NAMIC Wiki - User contributions [en]

2008 Winter Project Week:fmri var

2008-01-14T14:48:16Z

Tieu: /* References */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:fmri_var.png |thumb|100px |Hierarchical Model]]
|}

__NOTOC__
===Key Investigators===
* BWH: Kinh Tieu

<div style="margin: 20px;">

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

<h1>Objective</h1>

The goal is to construct Bayesian hierarchical models of fMRI activation to account for variation due to run, visit, subject, and site.

</div>

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

<h1>Approach, Plan </h1>

We will test various models with differing hierarchical structure and conditional distributions and compare inferences on the same data under each model.

</div>

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

<h1>Progress</h1>

We have built and tested a basic random effects model for data from each group and each load separately. The variance is largest for run which supports the hypothesis that using percent signal change minimizes overall site and subject variance. We formulated a new hierarchical model which encapsulates responses from both groups and all loads simultaneously, using a mixed effects setup. The advantage of of this new model is that it pools all of the data at once and can perform both the variance components analysis and the group difference estimation at the same time. The model is currently being tested.

</div>

<br style="clear: both;" />

</div>

===References===

2008 Winter Project Week:fmri var

2007-12-20T16:47:00Z

Tieu:

File:Fmri var.png

2007-12-20T16:45:00Z

Tieu:

2008 Winter Project Week:fmri var

2007-12-20T16:44:26Z

Tieu:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:fmri_var.png |thumb|320px|Hierarchical Model]]
|}

__NOTOC__
===Key Investigators===
* BWH: Kinh Tieu

<div style="margin: 20px;">

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

<h1>Objective</h1>

The goal is to construct Bayesian hierarchical models of fMRI activation to account for variation due to run, visit, subject, and site.

</div>

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

<h1>Approach, Plan </h1>

We will test various models with differing hierarchical structure and conditional distributions and compare inferences on the same data under each model.

</div>

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

<h1>Progress</h1>

</div>

<br style="clear: both;" />

</div>

===References===

2008 Winter Project Week:fmri var

2007-12-20T16:31:59Z

Tieu: New page: {| |Return to [[2008_Winter_Project_Week ]] |valign="top"|The Cingulum Bundle Anchor Tract |} __...

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:Case24-coronal-tensors-edit.png |thumb|320px|The Cingulum Bundle Anchor Tract]]
|}

__NOTOC__
===Key Investigators===
* BWH: Kinh Tieu

<div style="margin: 20px;">

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

<h1>Objective</h1>

</div>

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

<h1>Approach, Plan </h1>

</div>

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

<h1>Progress</h1>

</div>

<br style="clear: both;" />

</div>

===References===

2008 Winter Project Week

2007-12-20T16:29:01Z

Tieu: /* All Other Projects */

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

== Projects ==
*2008 Project Week [[2008_Winter_Project_Week_Template|'''Template''']]
*[[2007_Programming/Project_Week_MIT#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]
*Next Project Week is at MIT -- June 23-27, 2008

===DBP Roadmap Projects===
Please note that the first four categories below correspond to four clinical Roadmap application projects that will be pursued in focused parallel tracks at the meeting, each corresponding to a DBP problem.
====[[DBP2:Harvard:Brain_Segmentation_Roadmap|DBP Harvard Roadmap Project: Stochastic Tractography for Velocardio Facial Syndrome (VCFS)]]====
*[[2008_Winter_Project_Week:StochasticTract_Arcuate|Stochastic tractography of the arcuate fasciculus in schizophrenia]] (Marek Kubicki, Tri Ngo, Doug Markant)

====[[DBP2:UNC:Cortical_Thickness_Roadmap|DBP UNC Roadmap Project: Cortical Thickness Measurement for Autism]]====
*[[2008_Winter_Project_Week:Cortical_Thickness|Cortical thickness analysis of pediatric brains]] (Heather Cody Hazlett, Martin Styner, Clement Vachet, Jim Miller)

====[[DBP2:MIND:Roadmap|DBP MIND Roadmap Project: Brain Lesion Analysis in Neuropsychiatric Systemic Lupus Erythematosus]]====
*[[2008_Winter_Project_Week:Lesions|Towards an end to end lesion analysis feature in Slicer3]] (Mark Scully, Jeremy Bockholt, Brad Davis, Marcel Prastawa, Sonia Pujol, Vincent Magnotta)

====[[DBP2:JHU:Roadmap|DBP JHU Roadmap Project: Segmentation and Registration for Robotic Prostate Intervention]]====
#[[2008_Winter_Project_Week:Robotic_Prostate_Interventions | Robotic Prostate Interventions]] (David Gobbi, Csaba Csoma, Junichi Tokuda, Katie Hayes)
#[[2008_Winter_Project_Week:Prostate_Segmentation|Prostate Segmentation]], (Yi Gao, Ponnappan Arumuganainar, John Melonakos, Allen Tannenbaum, Gabor Fichtinger)

===All Other Projects===
# [[2008_Winter_Project_Week_GroupwiseReg | Groupwise Registration and Atlas Building]] (Brad Davis, Serdar Balci, Casey Goodlett)
# [[2008_Winter_Project_Week:MRISC|Joint Segmentation and Classification of MR Images Based on Structure-specific Affine Registration]] (Mert Sabuncu, Kilian Pohl)
# [[2008_Winter_Project_Week:CorPar|Cortical Surface Parcellation]] (Thomas Yeo, Mert Sabuncu)
# [[2008_Winter_Project_Week:Dorsolateral_Prefrontal_Cortex_Segmentation|Dorsolateral Prefrontal Cortex Segmentation]] (Marek Kubicki, Sylvain Bouix, John Melonakos, Brad Davis, Polina Golland)
#[[2008_Winter_Project_Week:Particle_Correspondence_DTI|Incorporating DTI data into entropy-based particle system for cortical correspondence]] (Ipek Oguz, Josh Cates, Tom Fletcher, Martin Styner)
#[[2008_Winter_Project_Week:Population_DTI|Integrating population based DTI tools into NAMIC Kit]] (Casey Goodlett)
#[[2008_Winter_Project_Week:Population_DTI_Application|Application of population based DTI tools to Schizophrenia]] (Casey Goodlett, Marek Kubicki)
#[[2008_Winter_Project_Week:Geodesic_Tractography_Segmentation|Geodesic Tractography Segmentation]], (John Melonakos, Allen Tannenbaum, Marek Kubicki)
#[[2008_Winter_Project_Week:Fluid_Mechanics_Tractography|Fluid Mechanics Based DTI Tractography]] (Nathan Hageman)
#[[2008_Winter_Project_Week:MRMLScenesForExecutionModel |MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
#Unstructured Grids and Mesh Support(Curt, Alex, Steve, Will, Vince, Bob O'Bara)
#[[2008_Winter_Project_Week:PythonSupport |Python Support in Slicer 3]] (Luca, Bryan Smith, Dan Blezek)
#[[2008_Winter_Project_Week:MRMLTransformHardening |Transform hardening in MRML]] (Luca Antiga, Steve Pieper)
#[[2008_Winter_Project_Week:EventBrokerInSlicer3 |Event broker in Slicer3]] (Jim, Steve, Alex Y, Luca, Dan Blezek)
#[[2008_Winter_Project_Week:CPack |CPack]], CTest, CMake infrastructure Improvements(Katie, Steve, Bill Hoffman, Sebastien)
#[[2008_Winter_ProjectWeek:SlicerCookbook | Slicer GUI Style Guide and Cookbook]] (Wendy Plesniak, Sebastien Barre)
#Shape Descriptor Functions for Dendritic Spine Morphometrics and Colon Polyps (Bryan Smith, Padma Sundaram, Martin Styner)
#[[2008_Winter_Project_Week_VolumeRendering|Volume rendering]] (Andy Freudling, Steve Pieper, Grauer)
#[[2008_Winter_Project_Week_VolumeRenderingUsingCuda|Volume rendering using Cuda]] (Andy Freudling, Steve Pieper, Grauer)
#[[2008_Winter_Project_Week:3DWWidgets |3D W Widgets and Picking]] (Will Schroeder, Nicole Aucoin, Curt Lisle, Kiran Shivana)
#[[2008_Winter_Project_Week:OutOfCoreMRML | MRML support for out of core processing with fMRI and DTI as use cases]] (Steve Pieper, Jim Miller, Wendy Plesniak, Alex Yarmakovich, Will Schroeder)
#[[2008_Winter_Project_Week:XNAT_Integration | XNAT Integration]] ([http://www.xnat.org XNAT], [http://www.slicer.org Slicer], [http://www.Xcede.org XCEDE], [http://www.batchmake.org Batchmake]) (Dan Marcus, Steve Pieper, Stephen Aylward, Jeff Grethe, Julien Jomier)
#KWWidgets Roadmap (Sebastien Barre, Wendy Plesniak, Katie Hayes)
#Circuit Annotation Capability (for example drawing arrows above regions that are connected functionally, structurally, etc), (Mark Scully, others)
#Astronomical coordinate system support (Mike Halle, Doug Alan)
#[[2008_Winter_Project_Week:Meshing Techniques into NA-MIC Toolkit|New Meshing Techniques into NA-MIC]] [Univ. of Iowa] (Nicole Grosland, Vince Magnotta)
#[[2008_Winter_Project_Week:Finite Element Meshing into NA-MIC|Meshing Workflow into Slicer]] [Univ. of Iowa] (Nicole Grosland, Vince Magnotta, Kiran Shivana, Steve Pieper, Curt Lisle, Brad Davis)
#[[2008_Winter_Project_Week:SmallAnimalEvalNCI |Evaluating NA-MIC Tools for Small Animal Imaging Workflows]] [NCI] (Curt Lisle, Jack Collins, Killian Pohl)
#[[2008_Winter_Project_Week:GoFigure |GoFigure:High-Level Microscopy Image analysis Application and Algorithms]] [CalTech-Harvard Medical School] (Alex G, Sean Megason, Arnaud Gelas?)
#[[2008_Winter_Project_Week:IGT_IGSTK_Slicer| IGSTK-Slicer]] [Georgetown] (Haiying Liu, Patrick Cheng, Noby Hata, Junichi Tokuda)
#[[2008_Winter_Project_Week:IGT_Intelligent_Surgical_Instrument_Projects| Japanese Intelligent Surgical Instrument Project]] [AIST] (Noby Hata, Chinzei, Hong)
#[[2008_Winter_Project_Week:microslicer_3 | Doing microscopy image analysis with Slicer3]] [The Ohio State University](Kishore Mosaliganti, Raghu Machiraju, Brad Davis,Stephen Aylward, Steve Pieper)
#[[2008_Winter_Project_Week:fmri_image_analysis | fMRI Analysis with Slicer 3]] [The Ohio State University](Firdaus Janoos,Raghu Machiraju, Luis Ibanez,Steve Pieper, Wendy Plesniak)
#[[2008_Winter_Project_Week:Resampling_DTIs_with_Slicer3|Resampling DTIs with Slicer 3]] (Francois Budin, Sylvain Bouix)
#[[2008_Winter_Project_Week:fmri_eeg_analysis | Analyzing fMRI and concurrent EEG with Slicer and SCIRun]] [BWH] (Padma Sundaram)
#[[2008_Winter_Project_Week:fmri_var | Bayesian hierarchical models for fMRI variance components analysis]] (Kinh Tieu)

== Dates.Venue.Registration ==

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

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

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

Please note that this information can also be found [[AHM_2008#Dates.Venue.Registration|here.]]

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

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

Please read the introduction to these events [[Project_Events#Introduction|here]].

=== Agenda===

[[AHM_2008#Agenda|Agenda for AHM 2008 and Project Week]]

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
# [[Engineering:TCON_2007#2007-11-29|November 29, 2007: Kickoff TCON#1 (w/ NA-MIC Engeering Core only) to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-12-06|December 6, 2007: TCON#2 with all participants to Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-12-13|December 13, 2007: TCON#3 with Breakout Session owners to review agendas]]
# [[Engineering:TCON_2007#2007-12-13|December 20, 2007: TCON#4 to discuss outstanding projects and teams]]
# [[Engineering:TCON_2007#2008-01-03|January 3, 2008: TCON#5 to discuss outstanding projects and teams]]
# December 20, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# January 3, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# By December 17, 2008: [[2008_Winter_Project_Week_Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== Previous Project Events ==

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

2007 December Slicer IGT Programming

2007-12-06T14:02:25Z

Tieu: /* Confirmed Attendees */

__NOTOC__
==Dates.Location.Hotels==
December 12-14, 2007
(Scheduled based on: http://www.doodle.ch/participation.html?pollId=a6pt4zn4wydey8kv)

SPL at 1249 Boylston Street, Boston MA. ([http://www.spl.harvard.edu/Directions#Getting_to_1249_Boylston_Street Directions])

Area hotels: [[Boston_Hotels]]

==Goal==
*Continued [[Leadership:SlicerIGT_2007|'''discussion''']] of Slicer IGT infrastructure, applications, and timelines
*Introduce each team's effort in Slicer in the context of IGT
*active funding&future submissions
*on-going technical development
*find unmet needs

=Agenda=
==Wednesday, December 12 ==
'''Theme: Where are we?'''
*12noon: lunch
*12:55pm: Welcome (Ferenc Jolesz)
*1-2pm:
**Slicer: overview of architecture, current status, and future plans (Pieper, Hata)
***History
***Clinical applications
***transition from 2.6 to 3
***resource
**IGSTK: overview of architecture, current status, and future plans (Ibanez, Cheng)
*2-3pm: Setting goals for meeting: Each IGT group present what they want to achieve at this meeting.
**2-2:15 - NA-MIC DBP Queens/JHU Gobbi/Csoma/Kazanzides
**2:15-2:30 - NA-MIC Collaborator Georgetown Cleary/Yaniv
**2:30-2:45 - NCIGT BWH Hata
**2:45-3:00 - Kitware
**3:00-3:15pm - NCIGT CIGL Stoll

*3:15-3:30pm: Coffee Break
*3:30pm Adjourn
*4-6pm (optional) demonstration of Slicer for control and display of MRI scanner (prostate module) @Advanced MRI center, 221 Longwood
**LINK
**LINK

==Thursday, December 13==
'''Morning Theme: Where are we?'''
*9:00am breakfast, start work

*9-1030am Discussion over Demos:
**Stoll (laproscopic ultrasound)
**Hata (Tracking at BWH)
**Yaniv (Tracking at Georgetown)
**Pieper (Volume rendering)

*10:30am: coffee break
*11am: continue work
Review of demos
**which function is cool?
**which functionality has to be shared
**what is the common needs?
**who has those missing functions outside of IGT?

*12:30: lunch
*1:30pm: continue work
'''Afternoon Theme: Where are we going?'''
**Resource shring
**priority tasks
**Hypothetical RO1

*3-4pm: Coffee break (and NA-MIC TCON)
*4:00pm: Plan for Hands on IGT Week
*5pm: Review day and plan for Friday (Hata)
*5:30pm: adjourn

==Friday, December 14==
----
*9:00am: breakfast, work
**Focus group discussion ('''What do we do now?''')
**Report to NCIGT
**Action items
*11:15am-noon: Wrapup/Suggestion to NCIGT PIs (Hata)
*noon: adjourn and head out to group lunch

----

==Confirmed Attendees==
#Noby Hata, BWH (NCIGT)
#Steve Pieper, Isomics - (All Days) (NAMIC, NAC)
#Patrick Cheng, Georgetown (NAMIC Collab)
#Ziv Yanev, Georgetown (NAMIC Collab)
#Kevin Cleary, Georgetown (Wed only) (NAMIC Collab)
#Luis Ibanez, Kitware (NAMIC)
#Sebastien Barre, Kitware (NCIGT)
#Stephen Aylward, Kitware (NCIGT)
#Jeff Stoll (except Thursday), BWH/CIMIT (NCIGT)
#Haiying Liu, BWH (NCIGT)
#Katie Hayes, BWH (NAC)
#Peter Kazanzides (except Friday), JHU (NAMIC Collab)
#Csaba Csoma, JHU (NAMIC/NCIGT Collab)
#Stephen Aylward, Kitware (NAMIC Collab)
#David Gobbi, Queens (NAMIC/NCIGT Collab)
#Tina Kapur,BWH (NAMIC/NCIGT)
#Ron Kikinis, BWH (NAMIC/NCIGT)
#Junichi Tokuda, BWH (NCIGT)
#Raul San Jose, BWH (NAC)
#Ferenc Jolesz, BWH (Wed only) (NCIGT/NAC)

P41-2007-Joint-Retreat

2007-02-02T02:07:06Z

Tieu: /* Participants */

=Joint Retreat =
* What is the objective
**To familiarize the others with the ongoing activties in the respective cores
**To identify opportunities for leverage and augmentation
* Who:
**The MGH Center for Functional Imaging Technologies (CFIT)
**The BWH Neuroimage Analysis Center (NAC)
**Core PI's for the two centers plus not more than 2 people per core
* Where:
**MIT Stata Center, Seminar Room G449 ([[Meeting_Locations:MIT_CSAIL_Star|Patil Conference Room / Kiva]])
* When:
**Monday, Jan. 29, 11am-5pm

=Agenda=
==11.00-12.30 MGH CFIT==
**11.00-11.15 Bruce Rosen, Overview
**11.15-11.40 Bruce Fischl, High resolution anatomical modeling
**11.40-11.55 Larry Wald, High resolution structural and functional MRI
**11.55-12.10 Graham Wiggins, Large-N arrays
**12.10-12.25 David Boas, Optical Imaging
**12.25-12.45 Matti Hamalainen, MEG and mulit-modal inverse problems.
**12.45-01.15 pm Lunch Break

==01.15-02.45 BWH NAC==
**01.15-01.20 Ron Kikinis: [[media:2007-01-29-NAC-Intro.ppt |Overview]]
**01.20-01.35 CF Westin: Diffusion MRI
**01.35-01.50 Sandy Wells: fMRI Informatics
**01.50-02.10 Andrea Mewes: Neonate Imaging
**02.10-02.20 Florin Talos: Computational Neuroanatomy
**02.25-02.35 Michael Halle: Visualization and representation for atlases
**02.35-02.45 Domink Meier: Time Series Analysis PI
**02.45-03.00 Steve Pieper: Status and plans for Slicer3 [[media:Pieper-eng-retreat2007-01-29.ppt | Slides]]

==02.30-03.00 Break==
*03.00-04.00 General Discussion (Sandy Wells, Bruce Fischl)
*04.00-05.00 DTI discussion (Bruce Rosen, Ron Kikinis)

=Participants=
#Ron Kikinis, PI, NAC
#Steve Pieper
#Bruce Fischl
#David Boas
#Larry Wald
#Matti Hamalainen
#Bruce Rosen, PI, CFIT
#Carl-Fredrik Westin
#Juliette Selb
#Lilla Zollei
#Jean Augustinack
#Anna Custo
#Thomas Witzel
#Wanmei Ou
#Florin Talos
#Michael Halle
#Andrea Mewes
#Polina Golland
#Sandy Wells
#Graham Wiggins

P41-2007-Joint-Retreat

2007-01-25T19:55:05Z

Tieu: /* Participants */