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| * '''Nov-Dec''': Connectivity tutorial | |
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| * Francois: Check the length needed to filter the recordings (after finishing tutorial #10) <<BR>>Section [[http://neuroimage.usc.edu/brainstorm/Tutorials/ArtifactsSsp#SSP_Algorithm_.5BTODO.5D|SSP Algorithm]] | [CODE] [ONLINE DOC] * Francois: Check the length needed to filter the recordings (after finishing #10) <<BR>>Section [[http://neuroimage.usc.edu/brainstorm/Tutorials/ArtifactsSsp#SSP_Algorithm_.5BTODO.5D|SSP Algorithm]] |
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| == Tutorial 20: Head modelling == [ONLINE DOC] * 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]] == 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 normalize unconstrained sources ? * Francois: Remove the warning messages in the interface * Francois: Call FieldTrip headmodels and beamformers [ONLINE DOC] * John, Richard, Sylvain: Section [[http://neuroimage.usc.edu/brainstorm/Tutorials/SourceEstimation#Source_estimation_options_.5BTODO.5D|Source estimation options]] * John, Richard, Sylvain: Section [[http://neuroimage.usc.edu/brainstorm/Tutorials/SourceEstimation#Advanced_options_.5BTODO.5D|Advanced options]] * John, Richard, Sylvain: Section [[http://neuroimage.usc.edu/brainstorm/Tutorials/SourceEstimation#Equations_.5BTODO.5D|Equations]] * John, Richard, Sylvain: Section [[http://neuroimage.usc.edu/brainstorm/Tutorials/SourceEstimation#References_.5BTODO.5D|References]] * John, Richard, Sylvain: Why are dSPM values 2x lower than Z-score ? * John, Richard, Sylvain: In-depth review of this sensitive tutorial == Tutorial 23: Scouts == [CODE] * Francois: Flip scouts: Make it an option == Tutorial 24: Time-frequency == [CODE] * 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) [ONLINE DOC] * Describe what happens with unconstrained sources * Hilbert: Link back to the filters tutorial (after finishing #10) * Description of "log freq scale" option == Tutorial 26: Statistics == [CODE] [ONLINE DOC] == Tutorial 27: Workflows == * Everything == Tutorial 28: Scripting == * Everything |
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| * Check that the script tutorial_introduction.m produces the same output as the screen captures * Check all the links in all the pages * Check the number of pages for each tutorial * Reference on ResearchGate, Academia and Google Scholar: <<BR>>http://neuroimage.usc.edu/brainstorm/Tutorials/AllIntroduction |
* 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 <<BR>>http://neuroimage.usc.edu/brainstorm/Tutorials/AllIntroduction <<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 == 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 |
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 [not started]
Richard Leahy: University of Southern California [validated 1-9]
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
- Francois: Add warning if recordings are not long enough
- Francois: Check that the bandpass filter is always used with enough data (Hilbert transform, SSP)
[ONLINE DOC]
Richard, John, Sylvain: Section What filters to apply?
Richard, John, Sylvain: Section Filters specifications
Tutorial 13: Artifact cleaning with SSP
[CODE] [ONLINE DOC]
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 normalize unconstrained sources ?
- 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 23: Scouts
[CODE]
- Francois: Flip scouts: Make it an option
Tutorial 24: Time-frequency
[CODE]
- 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)
[ONLINE DOC]
- Describe what happens with unconstrained sources
- Hilbert: Link back to the filters tutorial (after finishing #10)
- Description of "log freq scale" option
Tutorial 26: Statistics
[CODE]
[ONLINE DOC]
Tutorial 27: Workflows
- Everything
Tutorial 28: Scripting
- Everything
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
[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