DBP3:Iowa

Engineering Action Plan

Overview of the project

http://www.na-mic.org/pages/DBP:HD

In Progress / Completed (Reverse Chronological)

• (In Progress: Spring 2011) Write Tutorial for DTIPrep
• (In Progress: Spring 2011) Re-deidentify data subset and post to XNAT for NA-MIC purposes.
• (In Progress: Spring 2011) Identified a bug in Mattes mutual information metric related to multithreading the was affecting BRAINSFit. Working with the ITK community to correct it.
• (Complete: Spring 2011) Process data from raw DICOM data (enhanced DicomToNRRDConverter)
• (Complete: March 2011) Fixed BRAINSTools errors on Windows
• (Complete: Feb 2011) Moved all BRAINS testing data to midas.kitware.com and updated the tests to pull data from there.
• (Complete: Feb 2011) Final approval from the Predict Steering Committee to share data.
• (Complete: Jan 2011) Add testing data suite to DicomToNRRDConverter
• (Complete: Fall 2010) Over 2900 scan sessions collected.

Morphometric Processing

Goals: Have all the documentation and code in place for BRAINS3 to easily be used by the community.

• 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.

• 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.

• 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

Goals: Create a distributed batch processing pipeline that pulls data from and reports data to XNAT while distributing jobs across a cluster.

• 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

Goals: Share a meaningful, fully anonymized subset of the sMRI, fMRI, and DWI Huntington's data.

• (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

Goals: Inform community of the existence of tools and data sets as well as train them on their use.

• 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