Difference between revisions of "Slicer4:Diffusion"

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=Introduction=
 
=Introduction=
 
This page contains descriptions and plans for the dMRI framework in Slicer 4  
 
This page contains descriptions and plans for the dMRI framework in Slicer 4  
 +
-------------------------------
 +
==Periodical Meetings==
 +
=== Weekly Meeting ===
 +
Every Tuesday from 3pm to 4pm at 1249 Boylston, 2nd floor conference room (LMI Suite)
  
 +
=== Monthly Slicer4 coding sprint ===
 +
Third Tuesday of every month, from 12pm to 4pm, Boylston 1249, 2nd floor conference room (bring your friends and significant programming others)
  
−
=Jan 2011=
+
Upcoming Tuesdays:
−
==Outline of plans==
+
* June 22nd (exceptional 4th Tuesday meeting)
−
 
+
* March 15th
−
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===
+
=Features to be addressed before the Summer NA-MIC meeting=
 
[[image:Fiberbundles.png|right|thumb|400px|Draft of a GUI for Fiberbundles and Streamlines<br>The pull-down choices for each entry are listed, appearance will be similar to the annotation module]]
 
[[image:Fiberbundles.png|right|thumb|400px|Draft of a GUI for Fiberbundles and Streamlines<br>The pull-down choices for each entry are listed, appearance will be similar to the annotation module]]
  
Line 65: Line 48:
 
** CLI Support (Jim Miller?)
 
** CLI Support (Jim Miller?)
 
*** Diffusion CLI modules passing the data in memory as opposed to the actual file-based data interchange
 
*** Diffusion CLI modules passing the data in memory as opposed to the actual file-based data interchange
 +
-------------------------------
 +
=Schedule until June=
 +
 +
==Jan 2011==
 +
=== Kick-off, First meeting log ===
 +
 +
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
  
−
Plan to meet weekly on Tuesday afternoons, 1249 Boylston.
+
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.)
 
-------------------------------
 
-------------------------------
−
== 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, distribution of responsibilities.
−
-------------------------------
 
−
== Program ==
 
−
Feb 1, Discuss overall plan
 
  
−
Feb 8, Define new infrastructure to allow efficient tractography
+
Feb 8, Review overall plan.
  
−
Feb 15, Define new infrastructure to allow efficient tractography
+
Feb 15, Definition of dependencies. Deadlines for top priority functionalities and some independent tools.
  
−
Feb 22, Discuss user-interface work flow
+
Feb 22, First code sprint.
  
−
Deliverables Feb: Have detailed plan for March and April
+
Deliverables Feb: Have detailed plan for March and April (Done!)
  
 
-------------------------------
 
-------------------------------
  
 
Mar 1
 
Mar 1
−
* Getting CLI to a functioning state again (Demian is responsible - J2/JC)
+
* Getting CLI to a functioning state again (Demian is responsible - J2/JC will do the coding)
 
* Test the CLIs corresponding to (Isaiah)
 
* Test the CLIs corresponding to (Isaiah)
 
** Tensor estimation
 
** Tensor estimation
Line 102: Line 104:
 
Mar 29
 
Mar 29
  
−
Deliverables Mar: Interactive tractography
+
Deliverables Mar: CLI modules for tensor estimation and scalar extraction, tractography seeding. First version of DWI to Full brain tractography workflow
  
 
-------------------------------
 
-------------------------------

Revision as of 16:30, 17 February 2011

Home < Slicer4:Diffusion
Back to Slicer4 Projects

Introduction

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

Periodical Meetings

Weekly Meeting

Every Tuesday from 3pm to 4pm at 1249 Boylston, 2nd floor conference room (LMI Suite)

Monthly Slicer4 coding sprint

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

Upcoming Tuesdays:

  • June 22nd (exceptional 4th Tuesday meeting)
  • March 15th


Features to be addressed before the Summer NA-MIC meeting

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

Schedule until June

Jan 2011

Kick-off, First meeting log

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.)

Feb 1, Discuss overall plan, distribution of responsibilities.

Feb 8, Review overall plan.

Feb 15, Definition of dependencies. Deadlines for top priority functionalities and some independent tools.

Feb 22, First code sprint.

Deliverables Feb: Have detailed plan for March and April (Done!)

Mar 1

  • Getting CLI to a functioning state again (Demian is responsible - J2/JC will do the coding)
  • 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: CLI modules for tensor estimation and scalar extraction, tractography seeding. First version of DWI to Full brain tractography workflow

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

May17

May 24

May 31

Deliverable May:

June: debug, test

June (AHM),

Background

Workflows

JJL & WJP tractography workflow/UI discussion

PNL Diffusion MRI Lab Manual

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