Yi , UAB
# Girault , Alexis , University of North Carolina at Chapel Hill
# Golland , Polina , MIT CSAIL
# Harmouche , Rola , Brigham and Womens Hospital
# Jain , Saurabh , Johns Hopkins University
# Johnson , Chris , EAB Chair
# Johnson , Hans , University of Iowa
# Kalpathy-Cramer , Jayashree , MGH
# Kikinis , Ron , SPL, BWH, Harvard
# Kim , Eun Young , University of Iowa
# King , Franklin , Queens University
# Kochis , Donna , Kitware
# Kolesov , Ivan , Stony Brook University
# Lasso , Andras , Queens University
# Lorensen , William , William Lorensen
# Lowekamp , Bradley ,
# MacLeod , Rob , SCI Institute
# McCormick , Matthew , Kitware, Inc
# Alireza , Mehrtash BWH
# Miller , James , GE Research
# Nardelli , Pietro , Brigham and Womens Hospital
# Pace , Danielle , MIT
# Pieper , Steve , Steve Pieper
# Pinter , Csaba , Queens University
# Prastawa , Marcel , General Electric
# Pujol , Sonia , Sonia Pujol
# Ross , James , Brigham and Womens Hospital
# San Jose , Raul , Brigham and Womens Hospital
# Savadjiev , Peter , Brigham and Womens Hospital
# Sharma , Anuja , SCI Institute
# Sharp , Gregory , MGH
# Shusharina , Nadya , Massachusetts General Hospital
# Sridharan , Ramesh , MIT
# Styner , Martin , University of North Carolina
# Tannenbaum , Allen , Stony Brook University
# Toews , Matthew , BWH, Harvard Medical School
# Tokuda , Junichi ,
# Ulrich , Ethan , University of Iowa
# Vast , Erwin ,
# Wang , Bo , SCI Institute
# Wang , Kevin , Princess Margaret Cancer Centre
# Welch , David , University of Iowa
# Whitaker , Ross , SCI Institute
# Yamada , Atsushi , Shiga University of Medical Science
# Yarmarkovich , Alexander , Isomics
# Yoo , Terry , National Library of Medicine
# Zhu , Liangjia , Stony Brook University

Algorithm:SlicerModules

2013-08-31T16:03:41Z

Whitaker: Created page with ' = Algoirthms Core Slicer Models Under Development = * Left atrium segmentation: In collaboration with the Afib DBP. Graph-cut based segmentation that loads meshes, allows use…'

= Algoirthms Core Slicer Models Under Development =

* Left atrium segmentation: In collaboration with the Afib DBP. Graph-cut based segmentation that loads meshes, allows users to interactively "center" the model, perform the graph-cut segmentation, scan convert results into a volumetric format. Contact: Gopal Veni, University of Utah.

* Multimaterial meshing: Surface and volumetric meshing of multimaterial volumes with output surface triangles viewable within Slicer. Contact: Jonathan Bronson, University of Utah.

Algorithm:Main

2013-08-31T15:56:49Z

Whitaker: /* Data */

Back to [[Cores|NA-MIC Cores]]
__NOTOC__
='''Welcome to the NA-MIC Algorithms!'''=
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
The Algorithms Core (NA-MIC Core 1) investigates mathematical methods for medical image analysis. Algorithm design is an essential step in attempting to answer clinical questions based on medical imagery. The Algorithms Core collaborates with Core 2 to provide tools which Core 3 can leverage to enhance clinical studies. Our team members represent a broad cross-section of medical image groups. The links below showcase the work at each of the Core 1 sites and also showcase the collaborative work which we share with our Core 2 and 3 partners.
| style="background: #ebeced" colspan="2" align="center"| Volumetric Segmentation of the Arcuate Fasciculus[[Image:UtahArcuateFasciculusFeb10.png|center|200px]]
|-
| style="background: #ebeced"|
| style="background: #ebeced"|Microstructural Connectivity of the Arcuate Fasciculus in Adolescents with High-functioning Autism [[Algorithm:Past_Featured_Articles|Read more...]]
|}

= Algorithms Projects - Organized by Site =

* [[Algorithm:BU|Stony Brook]]
* [[Algorithm:MIT|MIT]]
* [[Algorithm:UNC|UNC]]
* [[Algorithm:Utah|Utah 1]]
* [[Algorithm:Utah2|Utah 2]]

= Algorithms Projects - Organized by Subject Matter =

* [[NA-MIC_Collaborations:New|NA-MIC Collaborations]]

= Data =

* [[Algorithm:DataRT|Radiotherapy]]

= [[Algorithm:SlicerModules|Slicer Modules]] =

Renewal-06-2013

2013-06-12T20:09:53Z

Whitaker: /* Participants */

[[2013_Summer_Project_Week#Agenda|Back to Summer project week Agenda]]

Closed Door Session with Ron. Room [[MIT_Project_Week_Rooms#32-D407|32-D407]]

=Agenda=
Getting together in one room will allow us to revisit the overall concept, to fine tune our approach, and to discuss open questions with respect to the grant as a whole.
=Participants=
TRD PI's and their delegates.
*Ron Kikinis
*Polina Golland (by google hangout)
*Allen Tannenbaum
*Sonia Pujol
*Steve Pieper
*Jim Miller
*Sylvain Bouix
*Andras Lasso
*Ross Whitaker (remote)

File:NAMIC-AHM-Jan2013-Ross.pptx

2013-01-10T14:58:40Z

Whitaker: uploaded a new version of "File:NAMIC-AHM-Jan2013-Ross.pptx"

File:NAMIC-AHM-Jan2013-Ross.pptx

2013-01-09T23:45:11Z

Whitaker: uploaded a new version of "File:NAMIC-AHM-Jan2013-Ross.pptx"

AHM 2013 alg core presentations

2012-12-24T19:02:57Z

Whitaker:

Presentations:

* Ross Whitaker [[Media:NAMIC-AHM-Jan2013-Ross.pptx]]
* Polina Golland
* Martin Styner
* Guido Gerig
* Allen Tannenbaum

AHM 2013 alg core presentations

2012-12-24T19:01:42Z

Whitaker:

Presentations:

* Ross Whitaker [[NAMIC-AHM-Jan2013-Ross.pptx]]
* Polina Golland
* Martin Styner
* Guido Gerig
* Allen Tannenbaum

File:NAMIC-AHM-Jan2013-Ross.pptx

2012-12-24T19:00:27Z

Whitaker:

AHM 2013 alg core presentations

2012-12-24T18:57:41Z

Whitaker:

Presentations:

* Ross Whitaker [[NAMIC-AHM-Jan2013-Ross.pptx|(slides)]]
* Polina Golland
* Martin Styner
* Guido Gerig
* Allen Tannenbaum

AHM 2013 alg core presentations

2012-12-24T18:56:42Z

Whitaker:

Presentations:

* Ross Whitaker [[NAMIC_AHM_Jan2013_Ross.pptx|(slides)]]
* Polina Golland
* Martin Styner
* Guido Gerig
* Allen Tannenbaum

File:NAMIC AHM Jan2013 Ross.pptx

2012-12-24T18:55:39Z

Whitaker: Draft of slides for AHM 2013.

Draft of slides for AHM 2013.

AHM 2013 alg core presentations

2012-12-24T18:48:37Z

Whitaker: Created page with 'Presentations: * Ross Whitaker * Polina Golland * Martin Styner * Guido Gerig * Allen Tannenbaum'

Presentations:

* Ross Whitaker
* Polina Golland
* Martin Styner
* Guido Gerig
* Allen Tannenbaum

AHM 2013

2012-12-24T18:46:16Z

Whitaker: /* Agenda */

__NOTOC__

Back to [[Events]]

[[Image:PW-SLC2013.png|300px]]

Dates: January 7-11, 2013.

Location: Salt Lake City, UT.

== Introduction ==
{| border="00" cellpadding="8" cellspacing="0"
|-
| rowspan="2" align="left" | '''This is the home page for the 2013 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 2013 project week, see below.

For information about Utah as a travel destination click [http://www.utah.com '''here'''].
| style="background: #ebeced" align="center"| [[Image:SLC.jpg|center|350px|View of the City]]
|-
| style="background: #ebeced"|The 2013 AHM, EAB and Project Week will be held '''January 7-11, 2013''', in '''Salt Lake City''', Utah.
|}

== Dates, Venue, Registration ==
{|
|align="left" style="width:60%"|
'''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'''.

'''Registration:''' Please click [http://www.sci.utah.edu/namic2013.html '''here'''] to register online before '''January 3, 2013'''. All participants must pay a registration fee ('''$250''' for AHM only, and '''$550''' for AHM+Project Week), which covers our catering and facilities costs.
After 12/25/12 registration prices will increase by $100. Last call registrations after 1/1/13 will be increased by $200.

'''Venue:''' The venue for the meeting is the Marriott City Center, Salt Lake City, Utah. Please either call the hotel at +1-866-961-8700 (toll free) and mention the group code "sciscia" or book online [http://www.marriott.com/hotels/travel/slccc-salt-lake-city-marriott-city-center/?toDate=1/12/13&groupCode=SCISCIA&fromDate=1/6/13&app=resvlink '''here''']. Please note that '''''we need attendees to use this hotel''''' in order not to incur additional charges for use of the conference rooms and keep registration fees low. The group rate is $149/night + tax.

|style="width:40%" |[[image:Marriott-floorplan.png|thumb |250px|'''Meeting Rooms:''' See [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ here] for the web version.]]
|}

== Agenda==
{| border="1" cellpadding="5"
|- style="background:#eeeeee; font-size:125%; color:#0063B6" align="center"
| style="width:5%"| '''Time'''
| style="width:15%" | '''Monday, January 7'''
| style="width:15%" | '''Tuesday, January 8'''
| style="width:15%" | '''Wednesday, January 9'''
| style="width:35%" | '''Thursday, January 10 '''
| style="width:15%" | '''Friday, January 11'''
|-
| style="background:#eeeeee; color:black"|
| style="background:#ffffff; color:#522200"| '''[[2013_Winter_Project_Week|Project Activities]] ''' ''(Capitol BC)''
| style="background:#dbf3ff; color:#522200"| '''[[2013_Winter_Project_Week|Project Activities]] ''' ''(Capitol BC)''
| style="background:#dbf3ff; color:#522200"| '''[[2013_Winter_Project_Week|Project Activities]] ''' ''(Capitol BC)''
| style="background:#F2E5D3; color:#522200"| '''AHM''' ''(Capitol ABC)'', '''[http://wiki.na-mic.org/Wiki/index.php/2013_EAB EAB]'''
| style="background:#dbf3ff; color:#522200"|'''[[2013_Winter_Project_Week|Project Activities]] ''' ''(Capitol BC)''
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#F2E5D3; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
| ''(Amethyst)''
|9-10am: Breakout Session: [[AHM2013-Performance_Evaluation_Tools|Performance Evaluation Tools]] ''(Capitol B)''
| ''(Amethyst)''
| '''8-8:05am:''' Welcome (Ron Kikinis) 
'''8:05-9:15am:''' [[AHM_2013_alg_core_presentations | Algorithms Core: Update and Future Plans]] '''9:20-9:55am:''' Recent Developments on Quantitative Multimodal Imaging at Fraunhofer MEVIS. Invited Speaker: Horst Hahn, PhD. 
| ''(Capitol BC)''
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#F2E5D3; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
| ''(Capitol A)''
| ''(Amethyst)''
|NA-MIC competitive renewal. [[ClosedSession2013|Closed session for TRD PIs and core personnel]] ''(Amethyst)''
| '''10:30-11:30am:''' [[AHM2013-Engineering_Updates | Engineering Core: Updates and Future Plans]] '''11:30am-12pm:''' Extensions - SlicerRT, Structured Reporting, iGyne, PET/CT review, Skull Stripper 
|
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)'' 
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)'' 
| style="background:#F2E5D3; color:black"| Lunch ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn ''(Olympus A)''
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''
| style="background:#dbf3ff; color:#522200"|[[2013_Winter_Project_Week|Project Presentations]] ''(Capitol BC)''
| ''(Capitol A)''
|'''DBP Team Meetings''' ''(Capitol A)'' '''1-2pm:''' [[DBP MGH Head and Neck Cancer]] '''2-3pm:''' [[DBP Utah Atrial Fibrillation]]
| '''1-2:40pm:''' DBP Update and Future Plans '''1-1:25pm:''' TBI (Jack Van Horn) '''1:25-1:50pm:''' Atrial Fibrillation (Rob McLeod) '''1:50-2:15pm:''' Huntington's Disease (Hans Johnson) '''2:15-240pm:''' Head and Neck Cancer (Greg Sharp) '''2:40-3:00pm:''' Outreach (Sonia Pujol, Steve Pieper) 
|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#F2E5D3; color:black"| Coffee ''(General area)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''3:00-5:00'''
|[[AHM2013-Extensions-Workshop|Breakout: Slicer Extensions for Developers]] [[AHM2013-PyXNAT|Breakout: PyXNAT]] ''(Capitol A)''
|3-4pm: Breakout Session: [[AHM2013-Real_World_DICOM|Real World DICOM]] ''(Capitol B)'' 4-5pm: [[AHM2013-Simple-ITK|Simple ITK Tutorial]]
|'''DBP Team Meetings''' ''(Capitol A)'' '''3-4pm:''' [[DBP UCLA Traumatic Brain Injury]] '''4-5pm:''' [[DBP Iowa Huntington's Disease]]
|'''3-4pm''': [[2013_EAB|EAB meeting]] (Core, Site, and DBP PIs to join) ''(Amethyst)'' '''4-5pm:''' EAB closed session ''(Amethyst)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''05:00-07:00'''
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#F2E5D3; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)
| style="background:#ffffff; color:black"|
|}

'''General Announcements:'''

**Will be added here

==Registered Attendees==

<big>'''NOTE:'''</big> The registered attendee list will be posted here by the organizers. '''DO NOT''' add your name to this list yourself. To register, please click [http://www.sci.utah.edu/namic2013-registration.html here].

As of 2:30 PM 12/21/2012
# Ackerman , Michael , National Library of Medicine, NIH, OHPCC
# Aucoin , Nicole , BWH
# Aylward , Stephen , Kitware, Inc.
# Batmanghelich , Kayhan , MIT
# Bengali , Salma , University of UtahSCI Institute
# Blumenfeld , Morry , EAB
# Budin , Francois , UNC
# Cates , Joshua , University of UtahSCI Institute
# Cavelier , German , NIH-NIMH
# Cevidanes , Lucia , University of Michigan
# Chauvin , Laurent , Laurent Chauvin
# Dalca , Adrian , MIT
# Datar , Manasi , University of UtahSCI Institute
# Fishbaugh , James , University of UtahSCI Institute
# Gao , Yi , BWH
# Gardner , Greg , University of UtahSCI Institute
# Haehn , Daniel , Boston Childrens Hospital
# Hata , Noby , BWH
# Ibanez , Luis , KITWARE Inc.
# Iftekahruddin , Khan , Old Dominion University
# Johnson , Chris , EAB
# Johnson , Hans , The University of Iowa
# Kaiser , Adrien , UNC
# Kapur , Tina , Harvard Medical School
# Karasev , Peter , Univ of Alabama at Birmingham
# Kikinis , Ron , SPL, BWH
# Kochis , Donna , Kitware
# Kolesov , Ivan , Univ of Alabama at Birmingham
# Kumar , Sunil , Washington University in St. Louis
# Li , Rui , GE Global Research
# Little , David , University of California, San Diego
# Lorensen , Bill , EAB
# Lowekamp , Bradley ,
# MacLeod , Rob , University of UtahSCI Institute
# McCormick , Matthew , Kitware, Inc
# Miller , Jim , GE Global Research
# Morris , Alan , University of UtahSCI Institute
# Napel , Sandy , EAB
# Onuma , Kazufumi , CANON INC.
# Padfield , Dirk , GE Global Research
# Paniagua , Beatriz , University of North Carolina at Chapel Hill
# Pieper , Steve , Isomics, Inc.
# Pinter , Csaba , Queens University
# Pujol , Sonia , Sonia Pujol
# Rankin , Adam , Queens University
# Sharma , Anauja , University of UtahSCI Institute
# Sharp , Gregory , MGH
# Shen , Dinggang , UNC-Chapel Hill
# Shusharina , Nadya , MGH
# Sridharan , Ramesh , MIT
# Styner , Martin , University of North Carolina
# Tannenbaum , Allen , Univ of Alabama at Birmingham
# Tokuda , Junichi , Brigham and Womens Hospital
# Ungi , Tamas , Queens University
# Van Horn , John , University of California Los Angeles
# Veeraraghavan , Harini , Memorial Sloan-Kettering Cancer Center
# Veni , Gopalkrishna , SCI Institute
# Wang , Bo , University of UtahSCI Institute
# Wang , Kevin , Princess Margaret Hospital
# Wassermann , Demian , Brigham and Womens Hospital
# Welch , David , The University of Iowa
# Yarmarkovich , Alexander , ISOMIC
# Yoo , Terry , National Library of Medicine, NIH, OHPCC
# Zhu , Liangjia , Univ of Alabama at Birmingham

2012-Nov-NIH-event-planning

2012-08-31T15:19:58Z

Whitaker: /* Potential Names */

=Background=
Peter:Regarding Nov 8-9 NCBC Showcase. Some items that need quick attention so
we can do a full court press on publicity.

# As soon as possible, send Jen and me a list of five high-profile individuals whom we can invite on the ‘testimonial’ panel (i.e., will make a 15 minute presentation about they have used your work/software, and sit on panel). Give us a ranking and brief statement of what the testimonial will be about. Extra points for anyone who can speak to more than one NCBC.
# If you haven’t sent us the list of five young people, can you do that. Also in rank order with brief explanation.
# Someone made the suggestion that since young trainees are so important we reinstate the lightening talks and reduce the NCBC PI presentation to 20 minutes. We’re ok with that. It will be busy, but the junior people are so important.

=email by R. K.=
Hi,

Peter Lyster at NIGMS is organizing an event in November to give the NCBC program more visibility. He wants to circulate the program to NIH folks in order to get it onto their schedules. See his email below on this topic.

We will have a tcon tomorrow to plan our contribution to this event, which is part of the effort to make a competitive renewal of NA-MIC happen. If you can not participate, please email me your thoughts. This whole procedure is on a short fuse.

The tcon will take place on '''Friday, August 31, from 11am - 11:30am EST'''. Please use the following number: 800-501-8979, access code: 7327389

Talk to you tomorrow

Ron

=Potential Names=
*Established:
**Medical
***Alex Golby
***Yoav Dori (JHU/CHOP; uses Slicer for pediatric cardiology)
***Heather Cody Hazlett/J. Piven
***Marek Kubicki/M. Shenton
***Nassir Marrouche
**Technical
***Gabor Fichtinger
***Terry Peters
***Russ Taylor
***Andras Lasso
***Marc Niethammer
***Nathalie Agar
***Kilian Pohl
***Gordon Kindlmann
***Jack van Horn
*Up and Coming
**Andrei Irimia
**Danielle Pace
**Andrey Fedorov
**Archana Venkataraman - just finished her PhD
**Mert Sabuncu - faculty at MGH, did his postdoc on NAMIC-related problems
**Yogesh Rathi
**Yi Gao
**Harini Veeraraghavan
**Casey Goodlett
**Samuel Gerber

Core 1 Retreat 2012

2012-08-19T20:50:19Z

Whitaker: /* Monday evening */

[[events|Back to NA-MIC events page]]

August 20 and 21

Park City, Utah

=Overview=
* Starting at 8:30am on Monday (please come in the night before). Finishing 2pm on Tuesday.
* Business issues
** DBPs
** Research interactions between groups
** Renewal planning
** Logistics of Core and NA-MIC
* Presentations from students, fellows, faculty - approximately 10 minutes each.
** Assume a tech savvy audience that knows these topics somewhat already
** Presentations should focus on technological developments - no need for "motivation", "introduction", etc.

=Agenda=
= Agenda =

==Monday morning==
*8am-9am: Breakfast
*9:00am-12:15pm: DBP updates (with break around 10am). Approx 40 mins each. Discuss: recent progress, papers published or planned, possible topics for final-year papers/impact.
**TBI - Guido
**Afib - Ross, Allen
**Huntington's - Martin
**Head&neck - Polina

==Monday afternoon==
*2:00-5:00: Project updates (10 mins each + questions)
**Polina Golland+
**Gopal Veni
**James Fishbaugh
**Allen Tannenbaum+
**Bo Wang
**Manasi Datar
**Martin Styner+
**Yi Gao+
**Suyash Awate
**Anuj Sharma

* 5:00-6:30: Renewal planning - Overview and DBP brainstorming

==Monday evening==
6:30: Dinner in Park City at the [http://www.purplesageparkcity.com/ Purple Sage].

==Tuesday morning ==
*7:30am-8:30am: Breakfast
*8:30-12:00: Renewal planning (short break around 10am)
*Scientific content
**Computer science objectives/goals
***algorithms, modeling, integration of imaging and non-imaging, info-viz,
*Platform Engineering and tool creation
**web technologies
*Biomedical drivers
**Remember the big 5 topics: neuro, cancer, heart, lung, infection
**humans, animals, cells, molecules
**our current portfolio of biomedical applications
**composition of teams
*Packaging/NIH program match
**Timing of grants/renewal and general status
**Discussion of funding alternatives
**Continued discussion of DBPs (TRDs)
**Discussion of organization and responsibilities
** Action items and next steps

= Attendees =
# Ross Whitaker
# Ron Kikinis
# Allen Tannenbaum
# Yi Gao
# Guido Gerig
# Bo Wang
# James Fishbaugh
# Anuja Sharma
# Martin Styner
# Polina Golland
# Kayhan Batmanghelich
# Manasi Datar
# Gopal Veni
# Suyash Awate

=Logistics=
*Venue: The Lodge at Deer Valley Resort ([http://www.deervalley.com/resources/Forms/SnowParkVillage.pdf see #18 on]).
*Hotel reservations. $125/night. Make reservations by filling out and mailing/faxing this [[:File:DV_lodge_hotel.pdf|form]].
*Fee $250.00 to cover breakfasts, lunches, and room fees. Please register [https://umarket.utah.edu/ecom/checkout.tpl?App_Type=0046&Item_Num=NAMICC1R here]
*Local transportation: you can reserve a shuttle on the hotel reservation form or go [http://www.expressshuttleutah.com/ here].

Core 1 Retreat 2012

2012-08-17T17:23:19Z

Whitaker: /* Monday afternoon */

[[events|Back to NA-MIC events page]]

August 20 and 21

Park City, Utah

=Overview=
* Starting at 8:30am on Monday (please come in the night before). Finishing 2pm on Tuesday.
* Business issues
** DBPs
** Research interactions between groups
** Renewal planning
** Logistics of Core and NA-MIC
* Presentations from students, fellows, faculty - approximately 10 minutes each.
** Assume a tech savvy audience that knows these topics somewhat already
** Presentations should focus on technological developments - no need for "motivation", "introduction", etc.

=Agenda=
= Agenda =

==Monday morning==
*8am-9am: Breakfast
*9:00am-12:15pm: DBP updates (with break around 10am). Approx 40 mins each. Discuss: recent progress, papers published or planned, possible topics for final-year papers/impact.
**TBI - Guido
**Afib - Ross, Allen
**Huntington's - Martin
**Head&neck - Polina

==Monday afternoon==
*2:00-5:00: Project updates (10 mins each + questions)
**Polina Golland+
**Gopal Veni
**James Fishbaugh
**Allen Tannenbaum+
**Bo Wang
**Manasi Datar
**Martin Styner+
**Yi Gao+
**Suyash Awate
**Anuj Sharma

* 5:00-6:30: Renewal planning - Overview and DBP brainstorming

==Monday evening==
Dinner in Park City at the [http://www.purplesageparkcity.com/ Purple Sage].

==Tuesday morning ==
*7:30am-8:30am: Breakfast
*8:30-12:00: Renewal planning (short break around 10am)
**Timing of grants/renewal and general status
**Discussion of funding alternatives
**Continued discussion of DBPs (TRDs)
**Discussion of organization and responsibilities
** Action items and next steps

= Attendees =
# Ross Whitaker
# Ron Kikinis
# Allen Tannenbaum
# Yi Gao
# Guido Gerig
# Bo Wang
# James Fishbaugh
# Anuja Sharma
# Martin Styner
# Polina Golland
# Kayhan Batmanghelich
# Manasi Datar
# Gopal Veni
# Suyash Awate

=Logistics=
*Venue: The Lodge at Deer Valley Resort
*Hotel reservations. $125/night. Make reservations by filling out and mailing/faxing this [[:File:DV_lodge_hotel.pdf|form]].
*Fee $250.00 to cover breakfasts, lunches, and room fees. Please register [https://umarket.utah.edu/ecom/checkout.tpl?App_Type=0046&Item_Num=NAMICC1R here]
*Local transportation: you can reserve a shuttle on the hotel reservation form or go [http://www.expressshuttleutah.com/ here].

Core 1 Retreat 2012

2012-08-17T17:22:58Z

Whitaker: /* Agenda */

[[events|Back to NA-MIC events page]]

August 20 and 21

Park City, Utah

=Overview=
* Starting at 8:30am on Monday (please come in the night before). Finishing 2pm on Tuesday.
* Business issues
** DBPs
** Research interactions between groups
** Renewal planning
** Logistics of Core and NA-MIC
* Presentations from students, fellows, faculty - approximately 10 minutes each.
** Assume a tech savvy audience that knows these topics somewhat already
** Presentations should focus on technological developments - no need for "motivation", "introduction", etc.

=Agenda=
= Agenda =

==Monday morning==
*8am-9am: Breakfast
*9:00am-12:15pm: DBP updates (with break around 10am). Approx 40 mins each. Discuss: recent progress, papers published or planned, possible topics for final-year papers/impact.
**TBI - Guido
**Afib - Ross, Allen
**Huntington's - Martin
**Head&neck - Polina

==Monday afternoon==
*2:00-5:00: Project updates (12 mins each + questions)
**Polina Golland+
**Gopal Veni
**James Fishbaugh
**Allen Tannenbaum+
**Bo Wang
**Manasi Datar
**Martin Styner+
**Yi Gao+
**Suyash Awate
**Anuj Sharma

* 5:00-6:30: Renewal planning - Overview and DBP brainstorming

==Monday evening==
Dinner in Park City at the [http://www.purplesageparkcity.com/ Purple Sage].

==Tuesday morning ==
*7:30am-8:30am: Breakfast
*8:30-12:00: Renewal planning (short break around 10am)
**Timing of grants/renewal and general status
**Discussion of funding alternatives
**Continued discussion of DBPs (TRDs)
**Discussion of organization and responsibilities
** Action items and next steps

= Attendees =
# Ross Whitaker
# Ron Kikinis
# Allen Tannenbaum
# Yi Gao
# Guido Gerig
# Bo Wang
# James Fishbaugh
# Anuja Sharma
# Martin Styner
# Polina Golland
# Kayhan Batmanghelich
# Manasi Datar
# Gopal Veni
# Suyash Awate

=Logistics=
*Venue: The Lodge at Deer Valley Resort
*Hotel reservations. $125/night. Make reservations by filling out and mailing/faxing this [[:File:DV_lodge_hotel.pdf|form]].
*Fee $250.00 to cover breakfasts, lunches, and room fees. Please register [https://umarket.utah.edu/ecom/checkout.tpl?App_Type=0046&Item_Num=NAMICC1R here]
*Local transportation: you can reserve a shuttle on the hotel reservation form or go [http://www.expressshuttleutah.com/ here].

Core 1 Retreat 2012

2012-08-17T17:21:10Z

Whitaker: /* Monday afternoon */

[[events|Back to NA-MIC events page]]

August 20 and 21

Park City, Utah

=Overview=
* Starting at 8:30am on Monday (please come in the night before). Finishing 2pm on Tuesday.
* Business issues
** DBPs
** Research interactions between groups
** Renewal planning
** Logistics of Core and NA-MIC
* Presentations from students, fellows, faculty - approximately 10 minutes each.
** Assume a tech savvy audience that knows these topics somewhat already
** Presentations should focus on technological developments - no need for "motivation", "introduction", etc.

=Agenda=
= Agenda =

==Monday morning==
*8am-9am: Breakfast
*9:00am-12:15pm: DBP updates (with break around 10am). Approx 40 mins each. Discuss: recent progress, papers published or planned, possible topics for final-year papers/impact.
**TBI - Guido
**Afib - Ross, Allen
**Huntington's - Martin
**Head&neck - Polina

==Monday afternoon==
*2:00-5:00: Project updates (12 mins each + questions)
**Polina Golland++
**Gopal Veni
**James Fishbaugh
**Allen Tannenbaum++
**Bo Wang
**Manasi Datar
**Martin Styner++
**Yi Gao
**Suyash Awate
**Anuj Sharma

* 5:00-6:30: Renewal planning - Overview and DBP brainstorming

==Tuesday morning ==
*7:30am-8:30am: Breakfast
*8:30-12:00: Renewal planning (short break around 10am)
**Timing of grants/renewal and general status
**Discussion of funding alternatives
**Continued discussion of DBPs (TRDs)
**Discussion of organization and responsibilities
** Action items and next steps

= Attendees =
# Ross Whitaker
# Ron Kikinis
# Allen Tannenbaum
# Yi Gao
# Guido Gerig
# Bo Wang
# James Fishbaugh
# Anuja Sharma
# Martin Styner
# Polina Golland
# Kayhan Batmanghelich
# Manasi Datar
# Gopal Veni
# Suyash Awate

=Logistics=
*Venue: The Lodge at Deer Valley Resort
*Hotel reservations. $125/night. Make reservations by filling out and mailing/faxing this [[:File:DV_lodge_hotel.pdf|form]].
*Fee $250.00 to cover breakfasts, lunches, and room fees. Please register [https://umarket.utah.edu/ecom/checkout.tpl?App_Type=0046&Item_Num=NAMICC1R here]
*Local transportation: you can reserve a shuttle on the hotel reservation form or go [http://www.expressshuttleutah.com/ here].

Core 1 Retreat 2012

2012-08-15T17:16:34Z

Whitaker: /* Monday morning */

[[events|Back to NA-MIC events page]]

August 20 and 21

Park City, Utah

=Overview=
* Starting at 8:30am on Monday (please come in the night before). Finishing 2pm on Tuesday.
* Business issues
** DBPs
** Research interactions between groups
** Renewal planning
** Logistics of Core and NA-MIC
* Presentations from students, fellows, faculty - approximately 10 minutes each.
** Assume a tech savvy audience that knows these topics somewhat already
** Presentations should focus on technological developments - no need for "motivation", "introduction", etc.

=Agenda=
= Agenda =

==Monday morning==
*8am-9am: Breakfast
*9:00am-12:15pm: DBP updates (with break around 10am). Approx 40 mins each. Discuss: recent progress, papers published or planned, possible topics for final-year papers/impact.
**TBI - Guido
**Afib - Ross, Allen
**Huntington's - Martin
**Head&neck - Polina

==Monday afternoon==
*2:00-5:00: Project updates (15mins each + questions)
**Polina Golland++
**Gopal Veni
**James Fishbaugh
**Allen Tannenbaum++
**Bo Wang
**Manasi Datar
**Martin Styner++
**Yi Gao
**Suyash Awate
**Anuj Sharma

* 5:00-6:30: Renewal planning - Overview and DBP brainstorming

==Tuesday morning ==
*7:30am-8:30am: Breakfast
*8:30-12:00: Renewal planning (short break around 10am)
**Timing of grants/renewal and general status
**Discussion of funding alternatives
**Continued discussion of DBPs (TRDs)
**Discussion of organization and responsibilities
** Action items and next steps

= Attendees =
# Ross Whitaker
# Ron Kikinis
# Allen Tannenbaum
# Yi Gao
# Guido Gerig
# Bo Wang
# James Fishbaugh
# Anuja Sharma
# Martin Styner
# Polina Golland
# Kayhan Batmanghelich
# Manasi Datar
# Gopal Veni
# Suyash Awate

=Logistics=
*Venue: The Lodge at Deer Valley Resort
*Hotel reservations. $125/night. Make reservations by filling out and mailing/faxing this [[:File:DV_lodge_hotel.pdf|form]].
*Fee $250.00 to cover breakfasts, lunches, and room fees. Please register [https://umarket.utah.edu/ecom/checkout.tpl?App_Type=0046&Item_Num=NAMICC1R here]
*Local transportation: you can reserve a shuttle on the hotel reservation form or go [http://www.expressshuttleutah.com/ here].

Core 1 Retreat 2012

2012-08-15T17:00:15Z

Whitaker: /* Agenda */

Core 1 Retreat 2012

2012-08-15T16:34:23Z

Whitaker: /* Attendees */

Core 1 Retreat 2012

2012-08-15T16:32:48Z

Whitaker: /* Logistics */

Core 1 Retreat 2012

2012-06-27T23:20:59Z

Whitaker: /* Logistics */

Core 1 Retreat 2012

2012-06-27T23:20:11Z

Whitaker: /* Logistics */

Core 1 Retreat 2012

2012-06-27T23:19:51Z

Whitaker: /* Logistics */

File:DV lodge hotel.pdf

2012-06-27T23:18:45Z

Whitaker: Registration form for hotel for 2012 Core 1 retreat in Deer Valley.

Registration form for hotel for 2012 Core 1 retreat in Deer Valley.

Core 1 Retreat 2012

2012-06-27T23:12:17Z

Whitaker: /* Logistics */

Core 1 Retreat 2012

2012-06-19T19:11:52Z

Whitaker: /* Logistics */

Core 1 Retreat 2012

2012-06-19T19:11:15Z

Whitaker: /* Logistics */

Core 1 Retreat 2012

2012-06-19T18:20:49Z

Whitaker:

Core 1 Retreat 2012

2012-02-20T16:44:10Z

Whitaker:

August 20 and 21

Park City, Utah

=== Attendees ===
# Ross Whitaker

Core 1 Retreat 2012

2012-02-20T16:40:51Z

Whitaker:

August 20 and 21

Park City, Utah

Core 1 Retreat 2012

2012-02-20T16:27:45Z

Whitaker:

August 20 and 21

Park City Utah

File:2012 01 Ross-Utah Update.pptx

2012-01-12T14:06:50Z

Whitaker: uploaded a new version of "File:2012 01 Ross-Utah Update.pptx"

File:2012 01 Ross-Utah Update.pptx

2012-01-12T05:43:00Z

Whitaker: uploaded a new version of "File:2012 01 Ross-Utah Update.pptx"

File:2012 01 Ross-Utah Update.pptx

2012-01-02T23:37:09Z

Whitaker:

AHM 2012

2012-01-02T23:35:56Z

Whitaker: /* Agenda */

Back to [[Events]]
[[Image:PW-SLC2012.png|300px]]

January 9-13, 2012, Salt Lake City, Utah
== Introduction ==
{| border="00" cellpadding="8" cellspacing="0"
|-
| rowspan="2" align="left" | '''This is the home page for the 2012 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 2012 project week, see below.

For information about Utah as a travel destination click [http://www.utah.com '''here'''].
| style="background: #ebeced" align="center"| [[Image:SLC.jpg|center|350px|View of the City]]
|-
| style="background: #ebeced"|The 2012 AHM, EAB and Project Week will be held '''January 9-13, 2012''', in '''Salt Lake City''', Utah.
|}

== Dates, Venue, Registration ==
{|
|align="left" style="width:60%"|
'''Dates:'''
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 12th'''.
* Project Activities will be held rest of the week between '''Monday, January 9th and Friday, January 13th'''.

'''Registration:''' Please click [http://www.sci.utah.edu/namic2012.html '''here'''] to register online before '''January 3, 2012'''. All participants must a pay registration fee ('''$200''' for AHM only, and '''$450''' for AHM+Project Week), which covers our catering and facilities costs.

'''Venue:''' The venue for the meeting is the Marriott, Salt Lake City, Utah. Please either call the hotel at +1-801-961-8700 (toll free) and mention the group code "sciscia" or book online [http://www.marriott.com/hotels/travel/slccc-salt-lake-city-marriott-city-center/ '''here''']. Please note that '''''we need attendees to use this hotel''''' in order not to incur additional charges for use of the conference rooms and keep registration fees low. The group rate is $149/night + tax and is valid for reservations made until '''December 9'''. After that it is $229/night + tax.

|style="width:40%" |[[image:Marriott-floorplan.png|thumb |250px|'''Meeting Rooms:''' See [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ here] for the web version.]]
|}

== Agenda==
{| border="1" cellpadding="5"
|- style="background:#eeeeee; color:black" align="left"
| style="width:4%" | '''Time'''
| style="width:12%" | '''Monday, January 9'''
| style="width:12%" | '''Tuesday, January 10'''
| style="width:12%" | '''Wednesday, January 11'''
| style="width:32%" | '''Thursday, January 12 '''
| style="width:12%" | '''Friday, January 13'''
|-
| style="background:#eeeeee; color:black"|
| style="background:#ffffff; color:#522200"| '''[[2012_Winter_Project_Week|Project Activities]] ''' ''(Capitol BC)''
| style="background:#dbf3ff; color:#522200"| '''[[2012_Winter_Project_Week|Project Activities]] ''' ''(Capitol BC)''
| style="background:#dbf3ff; color:#522200"| '''[[2012_Winter_Project_Week|Project Activities]] ''' ''(Capitol BC)''
| style="background:#F2E5D3; color:#522200"| '''AHM''' ''(Capitol ABC)'', '''[http://wiki.na-mic.org/Wiki/index.php/2012_EAB EAB]'''
| style="background:#dbf3ff; color:#522200"|'''[[2012_Winter_Project_Week|Project Activities]] ''' ''(Capitol BC)''
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
| style="background:#F2E5D3; color:black"| Breakfast ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Breakfast ''(Olympus A)''
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
|9-10am: DICOM General Breakout Session ''(Amethyst)''
|8-10am: [[AHM2012-Slicer-Overview-and-Migration|Slicer 4: Overview and Migration]] (for Developers) ''(Capitol A)''
|[[AHM2012-3D-US-Slicer-Breakout|Breakout: 3D Ultrasound in Slicer]] (Noby Hata) ''(Amethyst)''
| 8:05-9am: Keynote: iDASH: Integrating Data for Analysis, Anonymization, and Sharing, Lucila Ohno-Machado, PhD, UCSD 9-10am: Algorithms Core Update [[media:Bu.namic.ahm.zip|BU]], MIT, [[media:2012_01_UNC_Update.pptx‎|UNC]], [[media:2012_01_Ross-Utah_Update.pptx|Utah I]], [[media:UtahII-AHM2012-12Min.pptx|Utah II]]
| style="background:#dbf3ff; color:black"|[[2012_Winter_Project_Week|Project Review]] ''(Capitol BC)'' 
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#F2E5D3; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
| Core and Site PIs meeting with Ron ''(Capitol A)''
| [[2012_Winter_Project_Week_SimpleITK_and_Slicer4|Breakout: SimpleITK and Slicer 4.0]] (Hans Johnson & Bradley Lowekamp) ''(Amethyst)''
|
| 10:30-11:30am: Engineering Core Update 11:30-12pm: Outreach Update, Sonia Pujol
|
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)'' 
| style="background:#dbf3ff; color:black"| Lunch ''(Olympus A)'' 
| style="background:#F2E5D3; color:black"| Lunch ''(Olympus A)''
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn ''(Olympus A)''
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''
|[[2012_Winter_Project_Week|Project Presentations]] ''(Capitol BC)''
| [[2012_Winter_Project_Week_Slicer4_Module_Design_Breakout|Breakout: Slicer 4 Module Design with Individual Teams]] ''(Capitol A)''
|'''DBP Team Meetings''' ''(Capitol A)'' 1-2: [[2012_Winter_Project_Week_DBP_MGH_Team_Meeting|DBP MGH Head and Neck Cancer]] 2-3: [[2012_Winter_Project_Week_DBP_Utah_Team_Meeting|DBP Utah Atrial Fibrillation]]
| 1-1:45pm International Research Organizations contribute to NA-MIC: 1-1:30pm Best Practices from a Past DBP, Gabor FIchtinger, PhD, Queens University 1:30-1:45pm Neuroimage as a biomechanical model: New computational biomechanics of the brain, Karol Miller, University of Western Australia 1:45-3pm: Current DBP Updates 1:45: Huntington's Disease, Hans Johnson, U Iowa 2pm: Atrial Fibrillation, Rob McLeod, U Utah 2:15pm: Traumatic Brain Injury, Jack Van Horn, UCLA 2:30pm: Head and Neck Cancer, Greg Sharp, MGH
|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#dbf3ff; color:black"| Coffee ''(General area)''
| style="background:#F2E5D3; color:black"| Coffee ''(General area)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''3:00-5:00'''
|[[AHM2012-Slicer-with-Ron|Breakout: Slicer 4 with Ron (for Users)]] ''(Capitol A)''
| DICOM RT Breakout ''(Amethyst)''
|'''DBP Team Meetings''' ''(Capitol A)'' 3-4: [[2012_Winter_Project_Week_DBP_UCLA_Team_Meeting|DBP UCLA Traumatic Brain Injury]] 4-5: [[2012_Winter_Project_Week_DBP_Iowa_Team_Meeting|DBP Iowa Huntington's Disease]]
|3-4pm: [[2012_EAB|EAB meeting]] ''(Amethyst)'' 4-5pm EAB closed session ''(Amethyst)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''05:00-07:00'''
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#F2E5D3; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)
| style="background:#ffffff; color:black"|
|}

'''General Announcements:'''

**Will be added here

==Registered Attendees==

<big>'''NOTE:'''</big> The registered attendee list will be posted here by the organizers. '''DO NOT''' add your name to this list yourself. To register, please click [http://www.sci.utah.edu/namic2012-registration.html here].

# Ackerman Michael , National Library of Medicine, NIH, OHPPC
# Aucoin Nicole , BWH
# Aylward Stephen , Kitware
# Baumgartner Christian , Psychiatry Neuroimaging Lab - BWH Boston
# Berger Jean-Baptiste ,
# Blezek Daniel Mayo Clinic
# Blumenfeld Morry , EAB
# Blumfield Anthony , Radnostics
# Bowers Michael , Johns Hopkins University
# Cates Josh , University of Utah
# Chambers Micah , UCLA
# Chapman Brian , University of California, San Diego
# Chauvin Laurent , BWH
# Chen Xiaojun , Surgical Plan Lab,Brigham Womens Hospital
# Chen Elvis , Robarts Research Institute
# Datar Manasi , SCI Institute
# Diedrich Karl , AZE Research and Development
# Egger Jan , SPL, BWH, HMS
# Fedorov Andriy , BWH
# Fichtinger Gabor , Queens University
# Fillion-Robin Jean-Christophe , Kitware
# Finet Julien , Kitware
# Fishbaugh James , SCI Institute
# Gao Yi , Brigham And Womens Hospital
# Gardner Greg , SCI Institute
# George Ashvin , SCI Institute
# Gerig Guido , SCI Institute
# Ghosh Satrajit , Isomics, Inc.
# Golland Polina , MIT
# Hata Nobuhiko , BWH
# Iftekharuddin Khan , Old Dominion University
# Irimia Andrei , University of California, Los Angeles
# Johnson Hans , University of Iowa
# Johnson Chris , EAB
# Kalpathy-Cramer Jayashree , MGH
# Kikinis Ron , Brigham and Womens Hospital
# Kim Eun Young Regina , University of Iowa
# Kochis Donna , Kitware
# Kolesov Ivan Georgia Institute of Technology
# Lasso Andras , Queens University
# Long Benjamin , Kitware
# Lorensen Bill , EAB
# Lou Yifei , Georgia Tech
# MacLeod Rob , SCI Institute
# Marcus Daniel , Washington University
# Matsui Joy , University of Iowa
# Milchenko Mikhail , Washington University in St. Louis
# Miller James , GE Research
# Montillo Albert , GE
# Moradi Mehdi , BWH Harvard Medical School
# Morris Alan , SCI Institute
# Napel Sandy , EAB
# Oguz Ipek , UNC
# Ohno-Machado Lucila , plenary speaker
# Pace Danielle , Kitware
# Paniagua Beatriz , University of North Carolina at Chapel Hill
# Perry Daniel , SCI Institute
# Pieper Steve , Isomics, Inc.
# Pierpaoli Carlo EAB
# Pinter Csaba , Queens University
# Pohl Kilian
# Prastawa Marcel , SCI Institute
# Prior Fred , EAB
# Roger Gwendoline , UNC
# Ryan William Mayo Clinic
# Savadjiev Peter , Brigham and Womens Hospital
# Schroeder William , Kitware
# Scully Mark , University of Iowa
# Shackleford James MGH
# Sharma Anuja , SCI Institute
# Sharp Gregory , MGH
# Shusharina Nadya ,
# Sridharan Ramesh , MIT CSAIL
# Styner Martin University of North Carolina
# Tannenbaum Allen , Boston University
# Tibrewal Radhika ,
# Toews Matthew BWH HMS
# Tokuda Junichi ,
# Tustison Nick , University of Virginia
# Ungi Tamas , Queens University
# Vachet Clement , UNC Chapel Hill
# Van Horn John , UCLA
# Veeraraghavan Harini General Electric Research
# Veni Gopalkrishna , SCI Institute
# Wachinger Christian , MIT CSAIL
# Wang Bo , SCI Institute
# Wang Kevin University Health Network
# Wasserman Demian , Brigham and Womens Hospital
# Wedlake Chris , Robarts Research Institute
# Welch Dave , University of Iowa
# Whitaker Ross , SCI Institute
# Yarmarkovich Alexander , Isomics
# Yeniaras Erol , MD Anderson Cancer Center
# Yoo Terry , National Libraray of Medicine at NIH, OHPCC
# zhu yingxuan , GE Global Research
# Zhu Liang-jia , Georgia Institute of Technology

as of December 28, 2011 9:30 AM MST

Algorithm:Utah

2011-12-07T17:29:02Z

Whitaker: /* Shape Analysis Framework using SPHARM-PDM */

Back to [[Algorithm:Main|NA-MIC Algorithms]]
__NOTOC__
= Overview of Utah Algorithms (PI: Ross Whitaker) =

We are developing new methods in the areas of statistical shape analysis, MRI tissue segmentation, and diffusion tensor image processing and analysis. We are building shape analysis tools that can generate efficient statistical models appropriate for analyzing anatomical shape differences in the brain. We are developing a wide range of tools for diffusion tensor imaging, that span the entire pipeline from image processing to automatic white matter tract extraction to statistical testing of clinical hypotheses.

= Utah Projects =

{| cellpadding="10" style="text-align:left;"

| | [[Image:HeadRegressionResult.png|200px]]
| |

== [[Projects:ShapeRegression|Particle Based Shape Regression]] ==

Shape regression promises to be an important tool to study the relationship between anatomy and underlying clinical or biological parameters, such as age. We propose a new method to building shape models that incorporates regression analysis in the process of optimizing correspondences on a set of open surfaces. The method is applied to provide new results on clinical MRI data related to early development of the human head.

 M Datar, J Cates, P T Fletcher, S Gouttard, G Gerig, R Whitaker, Particle Based Shape Regression of Open Surfaces with Applications to Developmental Neuroimaging, MICCAI 2009.

|-
{| cellpadding="10" style="text-align:left;"

| | [[Image:sgerber_brainmanifold_oasis_manifold.png|200px]]
| |

== [[Projects:BrainManifold|Brain Manifold Learning]] ==

This work is concerned with modeling high dimensional spaces, such as the space of brain images. Common approach for representing populations are template or clustering based approaches. In this project we develop a data driven method to learn a manifold representation from a set of brain images. The presented approach is described and evaluated in the setting of brain MRI but generalizes to other application domains.

S Gerber, T Tasdizen, S Joshi, R Whitaker, On the Manifold Structure of the Space of Brain Images, MICCAI 2009.

S Gerber, T Tasdizen, R Whitaker, Dimensionality Reduction and Principal Surfaces via Kernel Map, ICCV 2009.

S. Gerber, T. Tasdizen, P.T. Fletcher, S. Joshi, R. Whitaker, Manifold Modeling for Brain Population Analysis, Medical Image Anal, 3, 2010.

|-
| style="width:15%" | [[Image:EPI.png|200px]]
| style="width:85%" |

== [[Projects:EPIDistortionCorrection| Correction for Geometric Distortion in Echo Planar Images]] ==

We have developed a variational image-based approach to correct the susceptibility artifacts in the alignment of diffusion weighted and structural MRI.The correction is formulated as an optimization of a penalty that captures the intensity difference between the jacobian corrected EPI baseline images and a corresponding T2-weighted structural image.

 R Tao, P T Fletcher, S Gerber, R Whitaker, A Variational Image-Based Approach to the Correction of Susceptibility Artifacts
in the Alignment of Diffusion Weighted and Structural MRI, IPMI 2009.

|-

| | [[Image:pipeline.png|150px]]
| |

== [[Projects:StructuralAndDWIPipeline| A Framework for Joint Analysis of Structural and Diffusion MRI]] ==

This framework addresses the simultaneous alignment and ﬁltering of DWI images to correct eddy current artifacts and the subsequent alignment of those images to structural, T1 MRI to correct for susceptibility artifacts, and this paper demonstrates the importance of performing these corrections. It also shows how a T1-based, group speciﬁc atlas can be used to generate grey-matter regions of interest that can drive subsequent connectivity analyses. The result is a system that can be combined with a variety of tools for MRI analysis for tissue classiﬁcation, morphometry, and cortical parcellation.

 Ran Tao, P. Thomas Fletcher, Ross T. Whitaker, in MICCAI 2008 on Computational Diffusion MRI.

|-

| | [[Image:Sulcaldepth.png|200px]]
| |

== [[Projects:CorticalCorrespondenceWithParticleSystem|Cortical Correspondence using Particle System]] ==

In this project, we want to compute cortical correspondence on populations, using various features such as cortical structure, DTI connectivity, vascular structure, and functional data (fMRI). This presents a challenge because of the highly convoluted surface of the cortex, as well as because of the different properties of the data features we want to incorporate together. [[Projects:CorticalCorrespondenceWithParticleSystem|More...]]

 Oguz I, Niethammer M, Cates J, Whitaker R, Fletcher T, Vachet C, Styner M. “Cortical Correspondence with Probabilistic Fiber Connectivity”. Proc. Information Processing in Medical Imaging, 2009.

|-

| | [[Image:CatesNamicFigure3.png|200px]]
| |

== [[Projects:ParticlesForShapesAndComplexes|Adaptive, Particle-Based Sampling for Shapes and Complexes]] ==

This research is a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wider range of problems than existing methods, including nonmanifold surfaces and objects of arbitrary topology. [[Projects:ParticlesForShapesAndComplexes|More...]]

 Particle-Based Shape Analysis of Multi-object Complexes. Cates J., Fletcher P.T., Styner M., Hazlett H.C., Whitaker R. Int Conf Med Image Comput Comput Assist Interv. 2008;11(Pt 1):477-485.

|-

| | [[Image:UNCShape_OverviewAnalysis_MICCAI06.gif|200px]]
| |

== [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|Shape Analysis Framework using SPHARM-PDM]] ==

The UNC shape analysis is based on an analysis framework of objects with spherical topology, described mainly by sampled spherical harmonics SPHARM-PDM. The input of the shape analysis framework is a set of binary segmentations of a single brain structure, such as the hippocampus or caudate. These segmentations are converted into a shape description (SPHARM) with correspondence and analyzed via Hotelling T^2 two sample metric. [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|More...]]

 Zhao Z., Taylor W., Styner M., Steffens D., Krishnan R., Macfall J. , Hippocampus shape analysis and late-life depression. PLoS ONE. 2008 Mar 19;3(3):e1837.

|-

| | [[Image:FiberTracts-angle.jpg|200px]]
| |

== [[Projects:DTIVolumetricWhiteMatterConnectivity|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. [[Projects:DTIVolumetricWhiteMatterConnectivity|More...]]

|-
| style="width:15%" | [[Image:DTIFiltering.jpg|200px]]
| style="width:85%" |

== [[Projects:DTIProcessingTools|DTI Processing and Statistics Tools]] ==

We implement the diffusion weighted image (DWI) registration model from the paper of G.K.Rohde et al. Patient head motion and eddy currents distortion cause artifacts in maps of diffusion parameters computer from DWI. This model corrects these two distortions at the same time including brightness correction.

|-

| | [[Image:Brain-seg-utah.png|200px]]
| |

== [[Projects:TissueClassificationWithNeighborhoodStatistics| Tissue Classification with Neighborhood Statistics]] ==

We have implemented an MRI tissue classification algorithm based on unsupervised non-parametric density estimation of tissue intensity classes.
[[Projects:TissueClassificationWithNeighborhoodStatistics|More...]]

|}

Algorithm:Utah

2011-12-07T17:28:46Z

Whitaker: /* Adaptive, Particle-Based Sampling for Shapes and Complexes */

Back to [[Algorithm:Main|NA-MIC Algorithms]]
__NOTOC__
= Overview of Utah Algorithms (PI: Ross Whitaker) =

We are developing new methods in the areas of statistical shape analysis, MRI tissue segmentation, and diffusion tensor image processing and analysis. We are building shape analysis tools that can generate efficient statistical models appropriate for analyzing anatomical shape differences in the brain. We are developing a wide range of tools for diffusion tensor imaging, that span the entire pipeline from image processing to automatic white matter tract extraction to statistical testing of clinical hypotheses.

= Utah Projects =

{| cellpadding="10" style="text-align:left;"

| | [[Image:HeadRegressionResult.png|200px]]
| |

== [[Projects:ShapeRegression|Particle Based Shape Regression]] ==

Shape regression promises to be an important tool to study the relationship between anatomy and underlying clinical or biological parameters, such as age. We propose a new method to building shape models that incorporates regression analysis in the process of optimizing correspondences on a set of open surfaces. The method is applied to provide new results on clinical MRI data related to early development of the human head.

 M Datar, J Cates, P T Fletcher, S Gouttard, G Gerig, R Whitaker, Particle Based Shape Regression of Open Surfaces with Applications to Developmental Neuroimaging, MICCAI 2009.

|-
{| cellpadding="10" style="text-align:left;"

| | [[Image:sgerber_brainmanifold_oasis_manifold.png|200px]]
| |

== [[Projects:BrainManifold|Brain Manifold Learning]] ==

This work is concerned with modeling high dimensional spaces, such as the space of brain images. Common approach for representing populations are template or clustering based approaches. In this project we develop a data driven method to learn a manifold representation from a set of brain images. The presented approach is described and evaluated in the setting of brain MRI but generalizes to other application domains.

S Gerber, T Tasdizen, S Joshi, R Whitaker, On the Manifold Structure of the Space of Brain Images, MICCAI 2009.

S Gerber, T Tasdizen, R Whitaker, Dimensionality Reduction and Principal Surfaces via Kernel Map, ICCV 2009.

S. Gerber, T. Tasdizen, P.T. Fletcher, S. Joshi, R. Whitaker, Manifold Modeling for Brain Population Analysis, Medical Image Anal, 3, 2010.

|-
| style="width:15%" | [[Image:EPI.png|200px]]
| style="width:85%" |

== [[Projects:EPIDistortionCorrection| Correction for Geometric Distortion in Echo Planar Images]] ==

We have developed a variational image-based approach to correct the susceptibility artifacts in the alignment of diffusion weighted and structural MRI.The correction is formulated as an optimization of a penalty that captures the intensity difference between the jacobian corrected EPI baseline images and a corresponding T2-weighted structural image.

 R Tao, P T Fletcher, S Gerber, R Whitaker, A Variational Image-Based Approach to the Correction of Susceptibility Artifacts
in the Alignment of Diffusion Weighted and Structural MRI, IPMI 2009.

|-

| | [[Image:pipeline.png|150px]]
| |

== [[Projects:StructuralAndDWIPipeline| A Framework for Joint Analysis of Structural and Diffusion MRI]] ==

This framework addresses the simultaneous alignment and ﬁltering of DWI images to correct eddy current artifacts and the subsequent alignment of those images to structural, T1 MRI to correct for susceptibility artifacts, and this paper demonstrates the importance of performing these corrections. It also shows how a T1-based, group speciﬁc atlas can be used to generate grey-matter regions of interest that can drive subsequent connectivity analyses. The result is a system that can be combined with a variety of tools for MRI analysis for tissue classiﬁcation, morphometry, and cortical parcellation.

 Ran Tao, P. Thomas Fletcher, Ross T. Whitaker, in MICCAI 2008 on Computational Diffusion MRI.

|-

| | [[Image:Sulcaldepth.png|200px]]
| |

== [[Projects:CorticalCorrespondenceWithParticleSystem|Cortical Correspondence using Particle System]] ==

In this project, we want to compute cortical correspondence on populations, using various features such as cortical structure, DTI connectivity, vascular structure, and functional data (fMRI). This presents a challenge because of the highly convoluted surface of the cortex, as well as because of the different properties of the data features we want to incorporate together. [[Projects:CorticalCorrespondenceWithParticleSystem|More...]]

 Oguz I, Niethammer M, Cates J, Whitaker R, Fletcher T, Vachet C, Styner M. “Cortical Correspondence with Probabilistic Fiber Connectivity”. Proc. Information Processing in Medical Imaging, 2009.

|-

| | [[Image:CatesNamicFigure3.png|200px]]
| |

== [[Projects:ParticlesForShapesAndComplexes|Adaptive, Particle-Based Sampling for Shapes and Complexes]] ==

This research is a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wider range of problems than existing methods, including nonmanifold surfaces and objects of arbitrary topology. [[Projects:ParticlesForShapesAndComplexes|More...]]

 Particle-Based Shape Analysis of Multi-object Complexes. Cates J., Fletcher P.T., Styner M., Hazlett H.C., Whitaker R. Int Conf Med Image Comput Comput Assist Interv. 2008;11(Pt 1):477-485.

|-

| | [[Image:UNCShape_OverviewAnalysis_MICCAI06.gif|200px]]
| |

== [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|Shape Analysis Framework using SPHARM-PDM]] ==

The UNC shape analysis is based on an analysis framework of objects with spherical topology, described mainly by sampled spherical harmonics SPHARM-PDM. The input of the shape analysis framework is a set of binary segmentations of a single brain structure, such as the hippocampus or caudate. These segmentations are converted into a shape description (SPHARM) with correspondence and analyzed via Hotelling T^2 two sample metric. [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|More...]]

'''New: ''' Zhao Z., Taylor W., Styner M., Steffens D., Krishnan R., Macfall J. , Hippocampus shape analysis and late-life depression. PLoS ONE. 2008 Mar 19;3(3):e1837.

|-

| | [[Image:FiberTracts-angle.jpg|200px]]
| |

== [[Projects:DTIVolumetricWhiteMatterConnectivity|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. [[Projects:DTIVolumetricWhiteMatterConnectivity|More...]]

|-
| style="width:15%" | [[Image:DTIFiltering.jpg|200px]]
| style="width:85%" |

== [[Projects:DTIProcessingTools|DTI Processing and Statistics Tools]] ==

We implement the diffusion weighted image (DWI) registration model from the paper of G.K.Rohde et al. Patient head motion and eddy currents distortion cause artifacts in maps of diffusion parameters computer from DWI. This model corrects these two distortions at the same time including brightness correction.

|-

| | [[Image:Brain-seg-utah.png|200px]]
| |

== [[Projects:TissueClassificationWithNeighborhoodStatistics| Tissue Classification with Neighborhood Statistics]] ==

We have implemented an MRI tissue classification algorithm based on unsupervised non-parametric density estimation of tissue intensity classes.
[[Projects:TissueClassificationWithNeighborhoodStatistics|More...]]

|}

Algorithm:Utah

2011-12-07T17:28:29Z

Whitaker: /* Cortical Correspondence using Particle System */

Back to [[Algorithm:Main|NA-MIC Algorithms]]
__NOTOC__
= Overview of Utah Algorithms (PI: Ross Whitaker) =

We are developing new methods in the areas of statistical shape analysis, MRI tissue segmentation, and diffusion tensor image processing and analysis. We are building shape analysis tools that can generate efficient statistical models appropriate for analyzing anatomical shape differences in the brain. We are developing a wide range of tools for diffusion tensor imaging, that span the entire pipeline from image processing to automatic white matter tract extraction to statistical testing of clinical hypotheses.

= Utah Projects =

{| cellpadding="10" style="text-align:left;"

| | [[Image:HeadRegressionResult.png|200px]]
| |

== [[Projects:ShapeRegression|Particle Based Shape Regression]] ==

Shape regression promises to be an important tool to study the relationship between anatomy and underlying clinical or biological parameters, such as age. We propose a new method to building shape models that incorporates regression analysis in the process of optimizing correspondences on a set of open surfaces. The method is applied to provide new results on clinical MRI data related to early development of the human head.

 M Datar, J Cates, P T Fletcher, S Gouttard, G Gerig, R Whitaker, Particle Based Shape Regression of Open Surfaces with Applications to Developmental Neuroimaging, MICCAI 2009.

|-
{| cellpadding="10" style="text-align:left;"

| | [[Image:sgerber_brainmanifold_oasis_manifold.png|200px]]
| |

== [[Projects:BrainManifold|Brain Manifold Learning]] ==

This work is concerned with modeling high dimensional spaces, such as the space of brain images. Common approach for representing populations are template or clustering based approaches. In this project we develop a data driven method to learn a manifold representation from a set of brain images. The presented approach is described and evaluated in the setting of brain MRI but generalizes to other application domains.

S Gerber, T Tasdizen, S Joshi, R Whitaker, On the Manifold Structure of the Space of Brain Images, MICCAI 2009.

S Gerber, T Tasdizen, R Whitaker, Dimensionality Reduction and Principal Surfaces via Kernel Map, ICCV 2009.

S. Gerber, T. Tasdizen, P.T. Fletcher, S. Joshi, R. Whitaker, Manifold Modeling for Brain Population Analysis, Medical Image Anal, 3, 2010.

|-
| style="width:15%" | [[Image:EPI.png|200px]]
| style="width:85%" |

== [[Projects:EPIDistortionCorrection| Correction for Geometric Distortion in Echo Planar Images]] ==

We have developed a variational image-based approach to correct the susceptibility artifacts in the alignment of diffusion weighted and structural MRI.The correction is formulated as an optimization of a penalty that captures the intensity difference between the jacobian corrected EPI baseline images and a corresponding T2-weighted structural image.

 R Tao, P T Fletcher, S Gerber, R Whitaker, A Variational Image-Based Approach to the Correction of Susceptibility Artifacts
in the Alignment of Diffusion Weighted and Structural MRI, IPMI 2009.

|-

| | [[Image:pipeline.png|150px]]
| |

== [[Projects:StructuralAndDWIPipeline| A Framework for Joint Analysis of Structural and Diffusion MRI]] ==

This framework addresses the simultaneous alignment and ﬁltering of DWI images to correct eddy current artifacts and the subsequent alignment of those images to structural, T1 MRI to correct for susceptibility artifacts, and this paper demonstrates the importance of performing these corrections. It also shows how a T1-based, group speciﬁc atlas can be used to generate grey-matter regions of interest that can drive subsequent connectivity analyses. The result is a system that can be combined with a variety of tools for MRI analysis for tissue classiﬁcation, morphometry, and cortical parcellation.

 Ran Tao, P. Thomas Fletcher, Ross T. Whitaker, in MICCAI 2008 on Computational Diffusion MRI.

|-

| | [[Image:Sulcaldepth.png|200px]]
| |

== [[Projects:CorticalCorrespondenceWithParticleSystem|Cortical Correspondence using Particle System]] ==

In this project, we want to compute cortical correspondence on populations, using various features such as cortical structure, DTI connectivity, vascular structure, and functional data (fMRI). This presents a challenge because of the highly convoluted surface of the cortex, as well as because of the different properties of the data features we want to incorporate together. [[Projects:CorticalCorrespondenceWithParticleSystem|More...]]

 Oguz I, Niethammer M, Cates J, Whitaker R, Fletcher T, Vachet C, Styner M. “Cortical Correspondence with Probabilistic Fiber Connectivity”. Proc. Information Processing in Medical Imaging, 2009.

|-

| | [[Image:CatesNamicFigure3.png|200px]]
| |

== [[Projects:ParticlesForShapesAndComplexes|Adaptive, Particle-Based Sampling for Shapes and Complexes]] ==

This research is a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wider range of problems than existing methods, including nonmanifold surfaces and objects of arbitrary topology. [[Projects:ParticlesForShapesAndComplexes|More...]]

'''New: ''' Particle-Based Shape Analysis of Multi-object Complexes. Cates J., Fletcher P.T., Styner M., Hazlett H.C., Whitaker R. Int Conf Med Image Comput Comput Assist Interv. 2008;11(Pt 1):477-485.

|-

| | [[Image:UNCShape_OverviewAnalysis_MICCAI06.gif|200px]]
| |

== [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|Shape Analysis Framework using SPHARM-PDM]] ==

The UNC shape analysis is based on an analysis framework of objects with spherical topology, described mainly by sampled spherical harmonics SPHARM-PDM. The input of the shape analysis framework is a set of binary segmentations of a single brain structure, such as the hippocampus or caudate. These segmentations are converted into a shape description (SPHARM) with correspondence and analyzed via Hotelling T^2 two sample metric. [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|More...]]

'''New: ''' Zhao Z., Taylor W., Styner M., Steffens D., Krishnan R., Macfall J. , Hippocampus shape analysis and late-life depression. PLoS ONE. 2008 Mar 19;3(3):e1837.

|-

| | [[Image:FiberTracts-angle.jpg|200px]]
| |

== [[Projects:DTIVolumetricWhiteMatterConnectivity|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. [[Projects:DTIVolumetricWhiteMatterConnectivity|More...]]

|-
| style="width:15%" | [[Image:DTIFiltering.jpg|200px]]
| style="width:85%" |

== [[Projects:DTIProcessingTools|DTI Processing and Statistics Tools]] ==

We implement the diffusion weighted image (DWI) registration model from the paper of G.K.Rohde et al. Patient head motion and eddy currents distortion cause artifacts in maps of diffusion parameters computer from DWI. This model corrects these two distortions at the same time including brightness correction.

|-

| | [[Image:Brain-seg-utah.png|200px]]
| |

== [[Projects:TissueClassificationWithNeighborhoodStatistics| Tissue Classification with Neighborhood Statistics]] ==

We have implemented an MRI tissue classification algorithm based on unsupervised non-parametric density estimation of tissue intensity classes.
[[Projects:TissueClassificationWithNeighborhoodStatistics|More...]]

|}

Algorithm:Utah

2011-12-07T17:28:14Z

Whitaker: /* A Framework for Joint Analysis of Structural and Diffusion MRI */

Back to [[Algorithm:Main|NA-MIC Algorithms]]
__NOTOC__
= Overview of Utah Algorithms (PI: Ross Whitaker) =

We are developing new methods in the areas of statistical shape analysis, MRI tissue segmentation, and diffusion tensor image processing and analysis. We are building shape analysis tools that can generate efficient statistical models appropriate for analyzing anatomical shape differences in the brain. We are developing a wide range of tools for diffusion tensor imaging, that span the entire pipeline from image processing to automatic white matter tract extraction to statistical testing of clinical hypotheses.

= Utah Projects =

{| cellpadding="10" style="text-align:left;"

| | [[Image:HeadRegressionResult.png|200px]]
| |

== [[Projects:ShapeRegression|Particle Based Shape Regression]] ==

Shape regression promises to be an important tool to study the relationship between anatomy and underlying clinical or biological parameters, such as age. We propose a new method to building shape models that incorporates regression analysis in the process of optimizing correspondences on a set of open surfaces. The method is applied to provide new results on clinical MRI data related to early development of the human head.

 M Datar, J Cates, P T Fletcher, S Gouttard, G Gerig, R Whitaker, Particle Based Shape Regression of Open Surfaces with Applications to Developmental Neuroimaging, MICCAI 2009.

|-
{| cellpadding="10" style="text-align:left;"

| | [[Image:sgerber_brainmanifold_oasis_manifold.png|200px]]
| |

== [[Projects:BrainManifold|Brain Manifold Learning]] ==

This work is concerned with modeling high dimensional spaces, such as the space of brain images. Common approach for representing populations are template or clustering based approaches. In this project we develop a data driven method to learn a manifold representation from a set of brain images. The presented approach is described and evaluated in the setting of brain MRI but generalizes to other application domains.

S Gerber, T Tasdizen, S Joshi, R Whitaker, On the Manifold Structure of the Space of Brain Images, MICCAI 2009.

S Gerber, T Tasdizen, R Whitaker, Dimensionality Reduction and Principal Surfaces via Kernel Map, ICCV 2009.

S. Gerber, T. Tasdizen, P.T. Fletcher, S. Joshi, R. Whitaker, Manifold Modeling for Brain Population Analysis, Medical Image Anal, 3, 2010.

|-
| style="width:15%" | [[Image:EPI.png|200px]]
| style="width:85%" |

== [[Projects:EPIDistortionCorrection| Correction for Geometric Distortion in Echo Planar Images]] ==

We have developed a variational image-based approach to correct the susceptibility artifacts in the alignment of diffusion weighted and structural MRI.The correction is formulated as an optimization of a penalty that captures the intensity difference between the jacobian corrected EPI baseline images and a corresponding T2-weighted structural image.

 R Tao, P T Fletcher, S Gerber, R Whitaker, A Variational Image-Based Approach to the Correction of Susceptibility Artifacts
in the Alignment of Diffusion Weighted and Structural MRI, IPMI 2009.

|-

| | [[Image:pipeline.png|150px]]
| |

== [[Projects:StructuralAndDWIPipeline| A Framework for Joint Analysis of Structural and Diffusion MRI]] ==

This framework addresses the simultaneous alignment and ﬁltering of DWI images to correct eddy current artifacts and the subsequent alignment of those images to structural, T1 MRI to correct for susceptibility artifacts, and this paper demonstrates the importance of performing these corrections. It also shows how a T1-based, group speciﬁc atlas can be used to generate grey-matter regions of interest that can drive subsequent connectivity analyses. The result is a system that can be combined with a variety of tools for MRI analysis for tissue classiﬁcation, morphometry, and cortical parcellation.

 Ran Tao, P. Thomas Fletcher, Ross T. Whitaker, in MICCAI 2008 on Computational Diffusion MRI.

|-

| | [[Image:Sulcaldepth.png|200px]]
| |

== [[Projects:CorticalCorrespondenceWithParticleSystem|Cortical Correspondence using Particle System]] ==

In this project, we want to compute cortical correspondence on populations, using various features such as cortical structure, DTI connectivity, vascular structure, and functional data (fMRI). This presents a challenge because of the highly convoluted surface of the cortex, as well as because of the different properties of the data features we want to incorporate together. [[Projects:CorticalCorrespondenceWithParticleSystem|More...]]

'''New: ''' Oguz I, Niethammer M, Cates J, Whitaker R, Fletcher T, Vachet C, Styner M. “Cortical Correspondence with Probabilistic Fiber Connectivity”. Proc. Information Processing in Medical Imaging, 2009.

|-

| | [[Image:CatesNamicFigure3.png|200px]]
| |

== [[Projects:ParticlesForShapesAndComplexes|Adaptive, Particle-Based Sampling for Shapes and Complexes]] ==

This research is a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wider range of problems than existing methods, including nonmanifold surfaces and objects of arbitrary topology. [[Projects:ParticlesForShapesAndComplexes|More...]]

'''New: ''' Particle-Based Shape Analysis of Multi-object Complexes. Cates J., Fletcher P.T., Styner M., Hazlett H.C., Whitaker R. Int Conf Med Image Comput Comput Assist Interv. 2008;11(Pt 1):477-485.

|-

| | [[Image:UNCShape_OverviewAnalysis_MICCAI06.gif|200px]]
| |

== [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|Shape Analysis Framework using SPHARM-PDM]] ==

The UNC shape analysis is based on an analysis framework of objects with spherical topology, described mainly by sampled spherical harmonics SPHARM-PDM. The input of the shape analysis framework is a set of binary segmentations of a single brain structure, such as the hippocampus or caudate. These segmentations are converted into a shape description (SPHARM) with correspondence and analyzed via Hotelling T^2 two sample metric. [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|More...]]

'''New: ''' Zhao Z., Taylor W., Styner M., Steffens D., Krishnan R., Macfall J. , Hippocampus shape analysis and late-life depression. PLoS ONE. 2008 Mar 19;3(3):e1837.

|-

| | [[Image:FiberTracts-angle.jpg|200px]]
| |

== [[Projects:DTIVolumetricWhiteMatterConnectivity|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. [[Projects:DTIVolumetricWhiteMatterConnectivity|More...]]

|-
| style="width:15%" | [[Image:DTIFiltering.jpg|200px]]
| style="width:85%" |

== [[Projects:DTIProcessingTools|DTI Processing and Statistics Tools]] ==

We implement the diffusion weighted image (DWI) registration model from the paper of G.K.Rohde et al. Patient head motion and eddy currents distortion cause artifacts in maps of diffusion parameters computer from DWI. This model corrects these two distortions at the same time including brightness correction.

|-

| | [[Image:Brain-seg-utah.png|200px]]
| |

== [[Projects:TissueClassificationWithNeighborhoodStatistics| Tissue Classification with Neighborhood Statistics]] ==

We have implemented an MRI tissue classification algorithm based on unsupervised non-parametric density estimation of tissue intensity classes.
[[Projects:TissueClassificationWithNeighborhoodStatistics|More...]]

|}

Algorithm:Utah

2011-12-07T17:27:52Z

Whitaker: /* Correction for Geometric Distortion in Echo Planar Images */

Back to [[Algorithm:Main|NA-MIC Algorithms]]
__NOTOC__
= Overview of Utah Algorithms (PI: Ross Whitaker) =

We are developing new methods in the areas of statistical shape analysis, MRI tissue segmentation, and diffusion tensor image processing and analysis. We are building shape analysis tools that can generate efficient statistical models appropriate for analyzing anatomical shape differences in the brain. We are developing a wide range of tools for diffusion tensor imaging, that span the entire pipeline from image processing to automatic white matter tract extraction to statistical testing of clinical hypotheses.

= Utah Projects =

{| cellpadding="10" style="text-align:left;"

| | [[Image:HeadRegressionResult.png|200px]]
| |

== [[Projects:ShapeRegression|Particle Based Shape Regression]] ==

Shape regression promises to be an important tool to study the relationship between anatomy and underlying clinical or biological parameters, such as age. We propose a new method to building shape models that incorporates regression analysis in the process of optimizing correspondences on a set of open surfaces. The method is applied to provide new results on clinical MRI data related to early development of the human head.

 M Datar, J Cates, P T Fletcher, S Gouttard, G Gerig, R Whitaker, Particle Based Shape Regression of Open Surfaces with Applications to Developmental Neuroimaging, MICCAI 2009.

|-
{| cellpadding="10" style="text-align:left;"

| | [[Image:sgerber_brainmanifold_oasis_manifold.png|200px]]
| |

== [[Projects:BrainManifold|Brain Manifold Learning]] ==

This work is concerned with modeling high dimensional spaces, such as the space of brain images. Common approach for representing populations are template or clustering based approaches. In this project we develop a data driven method to learn a manifold representation from a set of brain images. The presented approach is described and evaluated in the setting of brain MRI but generalizes to other application domains.

S Gerber, T Tasdizen, S Joshi, R Whitaker, On the Manifold Structure of the Space of Brain Images, MICCAI 2009.

S Gerber, T Tasdizen, R Whitaker, Dimensionality Reduction and Principal Surfaces via Kernel Map, ICCV 2009.

S. Gerber, T. Tasdizen, P.T. Fletcher, S. Joshi, R. Whitaker, Manifold Modeling for Brain Population Analysis, Medical Image Anal, 3, 2010.

|-
| style="width:15%" | [[Image:EPI.png|200px]]
| style="width:85%" |

== [[Projects:EPIDistortionCorrection| Correction for Geometric Distortion in Echo Planar Images]] ==

We have developed a variational image-based approach to correct the susceptibility artifacts in the alignment of diffusion weighted and structural MRI.The correction is formulated as an optimization of a penalty that captures the intensity difference between the jacobian corrected EPI baseline images and a corresponding T2-weighted structural image.

 R Tao, P T Fletcher, S Gerber, R Whitaker, A Variational Image-Based Approach to the Correction of Susceptibility Artifacts
in the Alignment of Diffusion Weighted and Structural MRI, IPMI 2009.

|-

| | [[Image:pipeline.png|150px]]
| |

== [[Projects:StructuralAndDWIPipeline| A Framework for Joint Analysis of Structural and Diffusion MRI]] ==

This framework addresses the simultaneous alignment and ﬁltering of DWI images to correct eddy current artifacts and the subsequent alignment of those images to structural, T1 MRI to correct for susceptibility artifacts, and this paper demonstrates the importance of performing these corrections. It also shows how a T1-based, group speciﬁc atlas can be used to generate grey-matter regions of interest that can drive subsequent connectivity analyses. The result is a system that can be combined with a variety of tools for MRI analysis for tissue classiﬁcation, morphometry, and cortical parcellation.

'''New: ''' Ran Tao, P. Thomas Fletcher, Ross T. Whitaker, in MICCAI 2008 on Computational Diffusion MRI.

|-

| | [[Image:Sulcaldepth.png|200px]]
| |

== [[Projects:CorticalCorrespondenceWithParticleSystem|Cortical Correspondence using Particle System]] ==

In this project, we want to compute cortical correspondence on populations, using various features such as cortical structure, DTI connectivity, vascular structure, and functional data (fMRI). This presents a challenge because of the highly convoluted surface of the cortex, as well as because of the different properties of the data features we want to incorporate together. [[Projects:CorticalCorrespondenceWithParticleSystem|More...]]

'''New: ''' Oguz I, Niethammer M, Cates J, Whitaker R, Fletcher T, Vachet C, Styner M. “Cortical Correspondence with Probabilistic Fiber Connectivity”. Proc. Information Processing in Medical Imaging, 2009.

|-

| | [[Image:CatesNamicFigure3.png|200px]]
| |

== [[Projects:ParticlesForShapesAndComplexes|Adaptive, Particle-Based Sampling for Shapes and Complexes]] ==

This research is a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wider range of problems than existing methods, including nonmanifold surfaces and objects of arbitrary topology. [[Projects:ParticlesForShapesAndComplexes|More...]]

'''New: ''' Particle-Based Shape Analysis of Multi-object Complexes. Cates J., Fletcher P.T., Styner M., Hazlett H.C., Whitaker R. Int Conf Med Image Comput Comput Assist Interv. 2008;11(Pt 1):477-485.

|-

| | [[Image:UNCShape_OverviewAnalysis_MICCAI06.gif|200px]]
| |

== [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|Shape Analysis Framework using SPHARM-PDM]] ==

The UNC shape analysis is based on an analysis framework of objects with spherical topology, described mainly by sampled spherical harmonics SPHARM-PDM. The input of the shape analysis framework is a set of binary segmentations of a single brain structure, such as the hippocampus or caudate. These segmentations are converted into a shape description (SPHARM) with correspondence and analyzed via Hotelling T^2 two sample metric. [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|More...]]

'''New: ''' Zhao Z., Taylor W., Styner M., Steffens D., Krishnan R., Macfall J. , Hippocampus shape analysis and late-life depression. PLoS ONE. 2008 Mar 19;3(3):e1837.

|-

| | [[Image:FiberTracts-angle.jpg|200px]]
| |

== [[Projects:DTIVolumetricWhiteMatterConnectivity|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. [[Projects:DTIVolumetricWhiteMatterConnectivity|More...]]

|-
| style="width:15%" | [[Image:DTIFiltering.jpg|200px]]
| style="width:85%" |

== [[Projects:DTIProcessingTools|DTI Processing and Statistics Tools]] ==

We implement the diffusion weighted image (DWI) registration model from the paper of G.K.Rohde et al. Patient head motion and eddy currents distortion cause artifacts in maps of diffusion parameters computer from DWI. This model corrects these two distortions at the same time including brightness correction.

|-

| | [[Image:Brain-seg-utah.png|200px]]
| |

== [[Projects:TissueClassificationWithNeighborhoodStatistics| Tissue Classification with Neighborhood Statistics]] ==

We have implemented an MRI tissue classification algorithm based on unsupervised non-parametric density estimation of tissue intensity classes.
[[Projects:TissueClassificationWithNeighborhoodStatistics|More...]]

|}

Algorithm:Utah

2011-12-07T17:27:32Z

Whitaker: /* Brain Manifold Learning */

Back to [[Algorithm:Main|NA-MIC Algorithms]]
__NOTOC__
= Overview of Utah Algorithms (PI: Ross Whitaker) =

We are developing new methods in the areas of statistical shape analysis, MRI tissue segmentation, and diffusion tensor image processing and analysis. We are building shape analysis tools that can generate efficient statistical models appropriate for analyzing anatomical shape differences in the brain. We are developing a wide range of tools for diffusion tensor imaging, that span the entire pipeline from image processing to automatic white matter tract extraction to statistical testing of clinical hypotheses.

= Utah Projects =

{| cellpadding="10" style="text-align:left;"

| | [[Image:HeadRegressionResult.png|200px]]
| |

== [[Projects:ShapeRegression|Particle Based Shape Regression]] ==

Shape regression promises to be an important tool to study the relationship between anatomy and underlying clinical or biological parameters, such as age. We propose a new method to building shape models that incorporates regression analysis in the process of optimizing correspondences on a set of open surfaces. The method is applied to provide new results on clinical MRI data related to early development of the human head.

 M Datar, J Cates, P T Fletcher, S Gouttard, G Gerig, R Whitaker, Particle Based Shape Regression of Open Surfaces with Applications to Developmental Neuroimaging, MICCAI 2009.

|-
{| cellpadding="10" style="text-align:left;"

| | [[Image:sgerber_brainmanifold_oasis_manifold.png|200px]]
| |

== [[Projects:BrainManifold|Brain Manifold Learning]] ==

This work is concerned with modeling high dimensional spaces, such as the space of brain images. Common approach for representing populations are template or clustering based approaches. In this project we develop a data driven method to learn a manifold representation from a set of brain images. The presented approach is described and evaluated in the setting of brain MRI but generalizes to other application domains.

S Gerber, T Tasdizen, S Joshi, R Whitaker, On the Manifold Structure of the Space of Brain Images, MICCAI 2009.

S Gerber, T Tasdizen, R Whitaker, Dimensionality Reduction and Principal Surfaces via Kernel Map, ICCV 2009.

S. Gerber, T. Tasdizen, P.T. Fletcher, S. Joshi, R. Whitaker, Manifold Modeling for Brain Population Analysis, Medical Image Anal, 3, 2010.

|-
| style="width:15%" | [[Image:EPI.png|200px]]
| style="width:85%" |

== [[Projects:EPIDistortionCorrection| Correction for Geometric Distortion in Echo Planar Images]] ==

We have developed a variational image-based approach to correct the susceptibility artifacts in the alignment of diffusion weighted and structural MRI.The correction is formulated as an optimization of a penalty that captures the intensity difference between the jacobian corrected EPI baseline images and a corresponding T2-weighted structural image.

'''New: ''' R Tao, P T Fletcher, S Gerber, R Whitaker, A Variational Image-Based Approach to the Correction of Susceptibility Artifacts
in the Alignment of Diffusion Weighted and Structural MRI, IPMI 2009.

|-

| | [[Image:pipeline.png|150px]]
| |

== [[Projects:StructuralAndDWIPipeline| A Framework for Joint Analysis of Structural and Diffusion MRI]] ==

This framework addresses the simultaneous alignment and ﬁltering of DWI images to correct eddy current artifacts and the subsequent alignment of those images to structural, T1 MRI to correct for susceptibility artifacts, and this paper demonstrates the importance of performing these corrections. It also shows how a T1-based, group speciﬁc atlas can be used to generate grey-matter regions of interest that can drive subsequent connectivity analyses. The result is a system that can be combined with a variety of tools for MRI analysis for tissue classiﬁcation, morphometry, and cortical parcellation.

'''New: ''' Ran Tao, P. Thomas Fletcher, Ross T. Whitaker, in MICCAI 2008 on Computational Diffusion MRI.

|-

| | [[Image:Sulcaldepth.png|200px]]
| |

== [[Projects:CorticalCorrespondenceWithParticleSystem|Cortical Correspondence using Particle System]] ==

In this project, we want to compute cortical correspondence on populations, using various features such as cortical structure, DTI connectivity, vascular structure, and functional data (fMRI). This presents a challenge because of the highly convoluted surface of the cortex, as well as because of the different properties of the data features we want to incorporate together. [[Projects:CorticalCorrespondenceWithParticleSystem|More...]]

'''New: ''' Oguz I, Niethammer M, Cates J, Whitaker R, Fletcher T, Vachet C, Styner M. “Cortical Correspondence with Probabilistic Fiber Connectivity”. Proc. Information Processing in Medical Imaging, 2009.

|-

| | [[Image:CatesNamicFigure3.png|200px]]
| |

== [[Projects:ParticlesForShapesAndComplexes|Adaptive, Particle-Based Sampling for Shapes and Complexes]] ==

This research is a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wider range of problems than existing methods, including nonmanifold surfaces and objects of arbitrary topology. [[Projects:ParticlesForShapesAndComplexes|More...]]

'''New: ''' Particle-Based Shape Analysis of Multi-object Complexes. Cates J., Fletcher P.T., Styner M., Hazlett H.C., Whitaker R. Int Conf Med Image Comput Comput Assist Interv. 2008;11(Pt 1):477-485.

|-

| | [[Image:UNCShape_OverviewAnalysis_MICCAI06.gif|200px]]
| |

== [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|Shape Analysis Framework using SPHARM-PDM]] ==

The UNC shape analysis is based on an analysis framework of objects with spherical topology, described mainly by sampled spherical harmonics SPHARM-PDM. The input of the shape analysis framework is a set of binary segmentations of a single brain structure, such as the hippocampus or caudate. These segmentations are converted into a shape description (SPHARM) with correspondence and analyzed via Hotelling T^2 two sample metric. [[Projects:ShapeAnalysisFrameworkUsingSPHARMPDM|More...]]

'''New: ''' Zhao Z., Taylor W., Styner M., Steffens D., Krishnan R., Macfall J. , Hippocampus shape analysis and late-life depression. PLoS ONE. 2008 Mar 19;3(3):e1837.

|-

| | [[Image:FiberTracts-angle.jpg|200px]]
| |

== [[Projects:DTIVolumetricWhiteMatterConnectivity|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. [[Projects:DTIVolumetricWhiteMatterConnectivity|More...]]

|-
| style="width:15%" | [[Image:DTIFiltering.jpg|200px]]
| style="width:85%" |

== [[Projects:DTIProcessingTools|DTI Processing and Statistics Tools]] ==

We implement the diffusion weighted image (DWI) registration model from the paper of G.K.Rohde et al. Patient head motion and eddy currents distortion cause artifacts in maps of diffusion parameters computer from DWI. This model corrects these two distortions at the same time including brightness correction.

|-

| | [[Image:Brain-seg-utah.png|200px]]
| |

== [[Projects:TissueClassificationWithNeighborhoodStatistics| Tissue Classification with Neighborhood Statistics]] ==

We have implemented an MRI tissue classification algorithm based on unsupervised non-parametric density estimation of tissue intensity classes.
[[Projects:TissueClassificationWithNeighborhoodStatistics|More...]]

|}