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| Deletions are marked like this. | Additions are marked like this. |
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| Reviewers ''[current reviewing status] '' | Reviewers: ''[current reviewing status] '' |
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| * '''Sylvain Baillet''': Montreal Neurological Institute ''[not started]'' * '''Richard Leahy''': University of Southern California ''[validated 1-9]'' * '''John Mosher''': Cleveland Clinic ''[not started]'' |
* '''Sylvain Baillet''': Montreal Neurological Institute ''[overview 1-14, edited 20-21]'' * '''Richard Leahy''': University of Southern California ''[validated 1-20]'' * '''John Mosher''': Cleveland Clinic ''[edited 22 only]'' |
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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 |
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| * Richard, John, Sylvain: Finish the evaluation of the band-pass filters used in Brainstorm * Richard, John, Sylvain: Why is the notch filter not working well at the beginning of the signal? * Francois: Mark with an extended event the time segments that we cannot trust (edge effect) * Francois: Add warning if recordings are not long enough * Francois: Check that the bandpass filter is always used with enough data (Hilbert transform, SSP) |
* Richard, Hossein: Define reasonable transient durations * Richard, Hossein: Describe the band-stop and notch filters in the same way * Richard, Hossein: Frequency resolution in the "freqz" plots for high-pass filters under 0.5Hz * Richard, John, Hossein, Sylvain: Weird PSD plots for Elekta recordings |
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| * Richard, John, Sylvain: Section [[http://neuroimage.usc.edu/brainstorm/Tutorials/ArtifactsFilter#What_filters_to_apply.3F_.5BTODO.5D|What filters to apply?]] * Richard, John, Sylvain: Section [[http://neuroimage.usc.edu/brainstorm/Tutorials/ArtifactsFilter#Filters_specifications_.5BTODO.5D|Filters specifications]] == Tutorial 12: Artifact detection == [ONLINE DOC] * Beth: Adding examples of the different detection processes. Section [[http://neuroimage.usc.edu/brainstorm/Tutorials/ArtifactsDetect#Other_detection_processes|Other detection processes]] |
* Richard, Hossein: Section [[http://neuroimage.usc.edu/brainstorm/Tutorials/ArtifactsFilter#Filters_specifications_.5BTODO.5D|Filters specifications]] for band-stop and notch filters |
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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: Inverse code: NAI |
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| * John, Richard, Sylvain: How to normalize unconstrained sources ? * Francois: Remove the warning messages in the interface |
* John: Explain the new results obtained with the epilepsy tutorial * John: Discuss and validate all the modifications with Alex and Matti * John: Cannot process GRAD and MAG at the same time ? * Francois: Make the "median" option the default? (changes a lot the range of values) |
| Line 72: | Line 55: |
| * Francois: Add note in Elekta tutorial: Process MAG and GRAD separately * Francois: Check respective values of dSPM and Z-score (dSPM 2x higher?) |
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| * John, Richard, Sylvain: In-depth review of this sensitive tutorial == Tutorial 23: Scouts == [CODE] * Francois: Flip scouts: Make it an option |
* John, Richard, Sylvain: What do with [[http://neuroimage.usc.edu/brainstorm/Tutorials/Beamformers|Hui-Ling Beamformers]]? |
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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 == Tutorial 26: Statistics == [CODE] [ONLINE DOC] |
* Francois: Hilbert: Link back to the filters tutorial (after finishing #10) |
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| * Everything | * Add Chi2(log) ? |
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| == Tutorial 28: Scripting == * Everything |
== Tutorial: Dipole scanning == * Add the description of all the measures in [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutDipScan#Significance_mesures_.5BTODO.5D|this section]]. == Tutorial EEG/Epilepsy == * Why sLORETA? * Location with the new code? |
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| * Francois: Check that the script tutorial_introduction.m produces the same output as tutorials | * Francois: Remove all the wiki pages that are not used |
| Line 115: | Line 89: |
| * Francois: Check the number of pages for each tutorial | * Francois: Remove useless images from all tutorials |
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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 |
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 [edited 22 only]
Dimitrios Pantazis: Massachusetts Institute of Technology [validated 1-15]
Tutorial 10: Power spectrum and frequency filters
[CODE]
- Richard, Hossein: Define reasonable transient durations
- Richard, Hossein: Describe the band-stop and notch filters in the same way
- Richard, Hossein: Frequency resolution in the "freqz" plots for high-pass filters under 0.5Hz
- Richard, John, Hossein, Sylvain: Weird PSD plots for Elekta recordings
[ONLINE DOC]
Richard, Hossein: Section Filters specifications for band-stop and notch filters
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: Inverse code: Mixed head models
- John: Explain the new results obtained with the epilepsy tutorial
- John: Discuss and validate all the modifications with Alex and Matti
- John: Cannot process GRAD and MAG at the same time ?
- Francois: Make the "median" option the default? (changes a lot the range of values)
Francois: Call FieldTrip headmodels and beamformers
- Francois: Add note in Elekta tutorial: Process MAG and GRAD separately
- Francois: Check respective values of dSPM and Z-score (dSPM 2x higher?)
[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: What do with Hui-Ling Beamformers?
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
- Add Chi2(log) ?
Tutorial: Dipole scanning
Add the description of all the measures in this section.
Tutorial EEG/Epilepsy
- Why sLORETA?
- Location with the new code?
Final steps
- Francois: Remove all the wiki pages that are not used
- Francois: Check all the links in all the pages
- Francois: Remove useless images from all tutorials
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