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Engineering Action Plan

Overview of the project

In Progress / Completed (Reverse Chronological)

Cross-sectional shape analysis will be performed via an ancillary grant in cooperation with Guido Gerig at Utah

  • (Completed: Feb 2013) Process data from raw DICOM data (enhanced DicomToNRRDConverter)
  • (In Progress: Winter 2012) SPHARM-PDM Slicer3 integration/dissemination
  • (In Progress: Winter 2012) Analyze 225 subjects with between 3-6 longitudinally collected scans including Caudate/Putamen/Thalamus using cross sectional tools.
  • (Completed: Winter 2011) Implemented in ITKv4: Identified a bug in Mattes mutual information metric related to multithreading the was affecting BRAINSFit. Working with the ITK community to correct it. This has been worked around in BRAINS Tools by forcing MI registration metric to be single threaded until the ITK community can correct it.
  • (Complete: Fall 2011) DTI noise estimation, Rician noise filtering
  • (Complete: Fall 2011) DTI pairwise registration (new Slicer module)
  • (Complete: Summer 2011) DTI estimation, property map generation
  • (Complete: Summer 2011) DTIPrep improvement
  • (Complete: Spring 2011) Write Tutorial for DTIPrep
  • (Complete: Spring 2011) Re-deidentify data subset and post to XNAT for NA-MIC purposes. Identified data and we are actively working on creating the data set as of March 2011.
  • (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 BRAINSTools to easily be used by the community.

  • 2011-02-15 (Mark, Dave): Prepare the BRAINSTools Toolkit for public use
    • Improve the consistency of the command line argument processing
    • (Hans Johnson) Improve merging strategies between BRAINSTools that are part of BRAINS3 and BRAINSTools that are part of Slicer3. A combination of git svn should ease the integration of these two platforms. -- This is not as easy as expected, and it is probably not a good use of our time to make this more automated. It will continue to be done manually.
  • 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):
    • Word doc Tutorial updated with visual inspection info
    • Create Media Wiki version of documentation
    • Create PPT presentation for DTIPrep.
  • (Complete: 2013-02-08) Process data from raw DICOM data (enhanced DicomToNRRDConverter)
    • (Complete: 2011-01-30) Add testing data suite to DicomToNRRDConverter
    • (Complete: 2010-12-31) CMake URL data download mechanisms (Look at Titan CMake has examples of this).
    • 2010-12-31 (Clement) DicomToNRRDConverter use of B-Matrix for vb13 data DTI_THP Iowa data.
  • Target 2011-05-01 (Revised: 2011-10-01) (Clement/Mahshid): DTI noise estimation, Rician noise filtering
    • Review status of code to determine how to modularize into stand alone library and executable
    • Include directly into DTIprep:
      • Optional Rician LMMSE image filtering - preprocessing
      • Optional Joint Rician LMMSE image filtering - before DTI creation
  • 2011-06-24 (Clement/Mahshid): DTI QC and motion/eddy current correction (enhanced DTIPrep)
    • Reporting standardization for easier report generation. Use of XML, extended reporting.
    • 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/Mahshid): 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 (Revised: 2011-10-15) (Clement): DTI pairwise registration (new Slicer module)
    • Develop pairwise registration module allowing:
      • Scalar feature (e.g FA) to drive the registration of a DTI image
      • Optional: Direct registration of the DTI image? (DTITK)
    • Slicer3-compatible module currently available on NITRC: DTI-Reg
      • Registration/Warping available via BRAINS (BRAINSFit/BRAINSDemonWarp) and via ANTS (Advanced Normalization Tools)
    • Investigate if both scalars and higher models can both be supported.
    • Optional: 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, alternative would be open source AtlasWorks
  • 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.
  • 2014-08-30 (Dave, Jessica): DTI processing wizard in Slicer
  • 2013-08-30 (Clement): Longitudinal DTI analysis module
    • Create processing pipeline for batch processing a 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
    • SPHARM shape summary tool
    • Statistical Shape Analysis Tools
      • 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
  • 2012-08-01 (Clement/Bea): Add support for particle shape analysis as part of shape pipeline
    • 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.


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.


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


  • DBP: Hans Johnson, DBP engineers Mark Scully and Dave Welch
  • Algo: Martin Styner, DBP engineer Clement Vachet, Mahshid Farzinfar (DTIPrep), Beatriz Paniagua (Shape)
  • Eng: Dan Marcus, Jeff Grethe, Marco Ruiz