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This page contains descriptions and plans for the dMRI framework in Slicer 4

Jan 2011

Outline of plans

Define new infrastructure to allow efficient tractography (Demain, Lauren, Alex)

  • Single ROI selection module
    • Generalization to model hierarchies
  • Labelmap selection module
  • Bundle representation
    • Reduce the memory footprint of bundles. First start, store in memory only the upper or lower triangular section of the matrix

Port the fiducial tractography seeding to new infrastructure (Alex)

Port tensor estimation tools (Demian)

Implement quick and fluid exploration of pre-calculated full-brain tractographies

Cluster interactive exploration, cluster labeling (Lauren)

Fiber laterality module (Lauren)

Define new infrastructure to allow several different representations of diffusivity (ODF, fODF, two-tensor, tensor, etc.)

Schedule until June

Features to be addressed

Draft of a GUI for Fiberbundles and Streamlines
The pull-down choices for each entry are listed, appearance will be similar to the annotation module
  • Porting/profiling of existing functionality (Alex)
    • Getting CLI to a functioning state again (J2/JC)
    • Volumes module including DWI / Tensor
    • Tensor estimation and scalar extraction
    • Tractography seeding (fiducial/labelmap)
    • Tensor Visualization (Basic visualization is priority)
    • Tractography Visualization
    • Displayable manager infrastructure
  • Workflows (Demian)
    • From DWI to full-brain tractography
    • Peritumoral tractography
  • DBP/High-end post-processing modules for tractography (Lauren)
    • Cluster interaction
    • Laterality analysis
    • Tumor distance-transform (Isaiah)
  • "Fluid" tractography exploration (Alex, this will be taken care of after the porting/profiling )
    • Picking of fibers
    • ROI-based selection of fibers
    • Labelmap selection of fibers
  • Usability testing / consultants (Isaiah, Ron, CF, Lauren, Demian)
  • Extraction of statistical indices from a fiber bundle ( e.g.: Mean / std FA, length, ??volume?? )
  • Test-cases for advanced functionality (Lauren/Antonio/Peter/Yogesh)
    • Python support
      • Multi-threading
      • Weave (without SciPy)
      • Fast LAPACK distribution (now comes with Slicer4)
      • Matplotlib (maybe this will come with PySide)
    • CLI Support (Jim Miller?)
      • Diffusion CLI modules passing the data in memory as opposed to the actual file-based data interchange

Plan to meet weekly on Tuesday afternoons, 1249 Boylston.

Proposed Monthly Slicer4 coding sprint:

Tuesdays from 12pm to 4pm, third Tuesday of every month, Boylston 1249, 2nd floor conference room (bring your friends and significant programming others)


Feb 1, Discuss overall plan

Feb 8, Define new infrastructure to allow efficient tractography

Feb 15, Define new infrastructure to allow efficient tractography

Feb 22, Discuss user-interface work flow

Deliverables Feb: Have detailed plan for March and April

Mar 1

  • Getting CLI to a functioning state again (Demian is responsible - J2/JC)
  • Test the CLIs corresponding to (Isaiah)
    • Tensor estimation
    • Tensor Scalar extraction
    • Tractography seeding (label-map)

Mar 8

Mar 15

  • DWI to Full brain tractography workflow (Demian)

Mar 22

Mar 29

Deliverables Mar: Interactive tractography

Apr 5

  • Finsler tractography CLI (Antonio)
  • Basic Diffusion Volume Display: FA and color-by-orientation and Glyphs (Alex)

Apr 12

Apr 19

Apr 26

Deliverables Apr:

May 3

May 10


May 24

May 31

Deliverable May:

June: debug, test

June (AHM),



JJL & WJP tractography workflow/UI discussion

PNL Diffusion MRI Lab Manual