2008 Core 1 UNC Utah DTI

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Time: 1pm-3pm MT, May 21, 2008

Attendees: Martin Styner, Guido Gerig, Casey Goodlett, Tom Fletcher

Agenda: Plan for collaborative tool development in NAMIC, specifically also with focus towards Zhexing Liu's work (new postdoc at UNC).

Tool development

For the end-to-end application use of the Utah atlas based analysis framework, 3 tools will need to be developed, which in part will rely on existing modules from Slicer, UNC and Utah.

DWI/DTI Preparation tool - DTIPrep

  • The tool will allow a "protocol" based execution via parameter files. The parameter files contain all the settings/preferences/options and this file can be created using the tool's GUI
  • This tool will handle the conversion of DICOM data to volumetric image formats (NRRD) using existing ITK-NAMIC classes
  • The tool performs automated quality control, corrects data if possible, possibly rejects parts of the data, and provides a reporting facility. The following functionalities will be supported:
    • Motion correction (using Utah modules)
    • Eddy current correction (using Utah modules)
    • Interpolation of data, e.g. to upinterpolate to isotropic data
    • Quality Control
      • Rejection of Interslice brightness, white or black slice at level of direction images
      • Local plausibility check with reconstructed DTI. Reject direction image if implausable results
      • FA/MD histogram comparison with atlas
      • Local dot product of principal direction with atlas,
      • Full brain tracking to check for possible flips, permutations of direction axes
      • Focus QC on white matter only, segment WM from baseline image via Slicer-itkEMS implementation
  • Furthermore, DTI data is generated (using Slicer/UNC modules), as well as directly derived images, such as FA/MD etc
  • Fltk vs KWWidget: can we use Fltk?

DTI Atlas Building tool

  • This tool computes an unbiased average atlas DTI image from a set of input DTI images
  • Individual steps exist as modules, need to be strung together
  • This provides support only for creating the atlases, tracking within the atlas is a semi-automatic process involving other tools such as Slicer

DTI Image/Atlas analysis tool

  • This tool will provide a series of analysis facilities
    • If deformable registration from Atlas to individual image is not yet present, then this is computed here
    • Applies atlas ROI's or fibertracts to individual images and extracts statistics
    • Maps images into atlas space for voxel based analysis for hypothesis generation
    • GLM supporting group comparisons for fiber and voxel based analysis
  • Several steps here need more research (done by Zhexing)