Slicer4:Diffusion

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Introduction

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)
  • Tensor estimation, visualization and scalar extraction
  • Tractography (fiducial/labelmap) and 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?? )

Plan to meet weekly on Tuesday afternoons, 1249 Boylston.

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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

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Mar 1

Mar 8

Mar 15

Mar 22

Mar 29

Deliverables Mar: Interactive tractography

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Apr 5

Apr 12

Apr 19

Apr 26

Deliverables Apr:

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May 3

May 10

May17

May 24

May 31

Deliverable May:

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June: debug, test

June (AHM),

Background

Workflows

JJL & WJP tractography workflow/UI discussion

PNL Diffusion MRI Lab Manual