2008 Core 1 UNC Utah DTI
From NAMIC Wiki
Home < 2008 Core 1 UNC Utah DTI
Contents
General
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)