NAMIC Wiki - User contributions [en]

AHM 2014

2014-01-09T21:10:04Z

Macleod: /* Agenda */

Back to [[Events]]

[[File:AHM-2014-in-session.JPG|thumb|right|600px|The 2014 AHM in session]]
[[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==

'''[https://www.google.com/calendar/embed?src=kitware.com_hmsjf9uq4e0mmft8ihj4aag1vg@group.calendar.google.com&ctz=America/Denver&mode=WEEK&showNav=0&showDate=0&showTabs=0&showCalendars=0&showTz=0&showPrint=0 Google Calendar version of 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: Wiro Niessen, Erasmus MC. [[media:NAMIC QIB ImagingGenetics Neuro 2014 Niessen.pdf|"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 2)''
| [[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-report2014-C.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, Ron Kikinis)]] ''(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:''' [[Media:TMJOA_Namic_2014.pptx|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: [[AHM2014-SubjectHierarchy|Breakout Session: 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) ''(Sundance)'' '''4-5pm:''' EAB closed session ''(Sundance)''
| 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:'''

*Murphy's Reception is on 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 , EAB
# Aucoin , Nicole , BWH
# Aylward , Stephen , Kitware
# Bengali , Salma , SCI Institute
# Binder , Polina , MIT
# Blumenfeld , Morry , EAB
# 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 , BWH
# 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
# Herrick , Rick , Neuroinformatics Research Group
# Jain , Saurabh , Johns Hopkins University
# Johnson , Chris , EAB
# 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
# Liang , Lichen , MGH
# Lorensen , Bill , EAB
# Lowekamp , Bradley ,
# Macleod , Rob , SCI Institute
# McCormick , Matthew , Kitware, Inc
# Mehrtash , Alireza , Brigham and Womens Hospital
# Miller , James , GE Research
# Napel , Sandy , EAB
# Nardelli , Pietro , Brigham and Womens Hospital
# ODonnell , Lauren , BWH
# Pace , Danielle , MIT
# Pieper , Steve , Isomics
# Pinter , Csaba , Queens University
# Prastawa , Marcel , General Electric
# Prior , Fred , EAB
# Pujol , Sonia , BWH
# 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 , BWH
# Ulrich , Ethan , University of Iowa
# Vast , Erwin ,
# Wang , Kevin , Princess Margaret Cancer Centre
# Wang , Bo , SCI Institute
# Welch , David , University of Iowa
# Whitaker , Ross , SCI Institute
# Yamada , Atsushi , Shiga University of Medical Science
# Yarmarkovich , Alexander , Isomics
# Yoo , Terry , EAB
# Zhu , Liangjia , Stony Brook University

File:DBP-AF-report2014-C.pdf

2014-01-09T21:02:01Z

Macleod:

AHM 2013

2013-01-10T15:58:15Z

Macleod: /* Agenda */

Back to [[Events]]

[[Image:PW-SLC2013.png|300px]] [[Image:H2013-Slicer2.png|270px]]

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]''' [[2013_Winter_Project_Week|Project Activities]]
| 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'''
| 
|9-10am: Breakout Session: [[AHM2013-Performance_Evaluation_Tools|Performance Evaluation Tools]] ''(Capitol B)'' [[AHM2013-Robotics|Breakout: Agile Robotics]] ''(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. 
| style="background:#dbf3ff; color:#522200"|[[2013_Winter_Project_Week|Project Presentations]] ''(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'''
|
| Breakout Session: [[AHM2013-IGT|Image Guided Therapy]] ''(Amethyst)'' [[AHM2013-Robotics|Breakout: Agile Robotics]] ''(Capitol A)''
|NA-MIC competitive renewal. [[ClosedSession2013|Closed session for TRD PIs and core personnel]] ''(Amethyst)''
| DBP Update and Future Plans '''10:30-10:55am:''' TBI (Jack Van Horn) '''10:55-11:20am:''' Atrial Fibrillation (Rob MacLeod, [[Media:DBP-AF-AHM2013.pdf|Slides]]) '''11:20-11:45am:''' Huntington's Disease (Hans Johnson) '''11:45-12:10pm:''' Head and Neck Cancer (Greg Sharp, [[Media:NAMIC-AHM-2013-01-Sharp.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'''
| style="background:#dbf3ff; color:#522200"|[[2013_Winter_Project_Week|Project Presentations]] ''(Capitol BC)''
| [[AHM2013-Robotics|Breakout: Agile Robotics]] ''(Capitol A)'' [[AHM2013-PatientHierarchy|Breakout: Slicer Patient Hierarchy and DICOM Export]] ''(Amethyst)''
|'''DBP Team Meetings''' ''(Capitol A)'' '''1-2pm:''' [[DBP MGH Head and Neck Cancer]] '''2-3pm:''' [[DBP Utah Atrial Fibrillation]]
| '''1:15-2pm:''' [[AHM2013-Engineering_Updates | Engineering Core: Updates and Future Plans]] '''2-2:30pm''' [[Media:AHM-2013-Extensions.ppt| Extensions]] (Tina Kapur, Jim Miller, Csaba Pinter, Tamas Ungi, Andriy Fedorov) '''2:30-3:00pm:''' 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]] ''(Capitol BC)'' [[AHM2013-PyXNAT|Breakout: PyXNAT]] ''(Capitol A)'' [[AHM2013-Robotics|Breakout: Agile Robotics]] ''(Amethyst)''
|3:15-4pm: Breakout Session: [[AHM2013-Real_World_DICOM|Real World DICOM]] ''(Amethyst)'' 4:15-5pm: [[AHM2013-Simple-ITK|Simple ITK Tutorial]] Amethyst [[AHM2013-Robotics|Breakout: Agile Robotics]] ''(Capitol A)''
|'''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 9:30 AM 1/2/2013
# Ackerman , Michael , National Library of Medicine, NIH, OHPCC
# Aucoin , Nicole , BWH
# Aylward , Stephen , Kitware, Inc.
# Batmanghelich , Kayhan , MIT
# Bengali , Salma , SCI Institute
# Blumenfeld , Morry , EAB
# Budin , Francois , UNC
# Cates , Joshua , SCI Institute
# Cavelier , German , NIH-NIMH
# Cevidanes , Lucia , University of Michigan
# Chauvin , Laurent , Brigham and Womens Hospital
# Dalca , Adrian , MIT
# Datar , Manasi , SCI Institute
# Fedorov , Andriy , Harvard Medical School
# Fillion-Robin , Jean-Christophe , Kitware Inc.
# Finet , Julien , Kitware Inc.
# Fishbaugh , James , SCI Institute
# Gao , Yi , BWH
# Gardner , Greg , SCI Institute
# Gerig , Guido , SCI Institute
# Grethe , Jeffrey , University of California, San Diego
# Haehn , Daniel , Boston Childrens Hospital
# Hata , Noby , BWH
# Ibanez , Luis , KITWARE Inc.
# Iftekahruddin , Khan , Old Dominion University
# Irimia , Andrei , University of California, Los Angeles
# Johnson , Chris , EAB
# Johnson , Hans , The University of Iowa
# Kaiser , Adrien , UNC
# Kapur , Tina , Harvard Medical School
# Karasev , Peter , Univ of Alabama at Birmingham
# Kato , Takahisa , Brigham and womens hospital
# Kikinis , Ron , SPL, BWH
# Kochis , Donna , Kitware
# Kolesov , Ivan , Univ of Alabama at Birmingham
# Kumar , Sunil , Washington University in St. Louis
# Kumekawa , Miki , Brigham Womens Hospital Chiba University
# Li , Rui , GE Global Research
# Little , David , University of California, San Diego
# Lorensen , Bill , EAB
# Lowekamp , Bradley ,
# MacLeod , Rob , SCI Institute
# McCormick , Matthew , Kitware, Inc
# Mehrtash , Alireza , Brigham and Womens Hospital
# Miller , Jim , GE Global Research
# Morris , Alan , SCI 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 , Brigham and Womens Hospital, Harvard Medical School
# Rankin , Adam , Queens University
# Ross , James , Brigham and Womens Hospital
# San Jose , Raul , Brigham and Womens Hospital
# Sharma , Anuja , SCI 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
# Toews , Matthew , BWH, Harvard Medical School
# 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 , SCI Institute
# Wang , Kevin , Princess Margaret Hospital
# Wassermann , Demian , Brigham and Womens Hospital
# Welch , David , The University of Iowa
# Wells , William , Brigham and Womens Hospital, HMS
# Whitaker , Ross , SCI Institute
# Yamada , Atsushi , Brigham and Womens Hospital
# Yarmarkovich , Alexander , ISOMIC
# Yoo , Terry , National Library of Medicine, NIH, OHPCC
# Zhu , Liangjia , Univ of Alabama at Birmingham

AHM 2013

2013-01-10T15:56:17Z

Macleod: /* Agenda */

Back to [[Events]]

[[Image:PW-SLC2013.png|300px]] [[Image:H2013-Slicer2.png|270px]]

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]''' [[2013_Winter_Project_Week|Project Activities]]
| 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'''
| 
|9-10am: Breakout Session: [[AHM2013-Performance_Evaluation_Tools|Performance Evaluation Tools]] ''(Capitol B)'' [[AHM2013-Robotics|Breakout: Agile Robotics]] ''(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. 
| style="background:#dbf3ff; color:#522200"|[[2013_Winter_Project_Week|Project Presentations]] ''(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'''
|
| Breakout Session: [[AHM2013-IGT|Image Guided Therapy]] ''(Amethyst)'' [[AHM2013-Robotics|Breakout: Agile Robotics]] ''(Capitol A)''
|NA-MIC competitive renewal. [[ClosedSession2013|Closed session for TRD PIs and core personnel]] ''(Amethyst)''
| DBP Update and Future Plans '''10:30-10:55am:''' TBI (Jack Van Horn) '''10:55-11:20am:''' Atrial Fibrillation (Rob MacLeod [[File:DBP-AF-AHM2013.pdf|Slides]]) '''11:20-11:45am:''' Huntington's Disease (Hans Johnson) '''11:45-12:10pm:''' Head and Neck Cancer (Greg Sharp, [[Media:NAMIC-AHM-2013-01-Sharp.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'''
| style="background:#dbf3ff; color:#522200"|[[2013_Winter_Project_Week|Project Presentations]] ''(Capitol BC)''
| [[AHM2013-Robotics|Breakout: Agile Robotics]] ''(Capitol A)'' [[AHM2013-PatientHierarchy|Breakout: Slicer Patient Hierarchy and DICOM Export]] ''(Amethyst)''
|'''DBP Team Meetings''' ''(Capitol A)'' '''1-2pm:''' [[DBP MGH Head and Neck Cancer]] '''2-3pm:''' [[DBP Utah Atrial Fibrillation]]
| '''1:15-2pm:''' [[AHM2013-Engineering_Updates | Engineering Core: Updates and Future Plans]] '''2-2:30pm''' [[Media:AHM-2013-Extensions.ppt| Extensions]] (Tina Kapur, Jim Miller, Csaba Pinter, Tamas Ungi, Andriy Fedorov) '''2:30-3:00pm:''' 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]] ''(Capitol BC)'' [[AHM2013-PyXNAT|Breakout: PyXNAT]] ''(Capitol A)'' [[AHM2013-Robotics|Breakout: Agile Robotics]] ''(Amethyst)''
|3:15-4pm: Breakout Session: [[AHM2013-Real_World_DICOM|Real World DICOM]] ''(Amethyst)'' 4:15-5pm: [[AHM2013-Simple-ITK|Simple ITK Tutorial]] Amethyst [[AHM2013-Robotics|Breakout: Agile Robotics]] ''(Capitol A)''
|'''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 9:30 AM 1/2/2013
# Ackerman , Michael , National Library of Medicine, NIH, OHPCC
# Aucoin , Nicole , BWH
# Aylward , Stephen , Kitware, Inc.
# Batmanghelich , Kayhan , MIT
# Bengali , Salma , SCI Institute
# Blumenfeld , Morry , EAB
# Budin , Francois , UNC
# Cates , Joshua , SCI Institute
# Cavelier , German , NIH-NIMH
# Cevidanes , Lucia , University of Michigan
# Chauvin , Laurent , Brigham and Womens Hospital
# Dalca , Adrian , MIT
# Datar , Manasi , SCI Institute
# Fedorov , Andriy , Harvard Medical School
# Fillion-Robin , Jean-Christophe , Kitware Inc.
# Finet , Julien , Kitware Inc.
# Fishbaugh , James , SCI Institute
# Gao , Yi , BWH
# Gardner , Greg , SCI Institute
# Gerig , Guido , SCI Institute
# Grethe , Jeffrey , University of California, San Diego
# Haehn , Daniel , Boston Childrens Hospital
# Hata , Noby , BWH
# Ibanez , Luis , KITWARE Inc.
# Iftekahruddin , Khan , Old Dominion University
# Irimia , Andrei , University of California, Los Angeles
# Johnson , Chris , EAB
# Johnson , Hans , The University of Iowa
# Kaiser , Adrien , UNC
# Kapur , Tina , Harvard Medical School
# Karasev , Peter , Univ of Alabama at Birmingham
# Kato , Takahisa , Brigham and womens hospital
# Kikinis , Ron , SPL, BWH
# Kochis , Donna , Kitware
# Kolesov , Ivan , Univ of Alabama at Birmingham
# Kumar , Sunil , Washington University in St. Louis
# Kumekawa , Miki , Brigham Womens Hospital Chiba University
# Li , Rui , GE Global Research
# Little , David , University of California, San Diego
# Lorensen , Bill , EAB
# Lowekamp , Bradley ,
# MacLeod , Rob , SCI Institute
# McCormick , Matthew , Kitware, Inc
# Mehrtash , Alireza , Brigham and Womens Hospital
# Miller , Jim , GE Global Research
# Morris , Alan , SCI 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 , Brigham and Womens Hospital, Harvard Medical School
# Rankin , Adam , Queens University
# Ross , James , Brigham and Womens Hospital
# San Jose , Raul , Brigham and Womens Hospital
# Sharma , Anuja , SCI 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
# Toews , Matthew , BWH, Harvard Medical School
# 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 , SCI Institute
# Wang , Kevin , Princess Margaret Hospital
# Wassermann , Demian , Brigham and Womens Hospital
# Welch , David , The University of Iowa
# Wells , William , Brigham and Womens Hospital, HMS
# Whitaker , Ross , SCI Institute
# Yamada , Atsushi , Brigham and Womens Hospital
# Yarmarkovich , Alexander , ISOMIC
# Yoo , Terry , National Library of Medicine, NIH, OHPCC
# Zhu , Liangjia , Univ of Alabama at Birmingham

File:DBP-AF-AHM2013.pdf

2013-01-10T15:53:38Z

Macleod: Slides from AHM 2013 of the AF DBP by Rob MacLeod

Slides from AHM 2013 of the AF DBP by Rob MacLeod

AHM 2013

2013-01-10T15:51:36Z

Macleod: /* Agenda */

Back to [[Events]]

[[Image:PW-SLC2013.png|300px]] [[Image:H2013-Slicer2.png|270px]]

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]''' [[2013_Winter_Project_Week|Project Activities]]
| 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'''
| 
|9-10am: Breakout Session: [[AHM2013-Performance_Evaluation_Tools|Performance Evaluation Tools]] ''(Capitol B)'' [[AHM2013-Robotics|Breakout: Agile Robotics]] ''(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. 
| style="background:#dbf3ff; color:#522200"|[[2013_Winter_Project_Week|Project Presentations]] ''(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'''
|
| Breakout Session: [[AHM2013-IGT|Image Guided Therapy]] ''(Amethyst)'' [[AHM2013-Robotics|Breakout: Agile Robotics]] ''(Capitol A)''
|NA-MIC competitive renewal. [[ClosedSession2013|Closed session for TRD PIs and core personnel]] ''(Amethyst)''
| DBP Update and Future Plans '''10:30-10:55am:''' TBI (Jack Van Horn) '''10:55-11:20am:''' Atrial Fibrillation (Rob MacLeod) '''11:20-11:45am:''' Huntington's Disease (Hans Johnson) '''11:45-12:10pm:''' Head and Neck Cancer (Greg Sharp, [[Media:NAMIC-AHM-2013-01-Sharp.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'''
| style="background:#dbf3ff; color:#522200"|[[2013_Winter_Project_Week|Project Presentations]] ''(Capitol BC)''
| [[AHM2013-Robotics|Breakout: Agile Robotics]] ''(Capitol A)'' [[AHM2013-PatientHierarchy|Breakout: Slicer Patient Hierarchy and DICOM Export]] ''(Amethyst)''
|'''DBP Team Meetings''' ''(Capitol A)'' '''1-2pm:''' [[DBP MGH Head and Neck Cancer]] '''2-3pm:''' [[DBP Utah Atrial Fibrillation]]
| '''1:15-2pm:''' [[AHM2013-Engineering_Updates | Engineering Core: Updates and Future Plans]] '''2-2:30pm''' [[Media:AHM-2013-Extensions.ppt| Extensions]] (Tina Kapur, Jim Miller, Csaba Pinter, Tamas Ungi, Andriy Fedorov) '''2:30-3:00pm:''' 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]] ''(Capitol BC)'' [[AHM2013-PyXNAT|Breakout: PyXNAT]] ''(Capitol A)'' [[AHM2013-Robotics|Breakout: Agile Robotics]] ''(Amethyst)''
|3:15-4pm: Breakout Session: [[AHM2013-Real_World_DICOM|Real World DICOM]] ''(Amethyst)'' 4:15-5pm: [[AHM2013-Simple-ITK|Simple ITK Tutorial]] Amethyst [[AHM2013-Robotics|Breakout: Agile Robotics]] ''(Capitol A)''
|'''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 9:30 AM 1/2/2013
# Ackerman , Michael , National Library of Medicine, NIH, OHPCC
# Aucoin , Nicole , BWH
# Aylward , Stephen , Kitware, Inc.
# Batmanghelich , Kayhan , MIT
# Bengali , Salma , SCI Institute
# Blumenfeld , Morry , EAB
# Budin , Francois , UNC
# Cates , Joshua , SCI Institute
# Cavelier , German , NIH-NIMH
# Cevidanes , Lucia , University of Michigan
# Chauvin , Laurent , Brigham and Womens Hospital
# Dalca , Adrian , MIT
# Datar , Manasi , SCI Institute
# Fedorov , Andriy , Harvard Medical School
# Fillion-Robin , Jean-Christophe , Kitware Inc.
# Finet , Julien , Kitware Inc.
# Fishbaugh , James , SCI Institute
# Gao , Yi , BWH
# Gardner , Greg , SCI Institute
# Gerig , Guido , SCI Institute
# Grethe , Jeffrey , University of California, San Diego
# Haehn , Daniel , Boston Childrens Hospital
# Hata , Noby , BWH
# Ibanez , Luis , KITWARE Inc.
# Iftekahruddin , Khan , Old Dominion University
# Irimia , Andrei , University of California, Los Angeles
# Johnson , Chris , EAB
# Johnson , Hans , The University of Iowa
# Kaiser , Adrien , UNC
# Kapur , Tina , Harvard Medical School
# Karasev , Peter , Univ of Alabama at Birmingham
# Kato , Takahisa , Brigham and womens hospital
# Kikinis , Ron , SPL, BWH
# Kochis , Donna , Kitware
# Kolesov , Ivan , Univ of Alabama at Birmingham
# Kumar , Sunil , Washington University in St. Louis
# Kumekawa , Miki , Brigham Womens Hospital Chiba University
# Li , Rui , GE Global Research
# Little , David , University of California, San Diego
# Lorensen , Bill , EAB
# Lowekamp , Bradley ,
# MacLeod , Rob , SCI Institute
# McCormick , Matthew , Kitware, Inc
# Mehrtash , Alireza , Brigham and Womens Hospital
# Miller , Jim , GE Global Research
# Morris , Alan , SCI 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 , Brigham and Womens Hospital, Harvard Medical School
# Rankin , Adam , Queens University
# Ross , James , Brigham and Womens Hospital
# San Jose , Raul , Brigham and Womens Hospital
# Sharma , Anuja , SCI 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
# Toews , Matthew , BWH, Harvard Medical School
# 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 , SCI Institute
# Wang , Kevin , Princess Margaret Hospital
# Wassermann , Demian , Brigham and Womens Hospital
# Welch , David , The University of Iowa
# Wells , William , Brigham and Womens Hospital, HMS
# Whitaker , Ross , SCI Institute
# Yamada , Atsushi , Brigham and Womens Hospital
# Yarmarkovich , Alexander , ISOMIC
# Yoo , Terry , National Library of Medicine, NIH, OHPCC
# Zhu , Liangjia , Univ of Alabama at Birmingham

AHM 2012

2012-01-13T03:00:28Z

Macleod: /* 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; font-size:125%; color:#0063B6" align="center"
| style="width:5%"| '''Time'''
| style="width:15%" | '''Monday, January 9'''
| style="width:15%" | '''Tuesday, January 10'''
| style="width:15%" | '''Wednesday, January 11'''
| style="width:35%" | '''Thursday, January 12 '''
| style="width:15%" | '''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''': [[AHM2012-DICOM-Huddle|DICOM General Breakout Session]] ''(Amethyst)''
|'''8-10am''': [[AHM2012-Slicer-Overview-and-Migration|Slicer 4: Overview and Migration]] (for Developers) ''(Capitol B)''
|[[AHM2012-3D-US-Slicer-Breakout|Breakout: 3D Ultrasound in Slicer]] (Noby Hata) ''(Amethyst)''
| '''8am''': [[AHM2012:Welcome|Welcome]] '''8:05-9am''': Keynote: iDASH: Integrating Data for Analysis, Anonymization, and Sharing, Lucila Ohno-Machado, PhD, UCSD '''9-10am''': Algorithms Core Update [[media:NAMIC-AHM-MIT-2012.pptx|MIT]], [[media:UNC_AHM2012.pptx‎‎|UNC]], [[media:2012_01_Ross-Utah_Update.pptx|Utah I]], [[media:UtahII-AHM2012-12Min.pptx|Utah II]], [[media:Bu.namic.ahm.final.zip|BU]]
| style="background:#dbf3ff; color:#522200"|8:00-9:00 Update your wiki pages! 9:00 [[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)''
| [[AHM2012-3D-US-Slicer-Breakout|Breakout: 3D Ultrasound in Slicer]] (Noby Hata) ''(Amethyst)''
| '''10:30-11:30am''': Engineering Core Update [[media:AHM2012-Core1b-Engineering-Introduction.pptx|Introduction]], [[media:AHM2012-Core1b-Engineering-EndUserPlatform.ppt|End user platform]], [[Media:AHM2012-Core1b-Engineering-ComputationalPlatform.ppt|Computational platform]], [[media:AHM2012-Core1b-Engineering-DataManagementPlatform.ppt|Data management platform]], [[media:AHM2012-Core1b-Engineering-SoftwareEngineeringAndSoftwareQuality.ppt|Software engineering and software quality]] '''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'''
| style="background:#dbf3ff; color:#522200"|[[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)'' '''1-2pm''': [[2012_Winter_Project_Week_DBP_MGH_Team_Meeting|DBP MGH Head and Neck Cancer]] '''2-3pm''': [[2012_Winter_Project_Week_DBP_Utah_Team_Meeting|DBP Utah Atrial Fibrillation]]
| '''1-1:30pm''': International Research Organizations contribute to NA-MIC '''1-1:30pm''': Best Practices from a Past DBP, Gabor Fichtinger, PhD, Queens University ([[media:Gabor-AHM-2012.pdf|slides]]) '''Current DBP Updates''' '''1:30pm''': Huntington's Disease, Hans Johnson, U Iowa '''1:50pm''': Atrial Fibrillation, Rob MacLeod, CARMA, U of Utah ([[media:DBP-AF-report.pdf|slides]]) ''' 2:10pm''': Traumatic Brain Injury, Jack Van Horn, UCLA '''2:30pm''': Head and Neck Cancer, Greg Sharp, MGH ([[media:2012-01-12-sharp-2.pdf|slides]])
|
|-
| 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)''
| [[2012_Winter_Project_Week_DICOM_RT_Breakout|Breakout: DICOM RT]] ''(Amethyst)''
|'''DBP Team Meetings''' ''(Capitol A)'' '''3-4pm''': [[2012_Winter_Project_Week_DBP_UCLA_Team_Meeting|DBP UCLA Traumatic Brain Injury]] '''4-5pm''': [[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 , Brigham and Womens Hospital
# Blumfield Anthony , Radnostics
# 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
# Gouaillard Alexandre , CoSMo Software
# Grethe Jeffrey , UCSD
# Hata Nobuhiko , BWH
# Iftekharuddin Khan , Old Dominion University
# Irimia Andrei , University of California, Los Angeles
# Johnson Chris , EAB, Chair
# Johnson Hans , University of Iowa
# 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
# Liang Jianming , Arizona State University
# Long Benjamin , Kitware
# Lorensen Bill , Brigham and Womens Hospital
# Lou Yifei , Georgia Tech
# Lowekamp Bradley ,
# 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 , Brigham and Womens Hospital
# Norton Isaiah , Brigham Womens Hospital
# Oguz Ipek , UNC
# Ohno-Machado Lucila , Plenary Speaker
# Pace Danielle , Kitware
# Pai Vinai , NIBIB NIH
# Paniagua Beatriz , University of North Carolina at Chapel Hill
# Patel Pratik , Brainlab
# Perry Daniel , SCI Institute
# Pieper Steve , Isomics, Inc.
# Pierpaoli Carlo , EAB
# Pinter Csaba , Queens University
# Pohl Kilian , UPEN
# Prior Fred , Brigham and Womens Hospital
# Pujol Sonia , BWH
# Roger Gwendoline , UNC
# Ryan William , Mayo Clinic
# San Jose Raul , BWH
# 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
# Toews Matthew , BWH HMS
# Tokuda Junichi , BWH
# 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 Kevin , University Health Network
# Wang Bo , SCI Institute
# Wasem Andrew , CoSMo Software
# 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 Liangjia , Georgia Institute of Technology
# zhu yingxuan , GE Global Research
# Zygmunt Kris , SCI Institute

as of January 12, 2012 1:00 PM MST

AHM 2012

2012-01-13T02:59:37Z

Macleod: /* 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; font-size:125%; color:#0063B6" align="center"
| style="width:5%"| '''Time'''
| style="width:15%" | '''Monday, January 9'''
| style="width:15%" | '''Tuesday, January 10'''
| style="width:15%" | '''Wednesday, January 11'''
| style="width:35%" | '''Thursday, January 12 '''
| style="width:15%" | '''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''': [[AHM2012-DICOM-Huddle|DICOM General Breakout Session]] ''(Amethyst)''
|'''8-10am''': [[AHM2012-Slicer-Overview-and-Migration|Slicer 4: Overview and Migration]] (for Developers) ''(Capitol B)''
|[[AHM2012-3D-US-Slicer-Breakout|Breakout: 3D Ultrasound in Slicer]] (Noby Hata) ''(Amethyst)''
| '''8am''': [[AHM2012:Welcome|Welcome]] '''8:05-9am''': Keynote: iDASH: Integrating Data for Analysis, Anonymization, and Sharing, Lucila Ohno-Machado, PhD, UCSD '''9-10am''': Algorithms Core Update [[media:NAMIC-AHM-MIT-2012.pptx|MIT]], [[media:UNC_AHM2012.pptx‎‎|UNC]], [[media:2012_01_Ross-Utah_Update.pptx|Utah I]], [[media:UtahII-AHM2012-12Min.pptx|Utah II]], [[media:Bu.namic.ahm.final.zip|BU]]
| style="background:#dbf3ff; color:#522200"|8:00-9:00 Update your wiki pages! 9:00 [[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)''
| [[AHM2012-3D-US-Slicer-Breakout|Breakout: 3D Ultrasound in Slicer]] (Noby Hata) ''(Amethyst)''
| '''10:30-11:30am''': Engineering Core Update [[media:AHM2012-Core1b-Engineering-Introduction.pptx|Introduction]], [[media:AHM2012-Core1b-Engineering-EndUserPlatform.ppt|End user platform]], [[Media:AHM2012-Core1b-Engineering-ComputationalPlatform.ppt|Computational platform]], [[media:AHM2012-Core1b-Engineering-DataManagementPlatform.ppt|Data management platform]], [[media:AHM2012-Core1b-Engineering-SoftwareEngineeringAndSoftwareQuality.ppt|Software engineering and software quality]] '''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'''
| style="background:#dbf3ff; color:#522200"|[[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)'' '''1-2pm''': [[2012_Winter_Project_Week_DBP_MGH_Team_Meeting|DBP MGH Head and Neck Cancer]] '''2-3pm''': [[2012_Winter_Project_Week_DBP_Utah_Team_Meeting|DBP Utah Atrial Fibrillation]]
| '''1-1:30pm''': International Research Organizations contribute to NA-MIC '''1-1:30pm''': Best Practices from a Past DBP, Gabor Fichtinger, PhD, Queens University ([[media:Gabor-AHM-2012.pdf|slides]]) '''Current DBP Updates''' '''1:30pm''': Huntington's Disease, Hans Johnson, U Iowa '''1:50pm''': Atrial Fibrillation, Rob MacLeod, U Utah ([[media:DBP-AF-report.pdf|slides]]) ''' 2:10pm''': Traumatic Brain Injury, Jack Van Horn, UCLA '''2:30pm''': Head and Neck Cancer, Greg Sharp, MGH ([[media:2012-01-12-sharp-2.pdf|slides]])
|
|-
| 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)''
| [[2012_Winter_Project_Week_DICOM_RT_Breakout|Breakout: DICOM RT]] ''(Amethyst)''
|'''DBP Team Meetings''' ''(Capitol A)'' '''3-4pm''': [[2012_Winter_Project_Week_DBP_UCLA_Team_Meeting|DBP UCLA Traumatic Brain Injury]] '''4-5pm''': [[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 , Brigham and Womens Hospital
# Blumfield Anthony , Radnostics
# 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
# Gouaillard Alexandre , CoSMo Software
# Grethe Jeffrey , UCSD
# Hata Nobuhiko , BWH
# Iftekharuddin Khan , Old Dominion University
# Irimia Andrei , University of California, Los Angeles
# Johnson Chris , EAB, Chair
# Johnson Hans , University of Iowa
# 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
# Liang Jianming , Arizona State University
# Long Benjamin , Kitware
# Lorensen Bill , Brigham and Womens Hospital
# Lou Yifei , Georgia Tech
# Lowekamp Bradley ,
# 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 , Brigham and Womens Hospital
# Norton Isaiah , Brigham Womens Hospital
# Oguz Ipek , UNC
# Ohno-Machado Lucila , Plenary Speaker
# Pace Danielle , Kitware
# Pai Vinai , NIBIB NIH
# Paniagua Beatriz , University of North Carolina at Chapel Hill
# Patel Pratik , Brainlab
# Perry Daniel , SCI Institute
# Pieper Steve , Isomics, Inc.
# Pierpaoli Carlo , EAB
# Pinter Csaba , Queens University
# Pohl Kilian , UPEN
# Prior Fred , Brigham and Womens Hospital
# Pujol Sonia , BWH
# Roger Gwendoline , UNC
# Ryan William , Mayo Clinic
# San Jose Raul , BWH
# 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
# Toews Matthew , BWH HMS
# Tokuda Junichi , BWH
# 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 Kevin , University Health Network
# Wang Bo , SCI Institute
# Wasem Andrew , CoSMo Software
# 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 Liangjia , Georgia Institute of Technology
# zhu yingxuan , GE Global Research
# Zygmunt Kris , SCI Institute

as of January 12, 2012 1:00 PM MST

File:DBP-AF-report.pdf

2012-01-13T02:42:39Z

Macleod: AF DBP Progress Report slides from Jan 12, 2012 all hands meeting.

AF DBP Progress Report slides from Jan 12, 2012 all hands meeting.

DBP3:Utah:RegSegPipeline

2011-04-23T14:41:41Z

Macleod: /* Pilot Studies on a Registration & Segmentation Pipeline & Workflow */

[[DBP3:Utah| back to DBP3 home]]
= The CARMA DBP: MRI-based study and treatment of atrial fibrillation =
== Pilot Studies on a Registration & Segmentation Pipeline & Workflow ==
Alex Zaitsev, Dominik Meier, Ron Kikinis

=== Background ===
By Rob MacLeod, PI AFib DBP

The Utah group carries out analysis of MRI scans from all patients coming to our clinical with symptoms of Atrial Fibrillation (AF) and continues to conduct regular MRI scans for patients once they undergo treatment by our physicians. The result is over 1000 MRI scans per year that we process using a set of heterogeneous tools. One goal of our collaboration with NAMIC is to explore new tools and capabilities to consolidate and streamline this processing pipeline. The goals of the process vary slightly depending on the timing of the imaging relative to patient care but all involve some combination of image correction, region of interest definition, segmentation of the left atrium (in some cases also right atrium and esophagus), and quantitative evaluation of enhancement in the images, due either to pre-existing fibrosis or post-treatment scar. In many cases, registration is also necessary to compare multiple images from the same patients over time and to compare multiple patients at the same stage of disease progression and treatment.

For more information, please see the following references:

R.S. Oakes, T.J. Badger, E.G. Kholmovski, N. Akoum, N.S. Burgon, E.N. Fish, J.J. Blauer, S.N. Rao, E.V. DiBella, N.M. Segerson, M. Daccarett, J. Windfelder, C.J. McGann, D. Parker, R.S. MacLeod, N.F. Marrouche. “Detection and quantification of left atrial structural remodeling with delayed-enhancement magnetic resonance imaging in patients with atrial fibrillation,” In Circulation, Vol. 119, No. 13, pp. 1758--1767. 2009. http://www.sci.utah.edu/publications/oaks09/Oaks_Circ2009.pdf

C.J. McGann, E.G. Kholmovski, R.S. Oakes, J.J. Blauer, M. Daccarett, N. Segerson, K.J. Airey, N. Akoum, E. Fish, T.J. Badger, E.V. DiBella, D. Parker, R.S. MacLeod, N.F. Marrouche. “New Magnetic Resonance Imaging-Based Method for Defining the Extent of Left Atrial Wall Injury After the Ablation of Atrial Fibrillation,” In Journal of the American College of Cardiology, Vol. 52, No. 15, pp. 1263--1271. Oct 7, 2008. http://www.sci.utah.edu/publications/mcgann08/mcg2008.pdf

C. Mahnkopf, T.J. Badger, N.S. Burgon, M. Daccarett, T.S. Haslam, C.T. Badger, C.J. McGann, N. Akoum, E. Kholmovski, R.S. Macleod, N.F. Marrouche. “Evaluation of the left atrial substrate in patients with lone atrial fibrillation using delayed-enhanced MRI: implications for disease progression and response to catheter ablation,” In Heart Rhythm, Vol. 7, No. 10, pp. 1475--1481. 2010. http://www.sci.utah.edu/publications/mahnkopf10/mahnkopf2010.pdf

We are in the process of making a small set of anonymized test data available for general use and more extensive deidentified data for exclusive use with NAMIC. Please contact me (macleod@sci.utah.edu) for more details.

=== Main processing pipeline ===
To facilitate the workflow, we can place all the automated steps at the beginning and cluster interactive elements at the end. Exception is the cropping step required as input for nonrigid registration. 
1. N4 bias field correction for the MRI (surface coils):
::*'''Input''': MRI_pre and MRI_post, each run separately with the same parameters below; '''Output:''' MRI_pre_n4 and MRI_post_n4
::*'''Module used:''' [http://www.slicer.org/slicerWiki/index.php/Modules:N4ITKBiasFieldCorrection-Documentation-3.6 N4 ITK]; '''Parameters:''' convergence: 1e-5, iterations: 50,40,30,20, shrink factor: 3
::*''Comments:'' a run on entire image gives some benefit that '''may''' be improved with masking: again the dominant intensity dropoff from the surface coil occurs along the chest wall and ribcage. Even if that is not the structure of interest, it is the low-freq. variation the bias correction algorithm is searching for, and masking that out can be counter-productive: via masking we may end up with a smoother image, but the intensity variations removed were not caused by the coil but are actually true signal.
2. affine registration MRA ->MRI (both pre and post)
::*'''Input''': MRI_pre_n4 (fixed) and MRA_pre ; '''Output:''' Xf1_pre_MRA-MRI.tfm"
::*'''Input''': MRI_post_n4 (fixed) and MRA_post ; '''Output:''' Xf2_post_MRA-MRI.tfm"
::*'''Module used:''' [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit]
::*'''Parameters:''' no initialization; samples: 200k, convergence: 1e-5, iterations:
::*''Comments:'' from the example dataset (P1) we infer that the two scans tend to have little initial alignment, hence initialization steps are not recommended. We choose registration parameters such that the chance of the registration making the alignment worse is minimized. Decide in a subsequent review/QC step if we keep the transform or the original pose. The MRA contains the same FOV and has surrounding structures (liver, chest, spine etc) visible also, despite lower intensities. A global affine is thus not necessarily going to benefit from masking the heart, unless the relative motion of the heart becomes the dominant reason for misalignment. We tried masking with both BrainsFit and RobustMultires modules. Both failed to provide better alignment with masking.
3. registration post -> pre: phase 1: AFFINE
::*'''Input''': MRI_pre_n4 (fixed) and MRI_post_n4 (moving) ; '''Output:''' Xf3_pre-post_affine.tfm
::*'''Module used:''' [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit]
::*'''Parameters:''' DOF: rigid+similarity+affine (possibly rigid only); initialization: Moments align ; samples: 200k, convergence: 1e-5, iterations:
::*''Comments:'' done on the entire image. The surrounding structures are useful in constraining the solution transform and should provide a more robust behavior. Cropping down to the cardiac only ROI is deferred to the nonrigid registration in phase 2. The inferior-superior FOV can differ, e.g. how much of the liver is included. If the two exams differ significantly (>30%) in that content, the above affine could fail and a prior cropping step is then suggested to better match image content before registration. Resampling to isotropic voxel size at this stage is also advantageous but will generate very large files > 100MB due to the full FOV.
4. Cropping to VOI:
::*'''Input''': MRI_pre_n4 (fixed) and MRI_post_n4 (moving) ; '''Output:''' MRI_pre_n4_cropped, MRI_post_n4_cropped
::*'''Module used:''' [http://www.slicer.org/slicerWiki/index.php/Modules:CropVolume-Documentation-3.6 Crop Volume]
::*''Comments:'' the [http://www.slicer.org/slicerWiki/index.php/Modules:VolumeRendering-Documentation-3.6 volume rendering module] may help in obtaining a good cropping ROI. Because of the high contrast, the MRA provides a good source for volume rendering.
5. registration post -> pre: phase 2: nonrigid / BSPLINE
::*'''Input''': MRI_pre_n4_cropped (fixed) and MRI_post_n4_cropped (moving) ; '''Output:''' Xf4_pre-post_BSpline.tfm"
::*'''Module used:''' [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit] or [http://www.slicer.org/slicerWiki/index.php/Modules:CMTK CMTK]
::*'''Parameters:''' DOF: BSpline only; initialization: Xf3_pre-post_affine.tfm ; samples: 200k, convergence: 1e-5, iterations:
::*''Comments:'' crop to volume of interest: [http://www.slicer.org/slicerWiki/index.php/Modules:CropVolume-Documentation-3.6 CropVolume module], use ''Resample to isotropic voxelsize'' option.
6. resample MRA: apply above BSpline to the pre MRA
::*'''Input Volume''': MRA_post_n4_cropped
::*'''Input Transform''': above Xf4_pre-post_BSpline.tfm; '''Output Volume''': MRA_post_n4_cropped_Xf4
::*'''Module used:''' [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleScalarVectorDWIVolume-Documentation-3.6 ResampleScalarVectorDWIVolume]
::*'''Parameters:''' output-to-input box checked, interpolation: linear
7. ROI definition (manual box ROI or automated via atlas)
::*'''Module used:''' [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit] or [http://www.slicer.org/slicerWiki/index.php/Modules:CMTK CMTK]
8. segmentation of LA from MRA -> inner wall
::*'''Module used:''' [http://www.slicer.org/slicerWiki/index.php/Modules:RobustStatisticsSeg-Documentation-3.6 Robust Statistics module] or [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor: thresholding] for thresholding within [http://www.slicer.org/slicerWiki/index.php/Modules:CMTK CMTK]
::*''Comments:'' as a dynamic image the MRA contains significant spread and likely requires interactive segmentation/thresholding to yield a satisfactory LA volume. For validation/visualization, use the :[http://www.slicer.org/slicerWiki/index.php/Modules:Volumes-Documentation-3.6 Volumes] thresholding option within ''Display'' tab, use ''iron'' colormap & low alpha setting to check for ventricular wall borders. (see figures below)
9. LA wall segmentation
::*'''Module used:''' ''Atrium Cardiac Wall Segmentation'' (Extension Module, no documentation yet, authors: Yi Gao, Behnood Gholami, Allen Tannenbaum)
10. segmentation of enhancement
::*'''Module:''' [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor: thresholding]
::*'''alternative Module:''' [http://wiki.na-mic.org/Wiki/index.php/Projects:AblationScarSegmentation AblationScarSegmentation]
::*''Comments:'; operate only on ROI within LA wall. Based on proper intensity statistics. An atlas-based set of intensity distributions may be more meaningful here than a simple Otsu, because both amount and location of enhancement is unknown and can in theory be 0.

<gallery perrow="4" widths="200px">
Image:DBP3_AFib_LV_overlay_1.jpg| Example contrast MRI with thresholded MRA as color overlay. Registration validation is not trivial: we can in theory use the position of the blood in the MRA relative to the LV wall as registration check, but the MRA itself does not provide a clear boundary at the lower intensities.
Image:DBP3_AFib_LA_overlay_2.jpg|Example contrast MRI with thresholded MRA as color overlay and areas of enhancement marked
Image:DBP3_histogramMRA.png|Histogram of MRA intensities: green = entire FOV, red: cardiac structures only (excl. aorta), which make only 6% of the total image content and thus are unlikely to disturb a registration based on the entire image.
Image:DBP3_Biasfield_masked-unmasked.png|Bias field correction results (N4ITK) with and without masking of the structures of interest. Masking causes a different correction not related to coil sensitivity but rather local image content. Masking is not recommended at this point.

</gallery>

=== Example Cases ===
* [[Media:AFib_Example_P1_Data.zip|Example Case P1 : pre-post N4 bias corregtion, registration, LA segmentation]]

Event:2011-04-UtahDBP-Training

2011-04-20T23:48:08Z

Macleod: /* Agenda */

=Slicer Hands-on Training for the UTAH CARMA Team=

== Logistics ==

*Date: Friday, April 22, 2011.
*Location: SCI Institute and CARMA center, Salt Lake City, Utah

== Agenda ==
* 09.30-11.00 Slicer tutorial for the Afib project (Ron Kikinis) and review of current Afib processing:Warnock Engineering Building Room 2570D, the Bioengineering Conference Room.
* 11.00-11.15 Break and Transfer to the CARMA Center
* 11.15-12.30 Private meeting with DBP engineers about image processing for Afib in Slicer: discuss strategy for integrating new capabilities into Slicer (Dillon Lee, Josh Cates, Josh B., Allen Butler, Alan Morris, Danny Perry, Greg Gardner, Rob MacLeod).
* 12:30-1:45 Lunch
* 2:00 SCI Distinguished Seminar Series Lecture: Rai Winslow, Warnock Engineering Building (Room TBD).
[[Events#2011|Back to Events 2011]]

Event:2011-04-UtahDBP-Training

2011-04-17T14:08:48Z

Macleod: /* Slicer Hands-on Training for the UTAH Afib Team */

=Slicer Hands-on Training for the UTAH CARMA Team=

== Logistics ==

*Date: Friday, April 22, 2011.
*Location: SCI Institute and CARMA center, Salt Lake City, Utah

== Agenda ==
* 09.30-11.00 Slicer tutorial for the Afib project (Ron Kikinis) and review of current Afib processing: SCI Institute E&S Conference Room
* 11.00-11.15 Break and Transfer to the CARMA Center
* 11.15-12.30 Private meeting with DBP engineers about image processing for Arib in Slicer: discuss strategy for integrating new capabilities into Slicer (Dillon Lee, Josh Cates, Josh B., Allen Butler, Danny Perry, Greg Gardner, Rob MacLeod).
* 12:30-1:45 Lunch
* 2:00 SCI Distinguished Seminar Series Lecture: Rai Winslow, Warnock Engineering Building (Room TBD).
[[Events#2011|Back to Events 2011]]

People

2011-01-13T21:22:40Z

Macleod: /* Personnel at least partially funded by NA-MIC */

== Personnel at least partially funded by NA-MIC ==

#Leadership Core
## [[User:Kikinis|Ron Kikinis]], Harvard (BWH SPL) PI
## [[User:Naucoin|Nicole Aucoin]], Harvard (BWH SPL)
## Wendy Plesniak, Harvard (BWH SPL)
## [[User:Marianna|Marianna Jakab]], Harvard (BWH SPL)
## [[User:Mastrogiacom|Katie Mastrogiacomo]], Harvard (BWH SPL)
# Algorithms Core
## [http://www.cs.utah.edu/~whitaker/ Ross Whitaker], Utah PI
## [http://www.sci.utah.edu/~gerig/ Guido Gerig], Utah
## [[Eric_Grimson|Eric Grimson]], MIT (CSAIL)
## [[Polina_Golland|Polina Golland]], MIT (CSAIL) PI
## [[User:Styner|Martin Styner]], UNC PI
## [http://www.ece.gatech.edu/faculty/fac_profiles/bio.php?empno=502435 Allen Tannenbaum], Georgia Tech, PI
## [http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=56 Bruce Fischl], Ph.D, Harvard (MGH)
## [[User:Gcasey|Casey Goodlett]], Utah
## Preston T. Fletcher, Utah
## Ran Tao, Utah
## [[User:FernD|Fern DeOliveira]], MIT CSAIL
## Ipek Oguz, UNC
## Vandana Mohan, Georgia Tech
# Engineering Core
## [[User:Will| Will Schroeder]], Kitware PI
## [[User:Ibanez|Luis Ibanez]], Kitware
## [http://www.kitware.com/profile/team/hoffman.html/ William Hoffman], Kitware
## [[User:Barre|Sebastien Barre]], Kitware
## [[User:Millerjv|Jim Miller]], GE PI
## [[User:Taox|Xiaodong Tao]], GE
## James Ross, GE
## [[User:Pieper|Steve Pieper]], Isomics PI
## Alex Yarmakovich, Isomics
## [http://nrg.wustl.edu Daniel Marcus], WUSTL
##Mikhail Milchenko, WUSTL
##Kevin Archie, WUSTL
## Arthur W. Toga, UCLA PI
## Nathan Hageman, UCLA
##Celia Cheung, UCLA
## Mark Ellisman, UCSD PI
## Jeff Grethe, UCSD
## Marco Ruiz, UCSD
# Driving Biological Problems (DBP)
## [http://www.sci.utah.edu/~macleod/ Rob MacLeod], University of Utah, PI DBP #1 Atrial Fibrillation
## [http://www.cisst.org/~gabor/ Gabor Fichtinger], Queen's University, PI
## [http://www.mrn.org/principal-investigators/h-jeremy-bockholt Jeremy Bockholt], The Mind Institute, PI
## [http://www.med.unc.edu/psych/directories/hazlett.htm/ Heather Cody Hazlett], UNC PI
## [http://lmi.bwh.harvard.edu/~kubicki/ Marek Kubicki], Harvard (BWH) Site PI
##[http://media.cs.queensu.ca/purang/ Purang Abolmaesumi], Queen's University
## [http://imaging.robarts.ca/~dgobbi/ David Gobbi], Queen's University
##Vikal, Queen's University
## Mark Scully, The Mind Institute
## Clement Vachet, UNC
## Rachel Gimpel Smith, UNC
## Gary Long, UNC
##Jorge Alvarado, Harvard (BWH)
##Padmapriya Srinivazan, Harvard (BWH)
##Jennifer Goodrich, Harvard (BWH)
# Service Core
## [[User:Will|Will Schroeder]], Kitware PI
## Zack Galbreath, Kitware
# Training Core
## [[User:Randy|Randy Gollub]], Harvard (MGH) PI
## [[User:SPujol|Sonia Pujol]], Harvard (BWH SPL) co-PI
# Dissemination Core
## [[User:Tkapur|Tina Kapur]], Harvard (BWH SPL) co-PI
## [[User:Pieper|Steve Pieper]], Isomics co-PI
# Management Core
## Rachana Manandhar, Harvard (BWH SPL)
## [[User:Sanjay|Sanjay Manandhar]], Harvard (BWH SPL)

== NA-MIC Collaborators ==
These NA-MIC collaborators are funded under the "Collaboration with NCBC" PAR.
#Nicole Grosland, UIowa
#Vincent Magnotta, UIowa
#Steve Pieper, Isomics
#James Daunais, Wake Forest
#Robert Kraft, Wake Forest
#Chris Wyatt, Virginia Tech
#Kilian Pohl, Harvard (BWH SPL)
#Sandy Wells, Harvard (BWH SPL)
#Kevin Cleary, Georgetown
#Enrique Campos-Nanez, George Washington U.
#Patrick (Peng) Cheng, Georgetown
#Ziv Yaniv, Georgetown
#Nobuhiko Hata, Harvard (BWH)
#Curtis Lisle, KnowledgeVis

==NA-MIC EAB==

Our External Advisory Board members are listed [[EAB|here]].

== NA-MIC alumni ==
* [http://marchingcubes.org Bill Lorensen]
* [[User:Lzollei|Lilla Zollei]], MIT (CSAIL)
* Lauren O'Donnell, MIT (CSAIL)
* [http://people.csail.mit.edu/wanmei/ Wanmei Ou], MIT (CSAIL)
* [[Mahnaz_Maddah|Mahnaz Maddah]], MIT (CSAIL)
* Ramsey Al-Hakim, Georgia Tech
* [[User:Melonakos|John Melonakos]], Georgia Tech
* [[User:Lankton|Shawn Lankton]], Georgia Tech
* [[User:Nain|Delphine Nain]], Georgia Tech
* Xavier Le Faucheur, Georgia Tech
* [[User:Mohan|Vandana Mohan]], Georgia Tech
* Tom Fletcher, Utah
* [http://www.sci.utah.edu/cgi-bin/SCIpersonnel.pl?username=tolga Tolga Tasdizen], Utah
* [http://www.cs.utah.edu/~sbasu/ Saurav Basu], Utah
* Josh Snyder, Harvard (MGH)
* [[User:DavidTuch|David Tuch]], Harvard (MGH)
* [[User:Karthik|Karthik Krishnan]],Kitware
* [http://www.kitware.com/profile/team/cedilnik.html/ Andy Cedilnik], Kitware
* [[User:Mathieu|Mathieu Malaterre]], Kitware
* [http://www.stat.ucla.edu/~dinov/ Ivo Dinov], UCLA
* [[User:MichaelPan|Michael Pan]], UCLA
* Brendan Flaherty, UCSD
* [[User:Adamc|Adam Cohen]], Harvard (BWH PNL)
* [[User:Markd|Mark Dreusicke]], Harvard (BWH PNL)
* Martha Shenton, Harvard (BWH PNL) PI
* [http://lmi.bwh.harvard.edu/~sylvain/ Sylvain Bouix], Harvard (BWH PNL)
* [http://lmi.bwh.harvard.edu/~marc/ Marc Niethammer], Harvard (BWH PNL)
* [http://synapse.hitchcock.org/bios/saykin.shtml Andy Saykin], Dartmouth PI
* Bob Roth, Dartmouth
* [http://synapse.hitchcock.org/bios/flashman.shtml Laura Flashman], Dartmouth
* [http://www.dhmc.org/providers/dhmc_provider_634.html Thomas McAllister], Dartmouth
* Alan Green, Dartmouth
* John West, Dartmouth
* [http://synapse.hitchcock.org/bios/mchugh.shtml/ Tara McHugh], Dartmouth
* [http://synapse.hitchcock.org/bios/pixley.shtml Heather Pixley], Dartmouth
* Stephen Guerin, Dartmouth
* John MacDonald, Dartmouth
* [http://www.bic.uci.edu/faculty/sgpotkin.htm/ Steve Potkin], UCI PI
* [[User:Jfallon|James Fallon]], UCI
* Jessica Turner, UCI
* Martina Panzenboeck, UCI
* David Medina, UCI
* [http://www.ics.uci.edu/~smyth/ Padhraic Smyth], UCI
* [http://www.ics.uci.edu/~sternh/ Hal Stern], UCI
* Diane Highum, UCI
* [http://www.ess.uci.edu/~yu/ Yi Jin], UCI
* Liv Trondsen, UCI
* Fabio Macciardi, Toronto
* [http://www.utpsychiatry.ca/dirsearch.asp?id=130 Jim Kennedy], Toronto
* Aristotle Voineskos, Toronto
* [http://kotaro.naist.jp/~meg/eindex.html Megumi Nakao], NAIST

== "Friends and Family" ==

=== NIH ===

* [[User:Lysterp|Peter M. Lyster]]

=== mBIRN ===

* [[User:Akolasny|Anthony Kolasny]]
* [[User:Dmarcus|Dan Marcus]]
* [[User:Kikinis|Ron Kikinis]]

=== fBIRN ===

* [[User:Kikinis|Ron Kikinis]]

=== IGT ===

* [[User:Ibanez|Luis Ibanez]]
* [[User:Noby| Nobuhiko Hata]]

=== Other ===

People

2011-01-13T21:21:43Z

Macleod: /* Personnel at least partially funded by NA-MIC */

== Personnel at least partially funded by NA-MIC ==

#Leadership Core
## [[User:Kikinis|Ron Kikinis]], Harvard (BWH SPL) PI
## [[User:Naucoin|Nicole Aucoin]], Harvard (BWH SPL)
## Wendy Plesniak, Harvard (BWH SPL)
## [[User:Marianna|Marianna Jakab]], Harvard (BWH SPL)
## [[User:Mastrogiacom|Katie Mastrogiacomo]], Harvard (BWH SPL)
# Algorithms Core
## [http://www.cs.utah.edu/~whitaker/ Ross Whitaker], Utah PI
## [http://www.sci.utah.edu/~gerig/ Guido Gerig], Utah
## [[Eric_Grimson|Eric Grimson]], MIT (CSAIL)
## [[Polina_Golland|Polina Golland]], MIT (CSAIL) PI
## [[User:Styner|Martin Styner]], UNC PI
## [http://www.ece.gatech.edu/faculty/fac_profiles/bio.php?empno=502435 Allen Tannenbaum], Georgia Tech, PI
## [http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=56 Bruce Fischl], Ph.D, Harvard (MGH)
## [[User:Gcasey|Casey Goodlett]], Utah
## Preston T. Fletcher, Utah
## Ran Tao, Utah
## [[User:FernD|Fern DeOliveira]], MIT CSAIL
## Ipek Oguz, UNC
## Vandana Mohan, Georgia Tech
# Engineering Core
## [[User:Will| Will Schroeder]], Kitware PI
## [[User:Ibanez|Luis Ibanez]], Kitware
## [http://www.kitware.com/profile/team/hoffman.html/ William Hoffman], Kitware
## [[User:Barre|Sebastien Barre]], Kitware
## [[User:Millerjv|Jim Miller]], GE PI
## [[User:Taox|Xiaodong Tao]], GE
## James Ross, GE
## [[User:Pieper|Steve Pieper]], Isomics PI
## Alex Yarmakovich, Isomics
## [http://nrg.wustl.edu Daniel Marcus], WUSTL
##Mikhail Milchenko, WUSTL
##Kevin Archie, WUSTL
## Arthur W. Toga, UCLA PI
## Nathan Hageman, UCLA
##Celia Cheung, UCLA
## Mark Ellisman, UCSD PI
## Jeff Grethe, UCSD
## Marco Ruiz, UCSD
# Driving Biological Problems (DBP)
## [http://www.sci.utah.edu/~macleod/ Rob MacLeod, University of Utah, PI DBP #1 Atrial Fibrillation
## [http://www.cisst.org/~gabor/ Gabor Fichtinger], Queen's University, PI
## [http://www.mrn.org/principal-investigators/h-jeremy-bockholt Jeremy Bockholt], The Mind Institute, PI
## [http://www.med.unc.edu/psych/directories/hazlett.htm/ Heather Cody Hazlett], UNC PI
## [http://lmi.bwh.harvard.edu/~kubicki/ Marek Kubicki], Harvard (BWH) Site PI
##[http://media.cs.queensu.ca/purang/ Purang Abolmaesumi], Queen's University
## [http://imaging.robarts.ca/~dgobbi/ David Gobbi], Queen's University
##Vikal, Queen's University
## Mark Scully, The Mind Institute
## Clement Vachet, UNC
## Rachel Gimpel Smith, UNC
## Gary Long, UNC
##Jorge Alvarado, Harvard (BWH)
##Padmapriya Srinivazan, Harvard (BWH)
##Jennifer Goodrich, Harvard (BWH)
# Service Core
## [[User:Will|Will Schroeder]], Kitware PI
## Zack Galbreath, Kitware
# Training Core
## [[User:Randy|Randy Gollub]], Harvard (MGH) PI
## [[User:SPujol|Sonia Pujol]], Harvard (BWH SPL) co-PI
# Dissemination Core
## [[User:Tkapur|Tina Kapur]], Harvard (BWH SPL) co-PI
## [[User:Pieper|Steve Pieper]], Isomics co-PI
# Management Core
## Rachana Manandhar, Harvard (BWH SPL)
## [[User:Sanjay|Sanjay Manandhar]], Harvard (BWH SPL)

== NA-MIC Collaborators ==
These NA-MIC collaborators are funded under the "Collaboration with NCBC" PAR.
#Nicole Grosland, UIowa
#Vincent Magnotta, UIowa
#Steve Pieper, Isomics
#James Daunais, Wake Forest
#Robert Kraft, Wake Forest
#Chris Wyatt, Virginia Tech
#Kilian Pohl, Harvard (BWH SPL)
#Sandy Wells, Harvard (BWH SPL)
#Kevin Cleary, Georgetown
#Enrique Campos-Nanez, George Washington U.
#Patrick (Peng) Cheng, Georgetown
#Ziv Yaniv, Georgetown
#Nobuhiko Hata, Harvard (BWH)
#Curtis Lisle, KnowledgeVis

==NA-MIC EAB==

Our External Advisory Board members are listed [[EAB|here]].

== NA-MIC alumni ==
* [http://marchingcubes.org Bill Lorensen]
* [[User:Lzollei|Lilla Zollei]], MIT (CSAIL)
* Lauren O'Donnell, MIT (CSAIL)
* [http://people.csail.mit.edu/wanmei/ Wanmei Ou], MIT (CSAIL)
* [[Mahnaz_Maddah|Mahnaz Maddah]], MIT (CSAIL)
* Ramsey Al-Hakim, Georgia Tech
* [[User:Melonakos|John Melonakos]], Georgia Tech
* [[User:Lankton|Shawn Lankton]], Georgia Tech
* [[User:Nain|Delphine Nain]], Georgia Tech
* Xavier Le Faucheur, Georgia Tech
* [[User:Mohan|Vandana Mohan]], Georgia Tech
* Tom Fletcher, Utah
* [http://www.sci.utah.edu/cgi-bin/SCIpersonnel.pl?username=tolga Tolga Tasdizen], Utah
* [http://www.cs.utah.edu/~sbasu/ Saurav Basu], Utah
* Josh Snyder, Harvard (MGH)
* [[User:DavidTuch|David Tuch]], Harvard (MGH)
* [[User:Karthik|Karthik Krishnan]],Kitware
* [http://www.kitware.com/profile/team/cedilnik.html/ Andy Cedilnik], Kitware
* [[User:Mathieu|Mathieu Malaterre]], Kitware
* [http://www.stat.ucla.edu/~dinov/ Ivo Dinov], UCLA
* [[User:MichaelPan|Michael Pan]], UCLA
* Brendan Flaherty, UCSD
* [[User:Adamc|Adam Cohen]], Harvard (BWH PNL)
* [[User:Markd|Mark Dreusicke]], Harvard (BWH PNL)
* Martha Shenton, Harvard (BWH PNL) PI
* [http://lmi.bwh.harvard.edu/~sylvain/ Sylvain Bouix], Harvard (BWH PNL)
* [http://lmi.bwh.harvard.edu/~marc/ Marc Niethammer], Harvard (BWH PNL)
* [http://synapse.hitchcock.org/bios/saykin.shtml Andy Saykin], Dartmouth PI
* Bob Roth, Dartmouth
* [http://synapse.hitchcock.org/bios/flashman.shtml Laura Flashman], Dartmouth
* [http://www.dhmc.org/providers/dhmc_provider_634.html Thomas McAllister], Dartmouth
* Alan Green, Dartmouth
* John West, Dartmouth
* [http://synapse.hitchcock.org/bios/mchugh.shtml/ Tara McHugh], Dartmouth
* [http://synapse.hitchcock.org/bios/pixley.shtml Heather Pixley], Dartmouth
* Stephen Guerin, Dartmouth
* John MacDonald, Dartmouth
* [http://www.bic.uci.edu/faculty/sgpotkin.htm/ Steve Potkin], UCI PI
* [[User:Jfallon|James Fallon]], UCI
* Jessica Turner, UCI
* Martina Panzenboeck, UCI
* David Medina, UCI
* [http://www.ics.uci.edu/~smyth/ Padhraic Smyth], UCI
* [http://www.ics.uci.edu/~sternh/ Hal Stern], UCI
* Diane Highum, UCI
* [http://www.ess.uci.edu/~yu/ Yi Jin], UCI
* Liv Trondsen, UCI
* Fabio Macciardi, Toronto
* [http://www.utpsychiatry.ca/dirsearch.asp?id=130 Jim Kennedy], Toronto
* Aristotle Voineskos, Toronto
* [http://kotaro.naist.jp/~meg/eindex.html Megumi Nakao], NAIST

== "Friends and Family" ==

=== NIH ===

* [[User:Lysterp|Peter M. Lyster]]

=== mBIRN ===

* [[User:Akolasny|Anthony Kolasny]]
* [[User:Dmarcus|Dan Marcus]]
* [[User:Kikinis|Ron Kikinis]]

=== fBIRN ===

* [[User:Kikinis|Ron Kikinis]]

=== IGT ===

* [[User:Ibanez|Luis Ibanez]]
* [[User:Noby| Nobuhiko Hata]]

=== Other ===

AHM 2011

2011-01-13T16:12:01Z

Macleod: /* Agenda */

Back to [[Events]]
[[Image:PW-SLC2011.png|300px]]

January 10-14, 2011, Salt Lake City, Utah
== Introduction ==
{| border="00" cellpadding="8" cellspacing="0"
|-
| rowspan="2" align="left" | '''This is the home page for the 2011 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 2011 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 2011 AHM, EAB and Project Week will be held '''January 10-14, 2011''', in '''Salt Lake City''', Utah.
|}

== Dates, Venue, Registration ==
'''Dates:'''
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 13th'''.
* Project Activities will be held rest of the week between '''Monday, January 10th and Friday, January 14th'''.

'''Venue:''' The venue for the meeting is the Sheraton, Salt Lake City, Utah. Please either call the hotel at +801-401-2000 (toll free) and mention the group code "SCI" or book online [http://www.starwoodmeeting.com/StarGroupsWeb/booking/reservation?id=1011029581&key=F0B2E '''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 $119/night + tax and is valid for reservations made until December 9, 2010. After that it is $199/night + tax.

'''Registration:''' Please click [http://www.sci.utah.edu/namic2011registration.html '''here'''] to register online before '''January 3, 2011'''. All participants must a pay registration fee ('''$200''' for AHM only, and '''$450''' for AHM+Project Week), which covers our catering and facilities costs.

'''Meeting Rooms:''' See [http://www.sheratonsaltlakecityhotel.com/floor-plans here] for the floorplan.

== Agenda==
{| border="1" cellpadding="5"
|- style="background:#eeeeee; color:black" align="left"
| style="width:4%" | '''Time'''
| style="width:12%" | '''Monday, January 10'''
| style="width:12%" | '''Tuesday, January 11'''
| style="width:12%" | '''Wednesday, January 12'''
| style="width:32%" | '''Thursday, January 13 '''
| style="width:12%" | '''Friday, January 14'''
|-
| style="background:#eeeeee; color:black"|
| style="background:#ffffff; color:#522200"| '''[[2011_Winter_Project_Week|Project Activities]] ''' [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Canyons)]
| style="background:#dbf3ff; color:#522200"| '''[[2011_Winter_Project_Week|Project Activities]] ''' [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Canyons)]
| style="background:#dbf3ff; color:#522200"| '''[[2011_Winter_Project_Week|Project Activities]] ''' [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Canyons)]
| style="background:#F2E5D3; color:#522200"| '''AHM, EAB''' [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Canyons, Arches, Deer Valley)]
| style="background:#dbf3ff; color:#522200"|'''[[2011_Winter_Project_Week|Project Activities]] ''' [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Canyons)]
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast
| style="background:#dbf3ff; color:black"| Breakfast
| style="background:#F2E5D3; color:black"| Breakfast
| style="background:#dbf3ff; color:black"| Breakfast
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"|8:00-9:00 [[AHM_2011:DBP-Briefing|DBP Briefing]] (Ron Kikinis) [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Deer Valley)] 9:30-10:00 [[AHM_2011:2011TrainingCoreVision|Training Core Strategy Session]] [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Deer Valley)] * Project Work 
| style="background:#dbf3ff; color:black"|Project Work 8-9:30am: [[2011 Winter Project Week:Breakout Multi-Image Engineering|Breakout: Engineering of Multi-Volume Data in Slicer]] [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Arches)] 
| style="background:#F2E5D3; color:black"|'''8:00''' Introduction, [http://www.spl.harvard.edu/~kikinis Ron Kikinis] 
'''8:05-10:00 Roadmap Projects''' 
: 8:05-8:25 Atrial Fibrillation, Rob MacLeod ([[Media:DBP-Afib-1up.pdf|slides (1up)‎]] and [[Media:DBP-Afib-2up.pdf|slides (2up)‎]]) 
: 8:25-8:45 Huntington's Diseases, Hans Johnson ([[Media:20110113_DTI_Intro.pdf|slides]]) 
: 8:45-9:05 Head and Neck Cancer, Greg Sharp ([[Media:AHM2011-DBP3-HN-Cancer.pdf|slides]]) 
: 9:05-9:25 Traumatic Brain Injury, Jack Van Horn 
: 9:25-9:45 Image Guided Therapy, Nobuhiko Hata ([[Media:AHM2011-IGT-Hata-talk.pptx|slides]]) 
| style="background:#dbf3ff; color:black"|Project Review 
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee
| style="background:#dbf3ff; color:black"| Coffee
| style="background:#F2E5D3; color:black"| Coffee
| style="background:#dbf3ff; color:black"| Coffee
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
| style="background:#ffffff; color:black"| '''Vision10'''
| style="background:#dbf3ff; color:black"|[[2011 Winter Project Week:Breakout Slicer|Breakout: Slicer 4 - Looking Forward]] (Steve Pieper, Julien Finet, Jean-Christophe Fillion-Robin) [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Arches)] * Project Work
| style="background:#dbf3ff; color:black"|[[2011 Winter Project Week:Breakout DTI|Breakout: DTI - Next Generation]] (Hans Johnson, C-F Westin) [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Deer Valley)] * Project Work

| style="background:#F2E5D3; color:black"|
'''10:30-12:00: Algorithms''' 
:10:30-10:45 Overview, Ross Whitaker ([[media:NAMIC_AHM_C1_intro_Jan11.ppt‎|slides]]) 
:10:45-11:00 Statistical models of anatomy and pathology, Polina Golland 
:11:00-11:15 Geometric correspondence, Guido Gerig ([[media:NAMIC-AHM-Geom-Registration.ppt‎|slides]]) 
:11:15-11:30 User interactive tools for segmentation, Allen Tannenbaum 
:11:30-11:45 Longitudinal and time-series analysis, Martin Styner ([[media:2011_01_NAMIC_LongTimeSeries.pptx‎|slides]]) 
| style="background:#dbf3ff; color:black"|Project Review
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch
| style="background:#dbf3ff; color:black"| Lunch 
| style="background:#dbf3ff; color:black"| Lunch 
| style="background:#F2E5D3; color:black"| Lunch
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''
| style="background:#dbf3ff; color:black"|1:00 '''Welcome''' Ron Kikinis [[2011_Winter_Project_Week:Segment-a-spine|Segment a spine challenge]] 1:10pm '''Project Introductions''' All Project Leads 
| style="background:#dbf3ff; color:black"|1-2pm: [[2011 Winter Project Week:Breakout Pathology and Longitudinal Followup|Breakout: Pathology and Longitudinal Followup]] (Guido Gerig) [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Deer Valley)] 
2-3pm: [[2011 Winter Project Week:Breakout ShapeWorks|Breakout: Particle Shape Correspondence]] (Martin Styner, Tom Fletcher, Ross Whitaker) (Arches) 
| style="background:#dbf3ff; color:black"|Project Work
| style="background:#F2E5D3; color:black"|

'''1:00-2:30 Engineering''' 
:1:00-1:15 2010 Highlights, Aims, Architecture, Will Schroeder 
:1:15-1:30 End User Platform Slicer 4, Steve Pieper ([[Media:AHM2011-Core1b-Engineering-EndUserPlatform.ppt|slides]]) 
:1:30-1:45 Computational Platform, CLI, Jim Miller ([[Media:AHM2011-Core1b-Engineering-ComputationalPlatform.ppt|slides]]) 
:1:45-2:00 Data Management Platform, Stephen Aylward ([[Media:AHM2011-Core1b-Engineering-DataManagement.ppt|slides]]) 
:2:00-2:15 Software Process, Stephen Aylward 
'''2:30-3:00 Outreach and Training''' (Sonia Pujol)
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee
| style="background:#dbf3ff; color:black"| Coffee
| style="background:#dbf3ff; color:black"| Coffee
| style="background:#F2E5D3; color:black"| Coffee
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''3:00-5:00'''
| style="background:#dbf3ff; color:black"|[[2011 Winter Project Week:Breakout Slicer with Ron|Breakout: Slicer with Ron]] (Ron Kikinis) [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Arches)] 
| style="background:#dbf3ff; color:black"|4:00-5:00 [[2011 Winter Project Week:BreakoutHD_UNC_Utah|Breakout: DTI analysis & longitudinal analysis for HD]] (Hans Johnson, Guido Gerig, Martin Styner) 
| style="background:#dbf3ff; color:black"|Project Work 
| style="background:#F2E5D3; color:black"|[[EAB]] [http://www.sheratonsaltlakecityhotel.com/assets/u/SI_1327_1flr.gif (Deer Valley)] '''3:00-4:00''' Discussion with NA-MIC Leadership '''4:00-5:00''' Closed Session
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''05:00-07:00'''
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|4:30-6:30 [[2011_Winter_Project_Week:Breakout_Slicer#Afternoon_Qt_Loadable_Module_Tutorial|How to write a loadable module]](J2, JC)
| 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:'''

*[[Summer 2011 Tutorial Contest]] Randy Gollub/Sonia Pujol

==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. [[User:Tkapur|Tkapur]] 01:19, 5 January 2011 (UTC)

# Michael Ackerman EAB
# Nicole Aucoin Brigham and Womens Hospital
# Stephen Aylward Kitware
# Dominique Belhachemi University of Pennsylvania
# Josh Blauer, SCI Institute
# Morry Blumenfeld EAB
# Anthony Blumfield Radnostics
# lucile bompard NIRAL
# Francois Budin UNC-NIRAL
# Anna Cariello University of Utah
# Josh Cates SCI Institute
# Micah Chambers UCLA
# Laurent Chauvin Brigham and Womens Hospital
# Min Chen Johns Hopkins University
# Zohara Cohen NIBIB
# Jason Crane UCSF
# Adrian Dalca MIT
# Manasi Datar SCI Institute
# Andriy Fedorov Brigham and Womens Hospital
# Jean-Christophe Fillion-Robin Kitware Inc.
# Julien Finet Kitware Inc.
# Tom Fletcher SCI Institute
# David Fuentes MD Anderson Cancer Center
# Yi Gao Georgia Tech
# Guido Gerig SCI Institute
# Behnood Gholami Georgia Institute of Technology
# Polina Golland MIT
# Randy Gollub Brigham and Womens Hospital
# Alexandre Gouaillard Cosmo Software Inc
# Daniel Haehn UPenn
# Xiang Hao SCI Institute
# Nobuhiko Hata Brigham and Womens Hospital
# Katie Hayes BWH
# Nicholas Herlambang AZE, Ltd.
# ANDREI IRIMIA University of California, Los Angeles
# Hans Johnson University of Iowa
# Chris Johnson EAB
# Peter Karasev Georgia Tech
# Ron Kikinis Brigham and Womens Hospital
# Ivan Kolesov Georgia Tech
# Janet Lainhart University of Utah
# Andras Lasso School of Computing, Queens University
# Gaetan Lehmann Cosmo Software Inc
# Feng Li Robarts Research Institute
# Yinpeng Li UNC
# Curtis Lisle KnowledgeVis, LLC
# Haiying Liu Covidien
# Bill Lorensen EAB
# Rob MacLeod SCI Institute
# Mahnaz Maddah SRI International
# Vincent Magnotta The University of Iowa
# Daniel Marcus Washington University
# Katie Mastrogiacomo Brigham and Womens Hospital
# Joy Matsui University of Iowa
# Dominik Meier Brigham and Womens Hospital
# bjoern menze CSAIL MIT
# Mikhail Milchenko Washington University in St Louis
# James Miller GE Research
# Karol Miller The University of Western Australia
# Zach Mullen Kitware, Inc
# Sandy Napel EAB
# Vladimir Nikonovskiy Physical Sciences, Inc.
# Lauren ODonnell Brigham and Womens Hospital
# Marram Olson
# Danielle Pace Kitware
# Beatriz Paniagua University of North Carolina at Chapel Hill
# David Partyka Kitware
# Godfrey Pearlson EAB
# Steve Pieper Isomics, Inc.
# Carlo Pierpaoli EAB
# Wendy Plesniak BWH
# Kilian Pohl UPenn
# Marcel Prastawa SCI Institute
# Fred Prior EAB
# Sonia Pujol Brigham Womens Hosp., Harvard University
# Martin Rajchl Robarts Research Institute
# Petter Risholm Brigham and Womens Hospital
# Marco Ruiz UCSD
# Will Schroeder Kitware
# Mark Scully University of Iowa
# Anuja Sharma SCI Institute
# Gregory Sharp MGH
# Dinggang Shen UNC-Chapel Hill
# Liao Shu UNC
# Nadya Shusharina MGH
# Martin Styner University of North Carolina
# Padmavathi Sundaram Children's Hospital Boston
# Suares Tamekue Tatuebu Brigham and Womens Hospital
# Allen Tannenbaum Georgia Tech
# Xiaodong Tao Xiaodong Tao
# Junichi Tokuda Brigham and Womens Hospital
# Tamas Ungi Queens University
#Mustafa Uzunbas Rutgers
# Clement Vachet UNC Chapel Hill
# John Van Horn UCLA
# Gopal Veni SCI Institute
# Bo Wang SCI Institute
# Qian Wang UNC
# Demian Wasserman Harvard Medical School
# Sandy Wells Brigham and Womens Hospital
# Carl-Fredrik Westin Brigham and Womens Hospital
# Ross Whitaker SCI Institute
# Alexander Yarmarkovich ISOMIC
# Terry Yoo National Library of Medicine at NIH
# Alex Zaitzev Brigham and Womens Hospital
# Kris Zygmunt SCI Institute

File:DBP-Afib-2up.pdf

2011-01-13T16:11:10Z

Macleod: DBP 1: AFib Slides from NA-MIC AHM 2011 in 2-up format

DBP 1: AFib Slides from NA-MIC AHM 2011 in 2-up format

File:DBP-Afib-1up.pdf

2011-01-13T15:52:27Z

Macleod: Slides from Rob MacLeod presentation at the NA-MIC All Hands Meeting in 1 slide per page format

Slides from Rob MacLeod presentation at the NA-MIC All Hands Meeting in 1 slide per page format

2011 Winter Project Week:Breakout Slicer with Ron

2010-11-18T17:57:35Z

Macleod: /* Attendees */

Back to [[AHM 2011#Agenda| Project Week Agenda]]

'''Moderator: Ron Kikinis'''
=Introduction=
*This is an advanced topic presentation on Slicer abilities. The intention is to familiarize the NA-MIC community with Slicer abilities.
*You have mastered the introductions and you are hungry for more.... :)
**This means that we expect you to at least have worked through the [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training Core Tutorials] before this class.
*Ron and the creators of modules will show you advanced capabilities in Slicer 3.6
=Logistics=
*What: Advanced capabilities in Slicer
*Who: All the new DBP engineers, all the participants new to NA-MIC
*When: Wednesday afternoon: 1pm through 3pm
*Where: Room XXXX

=Data=
<gallery caption="Image data used" widths="200px" heights="200px" perrow="3">
image:Central.xnat.org-Case-40.png|[http://central.xnat.org/app/action/DisplayItemAction/search_element/xnat%3AmrSessionData/search_field/xnat%3AmrSessionData.ID/search_value/CENTRAL_E00893/popup/false/project/IGT_FMRI_NEURO Case 40] from the fMRI neurosurgery data set on central.xnat.org
image:Case40-SPGR.png| T1 Weighted SPGR image
image:Case40-T2Baseline.png|T2 weighted Bzero image derived from the DWI acquisition
image:Case40-T2Flair.png|FLAIR image
image:Case40-SPGRwGD.png|SPGR after injection of Gd
image:Case40-DTI.png|DTI color by orientation overlayed over T2 baseline
</gallery>

=Preliminary Program=
*10 minutes or less per segment
*Comply with [http://www.slicer.org/slicerWiki/index.php/Documentation-Rons-Rules-For-Tools Rons Rules for Tools]

*Registration (Dominik Meier, Hans Johnson)
**Register everything to the SPGR data
***[[Projects:SlicerFAQ:DWI_Registration|basic concept and outline on FAQ]]
***[[Projects:SlicerFAQ:DWI_Registration#Caveats|List of special caveats pertaining to DTI registration and resampling]]
***[[Projects:RegistrationDocumentation:UseCaseInventory:BrainIntraDTI|overview of all DTI cases currently in the registration case library]]
***[[Projects:RegistrationLibrary:RegLib_C27|Similar case with step-by-step instructions, incl. DWI conversion and resampling]]
***[[Projects:RegistrationLibrary:RegLib_C29|Case showing 2-step registration DWI -> T2 -> T1 (direct to T1 fails)]]
***[[Projects:RegistrationLibrary:RegLib_C03|very complex case incl. anisotropy resampling, masking, manual initial alignment]]
**Resample as needed (DTI, T2 Baseline)
*Compareview (Jim Miller)
*Scenesnapshots (Wendy Plesniak, Alex Yarmarkovic)
*Simple measurements and fiducials (Nicole Aucoin)
*Interactive editor (Steve Pieper)
*Fast segmenters: Fast Marching, RSS, GrowCutSegment (Andrey Fedorov, Yi Gao, Harini Veeraraghavan)
** [[Media:AHM2011_CropVolume_FastMarching_demo.tgz|preliminary scene from Andrey (details to be added)]]
*DTI processing (Alex Yarmarkovic, Demian Wasserman)
*Volume Cropping (Andrey Fedorov)
*Keyboard and mouse shortcuts (Steve Pieper)
*Volume Rendering (Yanling Liu/Alex Yarmarkovic)
*EM segmentation (Kilian Pohl)

=Attendees=
#Ron Kikinis
#Steve Pieper
#UCLA DBP Engineer: Andrei Irimia
#Iowa DBP Engineer: Mark Scully
#MGH DBP Engineer:
#Utah DBP Engineer: Josh Cates
#Utah DBP Student: Josh Blauer
#Utah DBP PI: Rob MacLeod
#Utah DBP Student: Chris Gloschat

EngineeringRetreat2010

2010-11-18T17:09:20Z

Macleod: /* Utah */

[[Events|Back to Events]]

'''Goals''': Develop clarity and a plan for this year's work; establish broader strategic vision for the next four NAMIC years.

=Logistics=
* When: November 17-18 (Wednesday and Thursday). Start time: noon Wednesday, end time: early afternoon Thursday
* Where: Boston SPL, 1249 Facility
* Who: Engineering Core leaders and key personnel
* Hotel: Boston Marriott Cambridge, Two Cambridge Center, 50 Broadway, Cambridge, Massachusetts 02142, Phone: 1-617-494-6600

=Agenda=
*Review of current commitments and planned activities
**[[EngineeringRetreat2010/Kitware]]
**GE - Overview of renewal [[Media:Engineering retreat 11-17-2010 - GE.ppt | [ppt]]] [[Media:Engineering retreat 11-17-2010 - GE.pdf | [pdf]]]
**[[EngineeringRetreat2010/Isomics|Isomics]]
**St. Louis
**UCSD
*Review of wishlist from the DBP's
*Discussion of short term goals
*Discussion of long term goals

=Attendees=
#Steve Pieper
#Will Schroeder
#Stephen Aylward
#Jim Miller
#Ron Kikinis
#Alex Yarmarkovich
#Jeff Grethe (18th only - 17th @ Neuroscience/Committee meeting)

=Notes (currently in rough form)=
* Slicer the platform for anybody viewing and analyzing medical imaging data
* Strategizing about long-term NAMIC goals and funding
** The role and importance of long-term, international collaboration
** Long-term governance including consortium, MOU, etc. (federalist model, alternatives)
** The role of DBP: continued engagement vs. periodic cycling (developing solution pipelines)
** Long term scaling, maintenance, support
*** Development team and simultaneous support team
*** Push everything out of the core into modules (thereby distributing support, etc.)
** 510k support for scoped, viewing station
* Review of Core 1b Proposal Plan ([[Media:Engineering retreat 11-17-2010 - GE.ppt|Jim's Slides]])
* Greg Sharp reviewed his requirements
* Discussion of what Slicer "core" means
** Transition into core: what is the process?
*** Control of access to the core via git / gerrit / other processes (e.g., code review using Gerrit)
** Slicer core "bundled" with other capabilities (e.g., neuroscience core)
** How to test Slicer? CLI is covered, GUI is not there yet
** Supported: Core + any bundled algorithms
** Different categories of algorithms? in editor
*** Extensions that add an "effect" to editor
*** Adaptive GUI that changes based on data type, workflow, etc.
** Using CLI in workflow wizard
*** Need to make the wizard easier to use
**** One type of wizard is a "documentation guide" that directs the user what to do
**** Next level is a more formal wizard that controls the GUI
*** Creating workflows by scripting / recording GUI interaction
*** Defining workflow at a high level sequence of steps
*** Controlling "next" / "previous" in workflow; controlling display (after operations); controlling connection/auto update with interactors/widgets.
* Return to DBP review and discussion
** Utah
*** added some extra content related to interaction and histograms
*** An issue was raised: what about storing state in the CLI
** Iowa
*** SEM for MRML
*** Starting Slicer faster (loading modules is most of the delay, put in separate thread)
**** Slite (Slicer Lite)
*** One interesting discussion point: dealing with spatial/temporal scale (e.g., medical image combined with histological image). How to deal with units, GUI, interaction and rendering.
*** Consistent with Engineering Core plans (refer to wiki for further details)
** UCLA
*** File formats
*** DICOM to NRRD converter is the way to go in some cases
** MGH (revisited)
*** Adaptive radiotherapy: adjust plan as tumors shrink? Answer: not something we want to change. Maybe change is swelling occurs.
*** Improved segmentation and visualization tools
*** Monitoring secondary effects post-treatment (e.g., lobe shrinkage)

=Strategy=
* Slicer 3.6.x is in maintenance mode.
** Use it as a target for plug-in development
* New major development efforts are targeted at Slicer 4.
** Intention to stabilize by AHM 2011
* Communication with "Customers" is a top priority.
** For developers: stabilize the Slicer environment. '''Slicer has been a moving target for too long'''.
** For end-users: simplify the user interface, streamline and simplify common workflows
** Support the development of solutions
** We are '''not''' in the "early adopter game" for new tools for developers for the next two years

==Short term goals==
* Targeted for AHM
* Assign owners for each bullet item on this list
===Slicer 3===
*stabilize and [http://www.slicer.org/slicerWiki/index.php/Slicer3:3.6_Final_Issues debug Slicer 3.6]
*stabilize and document extensions and the process leading to them: My code is on NITRC. Now what?

===Slicer 4===
* Rons number 1: Augment scenes and scenesnapshots (see also its counterpart, the [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Download_Data Image Database UI])
** Thumbnails: user selectable toggle: 3d viewer (default), whole frame, red slice viewer, ability to replace thumbnails
** [[Projects:ARRA:miAnnotation:PriorityList|Annotation]]: User-provided description of scenesnapshot/scene (Daniel Haehn)
* Rons number 2: Make load/save easier to understand for new users.
** Single interface to all data sources based on [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerVolumesIODialog.png QSlicerVolumesIODialog].
** Plan and implement minimalist UI design for load
* Rons number 3: Review [http://www.na-mic.org/Bug/view_all_bug_page.php Slicer3 bug tracker] for issues and feature requests - in UI, particular widgets, command line modules, improved transforms/registration... (Steve)
* Rons number 4: Keep [[Projects:ARRA:SlicerUI|Slicer4 Qt port]] on schedule (JF, JC)
* Rons number 5: VTK widgets roadmap. [[WidgetDesign2010|See here for the minutes of the recent vtk widgets retreat]] (Will)
* Implement and package up module templates for developers of interactive modules to get a jump on consistent UXP.(wjp)
* Refine design of slice viewer's control panel to make more compact and quiet. (wjp)
* [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:SceneModule Scene module]: A new module to organize scenes and scenesnapshots
* Update Wiki pages:
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:CMAKESuperbuild CMAKE superbuild with support for extensions and extension dashboards] (Service Core)
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4 Slicer4]
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Developers Slicer4:Developers]
* Create a XML Schema for .mrml to check if a mrml document is 'well-formed' and 'valid'. Automatic generated (error free) parser can then be used for accessing/editing mrml files.
* Bug patches from Slicer 3.6 to Slicer 4

=== Requests from the DBPs ===
==== Utah ====
* need some extend support for DICOM I/O (ITK V.4 may take care of this)
* Deformable image registration (example applications exist in both clinical image management and in experiments) .)
* Tools for image registration, in general, is a big need that we have. Again, examples exist for both clinical and experimental data.
* GUI support for "steerable" segmentation methods like level-set methods, active contours, etc. (e.g. GA Tech's work on left atrium segmentation).
** Workflow
** Interaction widgets
*** Placing fudicials, guides, constraints, walls, sources, sinks, etc.
* "Show me a histogram, let me pick a range from the histogram" and provide means for histogram processing to suggest thresholds.

==== Iowa ====
See [http://www.na-mic.org/Wiki/index.php/DBP3:Iowa Engineering Action Plan]
* Create formal schema for SEM so that xml can be validated.
* Move SEM so that stand alone apps can easily use it
* Improve documentation of how to make SEM compliant programs work under windows with shared libraries.
* Document the many un-documented/partially documented attributes in SEM.
* Make slicer start faster
* When slicer3 is started in a directory, make a quick way to view the data from the current working directory.
* CMake options to download testing data from a URL. (Midas, Xnat, etc.)
* Support (and documentation) for workflows or wizards that can be made up of any number of other modules and that provide help / guidance on usage.
* Slicer compatibility with Sun Grid Engine
* Fiber profile measurement/visualization within Slicer
* CSV files as part of Slicer standards (Paths, variables, group associations, etc)
* A distributed batch processing pipeline that pulls data from and reports data to XNAT while distributing jobs across a cluster
* Refactor DicomToNrrdConverter
Would also like to second these [http://wiki.na-mic.org/Wiki/index.php/EngineeringRetreat2010#Longer_Term_Goals long term goals] that are listed further down:
* Identify standard workflows and allow CLI modules to declare which workflows they should be run within
* Reduce list of available modules when a user declares a field-of-interest (e.g., microscopy researchers should not be shown MRI-specific modules)
* Review all Slicer modules and determine which should be distribute with Slicer and which should be switched to being downloadable
** Determine support policies for Slicer-included modules versus downloadable modules
** Determine testing, documentation, review, and platform requirements to be a Slicer-included module
* extended save: save to local and remote destinations. Make plans for logic components, DB transaction, and UI design.
* Organizing multiple data sets from one subject: time series, image fusion etc.
* Make plans for a new and improved [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor] for slicer4
** Grow Cuts, RSS and fast Marching with volume cropping, integral volume rendering, (limited) GPU acceleration
* Investigate use of a binary mask used with volume rendering to specify non-rectilinear ROIs, to display segmentation results, and to display effects of interactive editing
* Define a "Core" Slicer that can be distributed with InsightApplications repository of ITKv4
** Review Slicer application framework to support modularization and customization
** Two audiences:
*** Create new GUI infrastructure where a simple Interface is created for each application area, e.g. one GUI for Radiologists reading brain MRI, another one for torso CT, ...
*** Simple, Extensible Platform for Developers (for custom apps/interfaces).
* Switch to GIT deferred. Reconsider after the first stable release of Slicer 4.
* Switch to client/server dashboards and take advantage of its benefits
** Each night binaries copied from client machines to Dashboard page/database that manages them
** Ensures Dashboards, builds, releases using common tags/svn#s
** Ensures available binaries include last-successful build, last-release build, and last-nights build.
** Dashboard specifies what should be build on what clients ("CDash@home" or "Client/Server CDash")
* Support scenes containing data that spans multiple scales in time and space
** visualize, indicate correspondence and support interactions with a scene in which the data differ by orders of magnitude and change over time
* Interactive/iterative command-line modules (e.g., tied to a vtkWidget)
* Batch processing (IPython) examples
** includes an algorithm validation framework
* Interact with [http://www.kitware.com/blog/home/post/49 ITKv4] (once released?), [http://commontk.org CTK], [http://nipy.sourceforge.net/software/projects/ NiPy], and other like-minded projects.

==== UCLA ====
* [http://trackvis.org/docs/?subsect=fileformat trackvis file format interoperability]
* [http://www.ncbi.nlm.nih.gov/pubmed/20206274 NIfTI DWI file format interoperability]
* [http://mind.loni.ucla.edu/specification/overview/ LONI MiND Framework]

==== MGH ====
*See planning document: http://wiki.na-mic.org/Wiki/index.php/DBP3:MGH

Big things we definitely need help with:
*Support for overlapping structures
*Improved support for extensions
*Isodose lines for RT dose

Big things we can probably do on our own:
*MRML node for demographics
*MRML node for (generic) deformable transforms
*Better DICOM support

Smaller items
*Pushing our CMake module bug fixes upstream
*Graphics glitches with image blending
*UI for structure names, colors
*Multiple refresh bugs
*Window/level slider issues
*Image reload button

Wishlist
*Display DVH in Slicer
*ITK iterator performance (needs benchmark)
*Margin tools
*Structure boolean operations
*DICOM Network I/O
*Vector field visualization
*Unevely spaced CT
*Dose comparison tools (difference, DTA, gamma index)
*Contour interpolation in editor
*Landmark markup tool

== Longer Term Goals ==
* Identify standard workflows and allow CLI modules to declare which workflows they should be run within
** Perhaps parallel's effort to associate CLI modules with Widgets
* Reduce list of available modules when a user declares a field-of-interest (e.g., microscopy researchers should not be shown MRI-specific modules)
* Simplify how tests are written for loadable modules
* Review all Slicer modules and determine which should be distribute with Slicer and which should be switched to being downloadable
** Determine support policies for Slicer-included modules versus downloadable modules
** Determine testing, documentation, review, and platform requirements to be a Slicer-included module
* DICOM read and write (local and remote) via CTK
* extended save: save to local and remote destinations. Make plans for logic components, DB transaction, and UI design.
* Organizing multiple data sets from one subject: time series, image fusion etc.
* Packaging/Superbuild fixes
** Package for linux
** Windows - clean registry on uninstall
** Mac - .dmg into application folder
* Creation of a [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:DisplayModule Display Module]
* Make plans for a new and improved [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor] for slicer4
** Grow Cuts, RSS and fast Marching with volume cropping, integral volume rendering, (limited) GPU acceleration
* Investigate use of a binary mask used with volume rendering to specify non-rectilinear ROIs, to display segmentation results, and to display effects of interactive editing
* Define a "Core" Slicer that can be distributed with InsightApplications repository of ITKv4
** Review Slicer application framework to support modularization and customization
** Two audiences:
*** Create new GUI infrastructure where a simple Interface is created for each application area, e.g. one GUI for Radiologists reading brain MRI, another one for torso CT, ...
*** Simple, Extensible Platform for Developers (for custom apps/interfaces).
* Switch to GIT deferred. Reconsider after the first stable release of Slicer 4.
* Switch to client/server dashboards and take advantage of its benefits
** Each night binaries copied from client machines to Dashboard page/database that manages them
** Ensures Dashboards, builds, releases using common tags/svn#s
** Ensures available binaries include last-successful build, last-release build, and last-nights build.
** Dashboard specifies what should be build on what clients ("CDash@home" or "Client/Server CDash")
* GUI Testing
** There is now an open-source method for automated testing of Qt-based applications: http://www.paraview.org/Wiki/Testing_design
* Support scenes containing data that spans multiple scales in time and space
** visualize, indicate correspondence and support interactions with a scene in which the data differ by orders of magnitude and change over time
* Infrastructure that supports simultaneous GPU-based volume rendering and GPU-based interactive segmentation methods (vtkWidgets)
* Guidelines and examples for GPU-based algorithms
* Interactive/iterative command-line modules (e.g., tied to a vtkWidget)
* Determine an alternative to Mantis/bug-tracking. We have over 495 bugs.
* Batch processing (IPython) examples
** includes an algorithm validation framework
* Interact with [http://www.kitware.com/blog/home/post/49 ITKv4] (once released?), [http://commontk.org CTK], [http://nipy.sourceforge.net/software/projects/ NiPy], and other like-minded projects.
* Consider ITKv4 module management tools being developed (after they have been released as stable release)
** Documentation prior to code development
** Module-specific dashboards
** forum-style commentaries on modules
* Improve support of Windows platform
** Simplify compilation of Slicer on Windows Machines
** Increase speed and stability of Slicer on Windows Machines
* Change release policy: A Slicer release version must not use/depend on ITK Review. If we do not make this modification then we cannot release Slicer as Debian package anymore.
* Command line module logic redesign
** DOM objects in shared memory
** WriteCLI in all mrml nodes

=See also=
*http://wiki.slicer.org/slicerWiki/index.php/Slicer4
*http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Developers