Slicer 3.0: Use Cases

1. Slicer 3.0: Use Cases Programmers Week: June 27, 2005 Tina Kapur, Ph.D.

2. Next 10 minutes… • Slicer 3.0 Target Users, Technologies, Applications • 30K foot User Requirements • Current State • Some Use Cases for Diffusion Analysis Module

3. Slicer 3.0 Target: Users, Technologies, Applications • Who are the target users? • Clinical Researchers • Computer Scientists • Software Developers • What technologies do we want to be “best of breed” in? • Visualization • Segmentation • Registration • Diffusion Image Analysis • fMRI Analysis • What applications do we want to specifically provide on top of these technologies? • Image-Editor for Schizophrenia Studies • Tractography

4. What are the “CTQs” (Critical To Quality factors) for target users • Clinical Researchers • Easy to Use, or at least well-documented • Must have cutting-edge algorithms • Must have “manual override” modes (e.g. manual editing…) • Computer Scientists • Easy to add new algorithms • Easy to test new algorithms • Software Developers • Easy to maintain • Easy to extend • Pleasure to program in

5. Some points to ponder… • Cutting-edge or Comprehensive? • How to intra-operate with other packages and not have to re-invent all the functionality in Slicer?

6. Strong user base Substantial software support Algorithms team Current State of Slicer (2.x)

7. Use Cases: What and Why? • Fit with “Extreme Programming” • Traditional method for capturing requirements is to synthesize use cases, system constraints, regulatory constraints etc. into Requirements and Design Documents • Extreme World: document use cases and use these (redundancy and all) to drive development. • Why? • +ve: less lossy process of documenting user needs • -ve: FDA still requires requirements/design docs

8. Use Cases: Diffusion Image Analysis • How were these gathered: • Observation/Discussions with users at NA-MIC workshops (Dartmouth, SLC, BWH, MIT) • Exploring software packages (Slicer,FiberTrack, …)

9. Use Cases: Diffusion Image Analysis • Visual Exploration of Data • Load any DICOM data set with specified conversion protocol • Visualize baseline, gradient directions, and gradient images • Compute/Visualize scalar measures of diffusivity or anisotropy (e.g. FA, ADC, RA, Lattice Index) • Compute/Visualize tensors for an ROI • Adjust parameters and visualize results • Tractography: Connectivity Exploration using Fiber Tracts • Draw tracts on scalar image using manually selected seed points • Include multiple tractography options: deflection, streamlines, stochastic • Draw tracts through a collection of ROIs (e.g. go from region A to B while avoiding C but going through D) • Manually edit and annotate fibers • Cluster fibers into bundles automatically and/or manually • Compute/Visualize cluster characteristics (e.g. mean curvature, mean length, underlying volume, standard deviation) • Define voxel ROIs based on tract locations

10. Use Cases: Diffusion Image Analysis (contd) • Distortion Correction • Eddy current correction • Using field maps to correct spatial distortion from susceptibility artifacts • Output • write out statistics (e.g. mean, std deviation) for a fiber or a bundle • Save (annotated) fiber tracts • Repeat Quantitative Output for multiple datasets (pipeline) • Map activation regions in fMRI to corresponding clusters in DTI (John West, Dartmouth) • Register subject(s) to labeled and annotated FA and tractography atlases in ICBM/MNI space.

11. Use Cases: Image Editor • http://www.na-mic.org/Wiki/index.php/Slicer:Image_Editor

12. End

13. “CTQ” (Critical to Quality) or Success Metrics • Number of user interactions needed (mouse clicks, keyboard strokes) • Ease of identifying the next step (how many “wrong” paths can user take while doing a task) • Progress Communication (progress bars, error messages and warnings)

14. What are typical current uses? • Exploration of a data set • Multiple operations on single-subject data set (eg. Surgical planning) • Clinical studies of Multiple-subject data sets (e.g. Schiz…)