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| * '''Sylvain Baillet''': Montreal Neurological Institute ''[not started]'' * '''Richard Leahy''': University of Southern California ''[validated 1-9]'' |
* '''Sylvain Baillet''': Montreal Neurological Institute ''[overview 1-14, edited 20-21]'' * '''Richard Leahy''': University of Southern California ''[validated 1-20]'' |
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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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| == Tutorial 20: Head modelling == | == Tutorial 20: Head modeling == |
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| * John, Richard, Sylvain: In-depth review of this sensitive tutorial * John, Richard, Sylvain: Section [[http://neuroimage.usc.edu/brainstorm/Tutorials/AllIntroduction#Tutorials.2FHeadModel.References_.5BTODO.5D|References]] |
* John: In-depth review of this sensitive tutorial * John: Section [[http://neuroimage.usc.edu/brainstorm/Tutorials/HeadModel#Additional_documentation_.5BTODO.5D|References]] |
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| * John: Dipole scanning: Wrong orientations * John: Inverse code: sLORETA |
* John: Noise covariance: Cannot regularize GRAD and MAG at the same time ? |
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| * John, Richard, Sylvain: How to normalize unconstrained sources ? | * Francois: Make the "no regularization" option the default? (changes a lot the range of values) |
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| * Francois: Add note in Elekta tutorial: Process MAG and GRAD separately | |
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| == Tutorial 23: Scouts == [CODE] * Francois: Flip scouts: Remove the sign flip cancelling based on the values ? |
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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) |
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| == Tutorial 26: Statistics == [CODE] |
== Tutorial 27: Workflows == |
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| == Tutorial 27: Workflows == * Everything == Tutorial 28: Scripting == * Everything |
* Add Chi2(log) ? |
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| * Francois: Check that the script tutorial_introduction.m produces the same output as tutorials | |
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| * Francois: Check the number of pages for each tutorial | |
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<<BR>><<BR>><<BR>><<BR>><<BR>>[Additional important stuff] == 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 == Other analysis scenarios == * Francois: Update all the tutorials (100 pages) * Francois: Add number of pages in the tutorials |
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| * Richard: How to assess significance from connectivity matrices * Francois: Preparation of a tutorial |
* Richard: How to deal with unconstrained sources?<<BR>> http://neuroimage.usc.edu/forums/showthread.php?2401 * Richard: How to assess significance from connectivity matrices? * Francois, Richard, Hossein: Preparation of a tutorial == Other analysis scenarios == * Beth: Update or delete: http://neuroimage.usc.edu/brainstorm/Tutorials/WorkflowGuide * Francois: Update all the tutorials (100+ pages) * Francois: Remove useless images from all tutorials |
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, edited 20-21]
Richard Leahy: University of Southern California [validated 1-20]
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 modeling
[ONLINE DOC]
- John: In-depth review of this sensitive tutorial
John: Section References
Tutorial 22: Source estimation
[CODE]
- John: Noise covariance: Cannot regularize GRAD and MAG at the same time ?
- John: Inverse code: NAI
- John: Inverse code: Mixed head models
- Francois: Make the "no regularization" option the default? (changes a lot the range of values)
- 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 27: Workflows
[ONLINE DOC]
- Add Chi2(log) ?
Final steps
- Francois: Check all the links in all the pages
Francois: Reference on ResearchGate, Academia and Google Scholar
http://neuroimage.usc.edu/brainstorm/Tutorials/AllIntroduction
Connectivity
- Not documented at all
- Richard, Sylvain: Define example dataset and precise results to obtain from them
Richard: How to deal with unconstrained sources?
http://neuroimage.usc.edu/forums/showthread.php?2401- Richard: How to assess significance from connectivity matrices?
- Francois, Richard, Hossein: Preparation of a tutorial
Other analysis scenarios
Beth: Update or delete: http://neuroimage.usc.edu/brainstorm/Tutorials/WorkflowGuide
- Francois: Update all the tutorials (100+ pages)
- Francois: Remove useless images from all tutorials