DBP3:Iowa

Engineering Action Plan

In Progress / Completed (Reverse Chronological)

• (In Progress: Fall 2010) Write Tutorial for DTIPrep
• (In Progress: Fall 2010) Add testing data suite to DicomToNRRDConverter
• (In Progress: Fall 2010) Process data from raw DICOM data (enhanced DicomToNRRDConverter)
• (In Progress: Fall 2010) 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.

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