Introduction tutorials: Editing process

http://neuroimage.usc.edu/brainstorm/Tutorials

Redactors:

• Francois Tadel: Montreal Neurological Institute

• Elizabeth Bock: Montreal Neurological Institute

Reviewers [current reviewing status]

• Sylvain Baillet: Montreal Neurological Institute [overview 1-14, no proofreading]

• Richard Leahy: University of Southern California [validated 1-19]

• John Mosher: Cleveland Clinic [not started]

• Dimitrios Pantazis: Massachusetts Institute of Technology [validated 1-15]

Expected timeline (2016)

• March: Tutorials #1-#21 (interface and pre-processing)

• April: Tutorials #22-#24 (source estimation and time-frequency)

• May-June: Tutorials #25-#28 (statistics and workflows)

• July-Sept: Cross-validation of the pipeline and the results with MNE, FieldTrip and SPM

• October: Presentation during a satellite meeting at the Biomag 2016 conference

• Nov-Dec: Connectivity tutorial

Tutorial 10: Power spectrum and frequency filters

[CODE]

• Richard, John, Sylvain: Finish the evaluation of the band-pass filters used in Brainstorm
• Francois: Mark with an extended event the time segments that we cannot trust (edge effect)
• Francois: Add warning if recordings are not long enough

[ONLINE DOC]

• Richard, John, Sylvain: Section What filters to apply?

• Richard, John, Sylvain: Section Filters specifications

Tutorial 12: Artifact detection

[ONLINE DOC]

• Beth: Adding examples of the different detection processes. Section Other detection processes

Tutorial 13: Artifact cleaning with SSP

[CODE]

• Francois: Check the length needed to filter the recordings (after finishing #10)
  Section SSP Algorithm

Tutorial 15: Import epochs

[ONLINE DOC]

• Richard, Sylvain, John, Francois: Define recommendations for epoch lengths (after finishing #10)
  Section Epoch length

Tutorial 20: Head modelling

[ONLINE DOC]

• John, Richard, Sylvain: In-depth review of this sensitive tutorial

• John, Richard, Sylvain: Section References

Tutorial 22: Source estimation

[CODE]

• John: Dipole scanning: Wrong orientations
• John: Inverse code: sLORETA
• John: Inverse code: NAI
• John: Inverse code: Mixed head models

• John, Richard, Sylvain: How to deal with unconstrained sources ?

  • For the Z-score normalization?

  • For the connectivity analysis? http://neuroimage.usc.edu/forums/showthread.php?2401

  • For the statistics?
  • Projection on a dominant orientation?
• Francois: Remove the warning messages in the interface

• Francois: Call FieldTrip headmodels and beamformers

[ONLINE DOC]

• John, Richard, Sylvain: Section Source estimation options

• John, Richard, Sylvain: Section Advanced options

• John, Richard, Sylvain: Section Equations

• John, Richard, Sylvain: Section References

• John, Richard, Sylvain: Why are dSPM values 2x lower than Z-score ?
• John, Richard, Sylvain: In-depth review of this sensitive tutorial

Tutorial 24: Time-frequency

[CODE]

• Enable option "Hide edge effects" for Hilbert (after finishing #10)

[ONLINE DOC]

• Hilbert: Link back to the filters tutorial (after finishing #10)

Tutorial 25: Difference

[ONLINE DOC]

• Validate order of the processes: Difference sources => Zscore => Low-pass filter
  Section: Difference deviant-standard

Tutorial 26: Statistics

[CODE]

• Francois: Implementation of Brainstorm-only permutation tests

[ONLINE DOC]

• Francois: Add the computation of power difference after a test on sources (|A|^2-|B|2)

Tutorial 27: Workflows

• Not evaluated yet

• Update: http://neuroimage.usc.edu/brainstorm/Tutorials/WorkflowGuide

Tutorial 28: Scripting

• Not evaluated yet

Final steps

• Francois: Check that the script tutorial_introduction.m produces the same output as tutorials
• Francois: Check all the links in all the pages
• Francois: Check the number of pages for each tutorial

• Francois: Reference on ResearchGate, Academia and Google Scholar
  http://neuroimage.usc.edu/brainstorm/Tutorials/AllIntroduction

• Francois: Remove useless images from all tutorials

[Additional important stuff]

Phantom tutorial (for validation)

• John: Prepare Elekta recordings to distribute on the tutorial page

• Francois: Prepare the Elekta phantom anatomy
• Francois: Prepare the analysis script
• Francois: Edit the tutorial page

Other analysis scenarios

• Francois: Update all the tutorials (100+ pages)
• Francois: Add number of pages in the tutorials

Connectivity

• Not documented at all
• Richard, Sylvain: Define example dataset and precise results to obtain from them
• Richard: How to assess significance from connectivity matrices
• Francois: Preparation of a tutorial