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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) | <<BR>><<BR>> |
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| * '''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 <<BR>> == Tutorial 10: Power spectrum and frequency filters == |
== Inverse models == === Tutorial 22: Source estimation === |
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| * 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) |
* John: Inverse code: Mixed head models * John: Explain the new (incorrect) results obtained with the epilepsy tutorial (see below) * John: Discuss and validate all the modifications with Alex and Matti * John: Cannot process GRAD and MAG at the same time ? * John, Richard, Sylvain: Why are dSPM values 2x lower than Z-score ? * The tutorial says "Z-normalized current density maps are also easy to interpret. They represent explicitly a "deviation from experimental baseline" as defined by the user. In contrast, dSPM indicates the deviation from the data that was used to define the noise covariance used in computing the min norm map. " * Therefore should we expect the dSPM values to deviate more from the noise recordings, than the Z-score from the pre-stim baseline? Instead of this we observe much lower values. Is there a scaling issue here? <<BR>><<BR>> {{attachment:diff_zscore_dspm.gif||width="385",height="138"}} * John: Send a message to Margot Taylor: She's been asking for your beamformers for about 3yrs. * 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 |
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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]] |
* John: Fix all the missing links * John, Richard, Sylvain: Section [[http://neuroimage.usc.edu/brainstorm/Tutorials/SourceEstimation#References_.5BTODO.5D|References]] * John, Richard, Sylvain: What do with [[http://neuroimage.usc.edu/brainstorm/Tutorials/Beamformers|Hui-Ling Beamformers]]? |
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| == Tutorial 13: Artifact cleaning with SSP == [CODE] [ONLINE DOC] |
=== Tutorial: Dipole scanning === * Add the description of all the measures in [[http://neuroimage.usc.edu/brainstorm/Tutorials/TutDipScan#Significance_mesures_.5BTODO.5D|this section]]. |
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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]] | === Tutorial EEG/Epilepsy === * Why sLORETA? * Location issues with the new code: <<BR>>dSPM is now localizing the spike in a much deeper spot (top=old version, bottom=new version) <<BR>><<BR>> {{attachment:epilepsy_dspm.gif||width="272",height="233"}} * '''Marcel Heers''': "Looking at the findings from the intracranial EEG in Matthias Dümpelmann's article (figure 1 panel a) and b)) it is '''very likely the new sources are wrong'''. Additionally, the older sources are much more in agreement with Matthias' sLORETA results and with cMEM findings. Sohrabopour et al. reported as well that their IRES method found results in agreement with sources shown in the tutorial." * Imported data for testing can be downloaded here:<<BR>> https://www.dropbox.com/s/42d9indpjr8ac1y/TutorialEpilepsy.zip?dl=0 |
| Line 45: | Line 49: |
| == Tutorial 15: Import epochs == [ONLINE DOC] * Richard, Sylvain, John, Francois: Define recommendations for epoch lengths (after finishing #10) <<BR>>Section [[http://neuroimage.usc.edu/brainstorm/Tutorials/Epoching#Epoch_length_.5BTODO.5D|Epoch length]] == 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 == |
== Filters == === Tutorial 10: Power spectrum and frequency filters === |
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| * 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 |
* 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 |
| Line 69: | Line 60: |
| * Richard, Hossein: Section [[http://neuroimage.usc.edu/brainstorm/Tutorials/ArtifactsFilter#Filters_specifications_.5BTODO.5D|Filters specifications]] for band-stop and notch filters | |
| Line 70: | Line 62: |
| === Tutorial 13: Artifact cleaning with SSP === * 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]] === Tutorial 15: Import epochs === * Richard, Sylvain, John, Francois: Define recommendations for epoch lengths (after finishing #10) <<BR>>Section [[http://neuroimage.usc.edu/brainstorm/Tutorials/Epoching#Epoch_length_.5BTODO.5D|Epoch length]] === Tutorial 22: Source estimation === * Francois: Update screen capture in section [[http://neuroimage.usc.edu/brainstorm/Tutorials/SourceEstimation#Averaging_in_source_space|Averaging in source space]] == 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) ? |
|
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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 <<BR>><<BR>><<BR>><<BR>> == 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 |
* 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 <<BR>>http://neuroimage.usc.edu/brainstorm/Tutorials/AllIntroduction |
| Line 92: | Line 92: |
| * 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]
Inverse models
Tutorial 22: Source estimation
[CODE]
- John: Inverse code: Mixed head models
- John: Explain the new (incorrect) results obtained with the epilepsy tutorial (see below)
- John: Discuss and validate all the modifications with Alex and Matti
- John: Cannot process GRAD and MAG at the same time ?
- John, Richard, Sylvain: Why are dSPM values 2x lower than Z-score ?
- The tutorial says "Z-normalized current density maps are also easy to interpret. They represent explicitly a "deviation from experimental baseline" as defined by the user. In contrast, dSPM indicates the deviation from the data that was used to define the noise covariance used in computing the min norm map. "
Therefore should we expect the dSPM values to deviate more from the noise recordings, than the Z-score from the pre-stim baseline? Instead of this we observe much lower values. Is there a scaling issue here?
- John: Send a message to Margot Taylor: She's been asking for your beamformers for about 3yrs.
- 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
[ONLINE DOC]
- John: Fix all the missing links
John, Richard, Sylvain: Section References
John, Richard, Sylvain: What do with Hui-Ling Beamformers?
Tutorial: Dipole scanning
Add the description of all the measures in this section.
Tutorial EEG/Epilepsy
- Why sLORETA?
Location issues with the new code:
dSPM is now localizing the spike in a much deeper spot (top=old version, bottom=new version)
Marcel Heers: "Looking at the findings from the intracranial EEG in Matthias Dümpelmann's article (figure 1 panel a) and b)) it is very likely the new sources are wrong. Additionally, the older sources are much more in agreement with Matthias' sLORETA results and with cMEM findings. Sohrabopour et al. reported as well that their IRES method found results in agreement with sources shown in the tutorial."
Imported data for testing can be downloaded here:
https://www.dropbox.com/s/42d9indpjr8ac1y/TutorialEpilepsy.zip?dl=0
Filters
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
Francois: Check the length needed to filter the recordings (after finishing #10)
Section SSP Algorithm
Tutorial 15: Import epochs
Richard, Sylvain, John, Francois: Define recommendations for epoch lengths (after finishing #10)
Section Epoch length
Tutorial 22: Source estimation
Francois: Update screen capture in section Averaging in source space
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) ?
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