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| * '''Sylvain Baillet''': Montreal Neurological Institute ''[not started]'' | * '''Sylvain Baillet''': Montreal Neurological Institute ''[overview 1-14, no proofreading]'' |
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| * Richard, John, Sylvain: Why is the notch filter not working well at the beginning of the signal? | |
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| * Francois: Check that the bandpass filter is always used with enough data (Hilbert transform, SSP) | |
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| [CODE] [ONLINE DOC] | [CODE] |
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| * John: Dipole scanning: Wrong orientations * John: Inverse code: sLORETA |
* John: Dipole scanning: Doesn't work with constrained sources |
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| * John, Richard, Sylvain: How to normalize unconstrained sources ? | * John: Noise covariance: Cannot regularize GRAD and MAG at the same time * 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? |
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| * Francois: Add note in Elekta tutorial: Process MAG and GRAD separately | |
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| * Review how to normalize the time-frequency maps * How to deal with magnitude (Hilbert) and power (Morlet) at the same time ? * Better keep track of the edge effects (maybe a mask of correctly estimated values ?) * Enable option "Hide edge effects" for Hilbert (after finishing #10) |
* Francois: Enable option "Hide edge effects" for Hilbert (after finishing #10) |
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| * Describe what happens with unconstrained sources * Hilbert: Link back to the filters tutorial (after finishing #10) * Description of "log freq scale" option |
* Francois: 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<<BR>>Section: [[http://neuroimage.usc.edu/brainstorm/Tutorials/Difference#Difference_deviant-standard|Difference deviant-standard]] |
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| * Francois: Implementation of Brainstorm-only permutation tests * Francois: Keep edge effects map (TFmask) for the stats on time-frequency maps |
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| * Francois: Add a section about unconstrained sources (after finishing #27) |
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| * Everything | * Update everything after: http://neuroimage.usc.edu/brainstorm/Tutorials/Workflows#Constrained_cortical_sources * Update: http://neuroimage.usc.edu/brainstorm/Tutorials/WorkflowGuide |
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| * Everything | * Not evaluated yet |
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| * Francois: Check the number of pages for each tutorial | |
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| == Phantom tutorial (for validation) == * John: Prepare Elekta recordings to distribute on the [[http://neuroimage.usc.edu/brainstorm/Tutorials/Phantom|tutorial page]] * Francois: Prepare the Elekta phantom anatomy * Francois: Prepare the analysis script * Francois: Edit the tutorial page |
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| * Francois: Update all the tutorials (100 pages) * Francois: Add number of pages in the tutorials |
* Francois: Update all the tutorials (100+ pages) * Francois: Remove useless images from all tutorials * Francois: Add number of pages for all the tutorials * Francois: Split list in columns |
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: Doesn't work with constrained sources
- John: Inverse code: NAI
- John: Inverse code: Mixed head models
- John: Noise covariance: Cannot regularize GRAD and MAG at the same time
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
- Francois: Add note in Elekta tutorial: Process MAG and GRAD separately
[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]
- Francois: Enable option "Hide edge effects" for Hilbert (after finishing #10)
[ONLINE DOC]
- Francois: 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
- Francois: Keep edge effects map (TFmask) for the stats on time-frequency maps
[ONLINE DOC]
- Francois: Add a section about unconstrained sources (after finishing #27)
Tutorial 27: Workflows
Update everything after: http://neuroimage.usc.edu/brainstorm/Tutorials/Workflows#Constrained_cortical_sources
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: Reference on ResearchGate, Academia and Google Scholar
http://neuroimage.usc.edu/brainstorm/Tutorials/AllIntroduction
[Additional important stuff]
Other analysis scenarios
- Francois: Update all the tutorials (100+ pages)
- Francois: Remove useless images from all tutorials
- Francois: Add number of pages for all the tutorials
- Francois: Split list in columns
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