|
Size: 5990
Comment:
|
Size: 6202
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 67: | Line 67: |
| * John, Richard, Sylvain: How to normalize unconstrained sources ? | * 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? |
| Line 70: | Line 74: |
| * All: Unconstrained: PCA vs Norm?<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/25230358<<BR>>[[http://www.nature.com/neuro/journal/v15/n6/full/nn.3101.html|Hipp|http://www.ncbi.nlm.nih.gov/pubmed/25230358]] <<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/25230358<<BR>>[[http://www.nature.com/neuro/journal/v15/n6/full/nn.3101.html|Hipp|http://www.nature.com/neuro/journal/v15/n6/full/nn.3101.html]] | |
| Line 89: | Line 92: |
| * ERS/ERD on Hilbert: Squared signal only? * Shouldn't we always use power?... Right now, even the averaging process for trials give inconsistent results across methods. |
== 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]] |
| Line 93: | Line 99: |
| * Not evaluated yet | [CODE] * Francois: Implementation of Brainstorm-only permutation tests [ONLINE DOC] * Francois: Add the computation of power difference after a test on sources (|A|^2^-|B|^2^) * Francois: Add a section about unconstrained sources (after finished #27) |
| Line 97: | Line 110: |
| * Update: http://neuroimage.usc.edu/brainstorm/Tutorials/WorkflowGuide |
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: Wrong orientations
- John: Inverse code: sLORETA
- John: Inverse code: NAI
- John: Inverse code: Mixed head models
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
[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]
- Enable option "Hide edge effects" for Hilbert (after finishing #10)
[ONLINE DOC]
- 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
[ONLINE DOC]
Francois: Add the computation of power difference after a test on sources (|A|2-|B|2)
- Francois: Add a section about unconstrained sources (after finished #27)
Tutorial 27: Workflows
- Not evaluated yet
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: Check the number of pages for each tutorial
Francois: Reference on ResearchGate, Academia and Google Scholar
http://neuroimage.usc.edu/brainstorm/Tutorials/AllIntroduction- Francois: Remove useless images from all tutorials
[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