Difference between revisions of "Iowa-NA-MIC-2010-Kickoff"

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  [[2010-09-Leadership-Brainstroming|Back to 2010 Brainstorming]]
 
  [[2010-09-Leadership-Brainstroming|Back to 2010 Brainstorming]]
 +
[[Events|Back to events page]]
 +
 
=What=
 
=What=
−
Planning the 3-year course:
+
== Planning the 3-year course of the Roadmap project ==
−
*Roadmap project
+
 
−
**What will the DBP engineer work on?
+
===Engineers ===
−
**Is the image data already in hand?
+
*Clement Vachet, DBP engineer, 20% at UNC, working on Iowa DBP, translating NA-MIC technology into use for PREDICT HD
−
*What modules for the NA-MIC Kit will result from this work?
+
*Mark Scully, DBP engineer at Iowa, Mark & Clement will work closely together, both will attend engineering tcons
−
*Outreach
+
*Two major areas: DTI processing and shape analysis
−
**Tutorial(s) on the wiki
+
*Marco Ruiz,  integration of XNAT with GridWizard to allow XNAT pipeline access to external computational resources
−
**Presentation at a DBP conference for year 2. The PI suggested the AAN (American Academy of Neurology) meeting in April 21-28, 2012 New Orleans as a possible venue. See http://www.aan.com/go/am10/education/proposals; Proposals for 2012 meeting are due May 2011.
+
 
−
**Hands-on teaching event for the DBP scientific community for year 3
+
=== Morphometric Processing ===
 +
* 2011-02-15 (Mark Scully):  Prepare the BRAINS3 Toolkit for public use
 +
** Improve the consistency of the command line argument processing
 +
*** Create an XML formal Schema from the SEM model examples
 +
*** Enhance the SEM schema with other optional tags needed for improved documentation
 +
*** Make SEM into it's own External_Add project to ease use by other packages
 +
*** Move internal documentation from https://www.icts.uiowa.edu/confluence/display/BRAINS/Command+line+argument+rules, to the SEM pages section
 +
** Improve merging strategies between BRAINS3Tools that are part of BRAINS3 and BRAINS3Tools that are part of Slicer3.  A combination of git svn should ease the integration of these two platforms.
 +
* 2012-01-15 (Mark Scully): Create documentation for a standard morphometric analysis
 +
* 2013-01-08 (Mark Scully): Create tutorial for full morphometric analysis suitable for basing a DWI based analysis on.
 +
 
 +
=== DTI Processing ===
 +
 
 +
Goals: Tools for a longitudinal analysis pipeline of changes measured by fiber tractography to identify white matter tracts that have strong co-morbid degenerative timelines compared to subcortical degeneration over time. Enable the use of the advanced DTI processing in NA-MIC within PREDICT HD. Specifically, adapt all NA-MIC tools to work as individual external Slicer modules (in part they already exist, but need further work), as well as combine them into a single Slicer DTI processing wizard.
 +
 
 +
Steps/Modules:
 +
* 2010-12-15 (Mark, Joy, UNC Team): Write Tutorial for DTIPrep
 +
** Create Media Wiki version of documentation with screen shots describing how visual inspections are to occur.
 +
** Create PPT presentation for DTIPrep.
 +
* Process data from raw DICOM data (enhanced DicomToNRRDConverter)
 +
** 2010-11-30 (Mark, Joy): Add testing data suite to DicomToNRRDConverter  (Joy to identify, Mark to implement)
 +
** Target 2010-12-31(Mark): CMake URL data download mechanisms (Look at Titan CMake has examples of this). 
 +
** Target 2010-12-31 (Clement): Document how to interpret B-Matrix for Siemens (extration from dicom) on the DicomToNrrd Wiki page
 +
** Target 2010-12-31 (Clement) Investigate DicomToNRRDConverter use of B-Matrix for vb13 data DTI_THP Iowa data.
 +
* Target 2011-03-01 (Clement): DTI noise estimation, Rician noise filtering
 +
** Review status of code to determine how to modularize into stand alone library and executable
 +
** Include directly into DTI-PREP
 +
* 2011-06-24 (Clement): DTI QC and motion/eddy current correction (enhanced DTIPrep)
 +
** Reporting standardization for easier report generation.
 +
** Loading reports so that batch processing mode and gui processing mode allow the same user
 +
** GUI should allow for manual individual rejection of DWI gradients
 +
* 2011-12-31 (Clement/Mark): DTI estimation, property map generation (existing Slicer modules)
 +
** Review and make command line interfaces and make a dictionary of common command line arguments across the tool sets.
 +
** Push DTIProcess tools into full Slicer Modules
 +
* 2011-08-15 (Clement): DTI atlas registration (new Slicer module)
 +
** Investigate if both scalars and higher models can both be supported.
 +
** Investigate DTITK inclusion Slicer3
 +
* 2012-05-01 (Clement): DTI atlas based fiber analysis (new Slicer module)
 +
** Tools need re-writing to make them slicer3 compatible.
 +
* 2012-07-01 (Clement): DTI atlas computation module (new Slicer module)
 +
** NITRC implementation FRAT needs rewrite with new greedy registration methods
 +
* 2012-09-01 (Clement): DWI atlas mapping tool (new Slicer module)
 +
** Need to move to NITRC and convert to Slicer3
 +
* 2013-01-01 (Clement/Mark/Jeff/All): Appropriate reporting of all steps
 +
** Reporting of tool status. Track the OpenProvenance project.
 +
** Use XML so that we can convert of OpenProvenance latter if desired.
 +
* 2013-08-30 (Mark): DTI processing wizard in Slicer
 +
* 2013-08-30 (Clement): Longitudinal DTI analysis module
 +
** Create processing pipeline for
 +
** Batch procesing for running large number of data sets
 +
* 2013-08-30 (Steve Pieper/Kitware/Core 2 involvement): Fiber profile measurement/visualization within Slicer
 +
 
 +
=== Shape Analysis ===
 +
 
 +
Goals: Tools for a longitudinal shape analysis pipeline to identify localized changes in basal ganglia tracts that have strong co-morbid degenerative timelines. Enable the use of the advanced SPHARM & particle shape analysis processing in NA-MIC within PREDICT HD.
 +
 
 +
Steps/Modules:
 +
* 2011-04-01 (Slicer Team/Core2):Sun Grid Engine compatibility
 +
* 2011-04-01 (Clement): Clean up existing tools for deployment at Iowa
 +
** Individual SPHARM tools (exists, needs polishing)
 +
** SPHARM shape summary tool (exists, needs polishing)
 +
** Statistical Shape Analysis Tools (exists, needs polishing)
 +
*** CSV files as part of Slicer standards (Paths, variables, group associations, etc)
 +
* 2012-01-01 (Mark):  Analyze 225 subjects with Cross sectional tools
 +
** With between 3-6 longitudinally collected scans.
 +
** With Caudate/Putamen/Thalamus
 +
* 2013-08-01 (Clement): Add support for particle shape analysis (new Slicer module)
 +
** Target of 2011-01-14:  have feasibility shape analysis done to identify outstanding work that needs to be done.
 +
 
 +
 
 +
=== BatchMake Processing and Grid Wizard ===
 +
* 2011-01-14 (Marco):  Contact BatchMake developers and determine what needs to be done in order to distribute computational load for the analysis of this project.
 +
** 2011-06-24 (Marco): Distribute from local data repositories.
 +
** 2012-06-24 (Marco/Kevin Archie/Tim Olsen): Distribute from XNAT
 +
** 2011-01-14 (Marco/Kevin Archie):  Define mechanism for deploying distributed computations with GridWizard as a backend tool that the end-user never sees.
 +
 
 +
=== Data ===
 +
 
 +
Is the image data already in hand?
 +
 
 +
*Yes. Over 2900 scan sessions collected.  We will need to identify the meaningful subset of this data, get final approval from the Predict Steering Committee for that subset,and then re-deidentify it and post to XNAT for NA-MIC purposes.
 +
* (Target date of 2010-12-10) Identified the FMRI_024 data (77 subjects, 2-3 years longitudinal) as a good candidate data set for collaborative algorithm development platform. This data set has 3 71direction+8B0 DTI data sets, 2 1.0^3 T1 data sets, and a 0.56x0.56x1.4 T2 data set.
 +
** Will likely need to collect clinical data for shape analysis work that includes: (Age, Gender, Dx, Burdon Score, Motor Score).
 +
** Will need to re-de-identify all the data to be used here.
 +
** Will need to run auto-workup for generating Caudate/putamen/hippocampus/thalmus masks.
 +
** Data exchange will be done through XNAT.  including derived data.
 +
* (Target date of 2011-01-14):  Share all DTI_THP to wide NAMIC group for validation of tools being developed.
 +
 
 +
== Outreach ==
 +
*Tutorial(s) on the wiki
 +
*Presentations at HBM, Euro-HD.net, HDSA (The Huntington's Disease Society of America) in year 2
 +
*Hands-on teaching event for the DBP scientific community for year 3
  
 
=Who=
 
=Who=
−
*DBP: Hans Johnson
+
*DBP: Hans Johnson, DBP engineer Mark Scully
 
*Algo: Martin Styner, DBP engineer Clement Vachet
 
*Algo: Martin Styner, DBP engineer Clement Vachet
−
*Eng: Dan Marcus, Jeff Grethe
+
*Eng: Dan Marcus, Jeff Grethe, Marco Ruiz
 +
 
 +
* Iowa Supporting Guests:  Shuhua Wu, Joy Matsui, Ben Rogers, Vince Magnotta
  
 
=When=
 
=When=
−
PROPOSAL:  November 1-2 or November 10-11.
+
* Monday  October 25th, 10:30am - 5:30pm
 +
** 10:30-12:00 Overview of project, and background of PREDICT-HD
 +
** 12:00- 1:00 Lunch
 +
** 1:00- 5:30 Working meeting focused on informatics, computations and processing
 +
**  6:30- 8:30 Dinnner @ One-Twenty-Six
 +
* Tuesday October 26th,  8:00am - 3:30pm
 +
**  8:00-12:00 Working meeting focused on algorithmic development
 +
** 12:00- 1:00 Lunch
 +
**  1:00- 3:30 Finalize timelines
 +
**  3:30- 5:30 Discuss current limitions of XNAT, and determine how to overcome them
 +
* Wednesday October 27th, 9:30am- 3:00pm
 +
**  GridWizard deployment
 +
       
 +
=Where=
 +
The University of Iowa Campus, Meet in W240 Boyd Tower.  The conference room is a short distance away from there in the Iowa Center for Translational Science.
 +
 
 +
Take elevator BW to the second floor, and take two immediate rights.  The conference room shares a wall with the BW elevator shaft.
 +
 
 +
== Travel Information ==
 +
The closest airport to Iowa City is the '''Cedar Rapids / Eastern Iowa Airport (CID)'''
 +
which is about 20 minutes from the hotel.
 +
 
 +
===Airport Shuttle Services===
 +
The easiest way to get from the airport to
 +
Iowa City is via one of the shuttle services:
 +
* [http://www.crshuttle.com/ Airport Shuttle Service]  (Phone: 1-800-725-8460)
 +
* [http://www.limosbyexpress.com/ Airport Express]    (Phone: 319-626-5466)
 +
Both are the same price and easiest to book before travel. The cost is roughly $60 round trip.
 +
 
 +
===Rental Cars===
 +
Rental cars are also available from the Airport. The following companies have desks at the airport
 +
* Avis
 +
** [http://www.avis.com/ Website]
 +
** Toll-Free Phone : 1-800-331-1212
 +
** Local Phone : (319) 366-6418
 +
* Hertz
 +
** [http://www.hertz.com/ Website]
 +
**Toll-Free Phone : 1-800-654-3131
 +
**Local Phone : (319) 365-9184
 +
* National and Alamo
 +
** [http://www.nationalcar.com/ Website]
 +
**Toll-Free Phone : 1-888-826-6890
 +
**Local Phone : (319) 363-0249
 +
*Enterprise
 +
**[http://www.enterprise.com/car_rental/home.do Website]
 +
**Local Phone : (319) 366-5522
 +
 
 +
 
 +
If you have any questions regarding travel, feel free to contact Joe Ekdahl either via e-mail(joe-ekdahl@uiowa.edu) or phone (319-384-3026).
 +
 
 +
== Hotel Information ==
 +
We reserved a block of hotel rooms at Hotel Vetro at a rate of $139. The group code to get this rate is ITK. These rooms will be held at this rate until October 22.
 +
* [http://www.hotelvetro.com/ Hotel Vetro]
 +
**Phone: 800-592-0355
 +
**Address: 201 South Linn Street, Iowa City, Iowa 52240
 +
 
  
−
=Where=
+
Other hotels that are close to the conference site, University of Iowa, and downtown include:
−
The University of Iowa Campus
+
*[http://www.Sheraton.com/IowaCity Sheraton hotel]
 +
**Phone: 319-337-4058
 +
**Address: 210 South Dubuque St, Iowa City, IA 52240
 +
*[http://imu.uiowa.edu/iowahouse/ Iowa House Hotel]
 +
**Phone: 319-335-3513
 +
**Address: 125 North Madison St, Iowa City, IA 52242
 +
 
 +
 
 +
== Meeting Room ==
 +
 
 +
TBD

Latest revision as of 15:08, 27 October 2010

Home < Iowa-NA-MIC-2010-Kickoff
Back to 2010 Brainstorming
Back to events page

What

Planning the 3-year course of the Roadmap project

Engineers

  • Clement Vachet, DBP engineer, 20% at UNC, working on Iowa DBP, translating NA-MIC technology into use for PREDICT HD
  • Mark Scully, DBP engineer at Iowa, Mark & Clement will work closely together, both will attend engineering tcons
  • Two major areas: DTI processing and shape analysis
  • Marco Ruiz, integration of XNAT with GridWizard to allow XNAT pipeline access to external computational resources

Morphometric Processing

  • 2011-02-15 (Mark Scully): Prepare the BRAINS3 Toolkit for public use
    • Improve the consistency of the command line argument processing
    • Improve merging strategies between BRAINS3Tools that are part of BRAINS3 and BRAINS3Tools that are part of Slicer3. A combination of git svn should ease the integration of these two platforms.
  • 2012-01-15 (Mark Scully): Create documentation for a standard morphometric analysis
  • 2013-01-08 (Mark Scully): Create tutorial for full morphometric analysis suitable for basing a DWI based analysis on.

DTI Processing

Goals: Tools for a longitudinal analysis pipeline of changes measured by fiber tractography to identify white matter tracts that have strong co-morbid degenerative timelines compared to subcortical degeneration over time. Enable the use of the advanced DTI processing in NA-MIC within PREDICT HD. Specifically, adapt all NA-MIC tools to work as individual external Slicer modules (in part they already exist, but need further work), as well as combine them into a single Slicer DTI processing wizard.

Steps/Modules:

  • 2010-12-15 (Mark, Joy, UNC Team): Write Tutorial for DTIPrep
    • Create Media Wiki version of documentation with screen shots describing how visual inspections are to occur.
    • Create PPT presentation for DTIPrep.
  • Process data from raw DICOM data (enhanced DicomToNRRDConverter)
    • 2010-11-30 (Mark, Joy): Add testing data suite to DicomToNRRDConverter (Joy to identify, Mark to implement)
    • Target 2010-12-31(Mark): CMake URL data download mechanisms (Look at Titan CMake has examples of this).
    • Target 2010-12-31 (Clement): Document how to interpret B-Matrix for Siemens (extration from dicom) on the DicomToNrrd Wiki page
    • Target 2010-12-31 (Clement) Investigate DicomToNRRDConverter use of B-Matrix for vb13 data DTI_THP Iowa data.
  • Target 2011-03-01 (Clement): DTI noise estimation, Rician noise filtering
    • Review status of code to determine how to modularize into stand alone library and executable
    • Include directly into DTI-PREP
  • 2011-06-24 (Clement): DTI QC and motion/eddy current correction (enhanced DTIPrep)
    • Reporting standardization for easier report generation.
    • Loading reports so that batch processing mode and gui processing mode allow the same user
    • GUI should allow for manual individual rejection of DWI gradients
  • 2011-12-31 (Clement/Mark): DTI estimation, property map generation (existing Slicer modules)
    • Review and make command line interfaces and make a dictionary of common command line arguments across the tool sets.
    • Push DTIProcess tools into full Slicer Modules
  • 2011-08-15 (Clement): DTI atlas registration (new Slicer module)
    • Investigate if both scalars and higher models can both be supported.
    • Investigate DTITK inclusion Slicer3
  • 2012-05-01 (Clement): DTI atlas based fiber analysis (new Slicer module)
    • Tools need re-writing to make them slicer3 compatible.
  • 2012-07-01 (Clement): DTI atlas computation module (new Slicer module)
    • NITRC implementation FRAT needs rewrite with new greedy registration methods
  • 2012-09-01 (Clement): DWI atlas mapping tool (new Slicer module)
    • Need to move to NITRC and convert to Slicer3
  • 2013-01-01 (Clement/Mark/Jeff/All): Appropriate reporting of all steps
    • Reporting of tool status. Track the OpenProvenance project.
    • Use XML so that we can convert of OpenProvenance latter if desired.
  • 2013-08-30 (Mark): DTI processing wizard in Slicer
  • 2013-08-30 (Clement): Longitudinal DTI analysis module
    • Create processing pipeline for
    • Batch procesing for running large number of data sets
  • 2013-08-30 (Steve Pieper/Kitware/Core 2 involvement): Fiber profile measurement/visualization within Slicer

Shape Analysis

Goals: Tools for a longitudinal shape analysis pipeline to identify localized changes in basal ganglia tracts that have strong co-morbid degenerative timelines. Enable the use of the advanced SPHARM & particle shape analysis processing in NA-MIC within PREDICT HD.

Steps/Modules:

  • 2011-04-01 (Slicer Team/Core2):Sun Grid Engine compatibility
  • 2011-04-01 (Clement): Clean up existing tools for deployment at Iowa
    • Individual SPHARM tools (exists, needs polishing)
    • SPHARM shape summary tool (exists, needs polishing)
    • Statistical Shape Analysis Tools (exists, needs polishing)
      • CSV files as part of Slicer standards (Paths, variables, group associations, etc)
  • 2012-01-01 (Mark): Analyze 225 subjects with Cross sectional tools
    • With between 3-6 longitudinally collected scans.
    • With Caudate/Putamen/Thalamus
  • 2013-08-01 (Clement): Add support for particle shape analysis (new Slicer module)
    • Target of 2011-01-14: have feasibility shape analysis done to identify outstanding work that needs to be done.


BatchMake Processing and Grid Wizard

  • 2011-01-14 (Marco): Contact BatchMake developers and determine what needs to be done in order to distribute computational load for the analysis of this project.
    • 2011-06-24 (Marco): Distribute from local data repositories.
    • 2012-06-24 (Marco/Kevin Archie/Tim Olsen): Distribute from XNAT
    • 2011-01-14 (Marco/Kevin Archie): Define mechanism for deploying distributed computations with GridWizard as a backend tool that the end-user never sees.

Data

Is the image data already in hand?

  • Yes. Over 2900 scan sessions collected. We will need to identify the meaningful subset of this data, get final approval from the Predict Steering Committee for that subset,and then re-deidentify it and post to XNAT for NA-MIC purposes.
  • (Target date of 2010-12-10) Identified the FMRI_024 data (77 subjects, 2-3 years longitudinal) as a good candidate data set for collaborative algorithm development platform. This data set has 3 71direction+8B0 DTI data sets, 2 1.0^3 T1 data sets, and a 0.56x0.56x1.4 T2 data set.
    • Will likely need to collect clinical data for shape analysis work that includes: (Age, Gender, Dx, Burdon Score, Motor Score).
    • Will need to re-de-identify all the data to be used here.
    • Will need to run auto-workup for generating Caudate/putamen/hippocampus/thalmus masks.
    • Data exchange will be done through XNAT. including derived data.
  • (Target date of 2011-01-14): Share all DTI_THP to wide NAMIC group for validation of tools being developed.

Outreach

  • Tutorial(s) on the wiki
  • Presentations at HBM, Euro-HD.net, HDSA (The Huntington's Disease Society of America) in year 2
  • Hands-on teaching event for the DBP scientific community for year 3

Who

  • DBP: Hans Johnson, DBP engineer Mark Scully
  • Algo: Martin Styner, DBP engineer Clement Vachet
  • Eng: Dan Marcus, Jeff Grethe, Marco Ruiz
  • Iowa Supporting Guests: Shuhua Wu, Joy Matsui, Ben Rogers, Vince Magnotta

When

  • Monday October 25th, 10:30am - 5:30pm
    • 10:30-12:00 Overview of project, and background of PREDICT-HD
    • 12:00- 1:00 Lunch
    • 1:00- 5:30 Working meeting focused on informatics, computations and processing
    • 6:30- 8:30 Dinnner @ One-Twenty-Six
  • Tuesday October 26th, 8:00am - 3:30pm
    • 8:00-12:00 Working meeting focused on algorithmic development
    • 12:00- 1:00 Lunch
    • 1:00- 3:30 Finalize timelines
    • 3:30- 5:30 Discuss current limitions of XNAT, and determine how to overcome them
  • Wednesday October 27th, 9:30am- 3:00pm
    • GridWizard deployment

Where

The University of Iowa Campus, Meet in W240 Boyd Tower. The conference room is a short distance away from there in the Iowa Center for Translational Science.

Take elevator BW to the second floor, and take two immediate rights. The conference room shares a wall with the BW elevator shaft.

Travel Information

The closest airport to Iowa City is the Cedar Rapids / Eastern Iowa Airport (CID) which is about 20 minutes from the hotel.

Airport Shuttle Services

The easiest way to get from the airport to Iowa City is via one of the shuttle services:

Both are the same price and easiest to book before travel. The cost is roughly $60 round trip.

Rental Cars

Rental cars are also available from the Airport. The following companies have desks at the airport

  • Avis
    • Website
    • Toll-Free Phone : 1-800-331-1212
    • Local Phone : (319) 366-6418
  • Hertz
    • Website
    • Toll-Free Phone : 1-800-654-3131
    • Local Phone : (319) 365-9184
  • National and Alamo
    • Website
    • Toll-Free Phone : 1-888-826-6890
    • Local Phone : (319) 363-0249
  • Enterprise
    • Website
    • Local Phone : (319) 366-5522


If you have any questions regarding travel, feel free to contact Joe Ekdahl either via e-mail(joe-ekdahl@uiowa.edu) or phone (319-384-3026).

Hotel Information

We reserved a block of hotel rooms at Hotel Vetro at a rate of $139. The group code to get this rate is ITK. These rooms will be held at this rate until October 22.

  • Hotel Vetro
    • Phone: 800-592-0355
    • Address: 201 South Linn Street, Iowa City, Iowa 52240


Other hotels that are close to the conference site, University of Iowa, and downtown include:

  • Sheraton hotel
    • Phone: 319-337-4058
    • Address: 210 South Dubuque St, Iowa City, IA 52240
  • Iowa House Hotel
    • Phone: 319-335-3513
    • Address: 125 North Madison St, Iowa City, IA 52242


Meeting Room

TBD

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