Introduction tutorials: Editing process

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 are still not supported.

• John: Explain the new (incorrect) results obtained with the epilepsy tutorial (see below)

• John: Drop the option "RMS source amplitude"?

  • The documentation is not informative and not encouraging at all: "RMS source amplitude: An alternative definition of SNR, but still under test and may be dropped."
  • The option is not even accessible in the interface: you successively asked me to disable it for the min norm, and then made me hide the entire section "Regularization parameter" for the dipole modelling and the beamformer.
  • Can I just remove it from the interface?
  • Francois: Update code, tutorials and screen captures accordingly

• John, Richard, Sylvain, Matti, Alex: Make the "median eigenvalue" option the default?

  • John suggests to use the "median eigenvalue" option by default instead of the option "Regularize noise covariance", which as been used for many years.

  • In this section of the tutorials, John wrote: "Recommended option: This author (Mosher) votes for the median eigenvalue as being generally effective. The other options are useful for comparing with other software packages that generally employ similar regularization methods."

  • However this modifies a lot the results: the localization results and the MN amplitudes can be very different. If this is a clear improvement, it's good to promote it. But it cannot be done randomly like this, this has to be discussed (especially with Matti and Alex) and tested.
  • John: Please arrange a meeting so you can discuss this question.

• 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: Mixing GRAD and MAG:

  • John: You do not recommend processing GRAD and MAG at the same time? This is currently the default behavior in the interface...

  • John: Please discuss this with Matti and Alex

  • Francois: Change the default + add note in Elekta tutorial if change is validated

• John: Send a message to Margot Taylor: She's been asking for your beamformers for about 2yrs.

• Francois: Call FieldTrip headmodels and beamformers

[ONLINE DOC]

• John: Fix all the missing links

• John: Data covariance:

  • Recommendations moved to the Noise and data covariance tutorial.

  • You said: "Our recommendation for evoked responses is to use a window that spans prestim through the end of the response of interest, with a minimum of 500ms total duration. "
  • Should I modify the interface (and screen capture of the example) to always include the pre-stim baseline (eg. from -100ms to +500ms, instead of from 0ms to +500ms) ?

  • Francois: Update the screen capture + code for default selection of the time window

Tutorial: Dipole scanning

• John: Unfinished sentence in this section.

Tutorial EEG/Epilepsy

• John: Why sLORETA?

• John: Please address the 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 wrote: "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: Update the code for the band-stop and notch filters in the same way

• Francois, Richard, Hossein, Alex: Address the issue of the weird PSD plots for Elekta recordings

[ONLINE DOC]

• Francois: Add to the documentation that wavelets are safer for epoched data and averages

• Richard, Hossein: Section Filters specifications for band-stop and notch filters

• Hossein: Add the example of a chirp in the documentation: "A chirp is a nice example to show this on, illustrating bandpass filtering into two bands say - if the frequency range of the chirp is broad enough you should see it move from one band to the other, but it both cases with no delay relative to the original signal - so 3 curves - original signal, signal in lower band, signal in upper band."

• Francois: Update section "Apply a notch filter" to add the transients in screen capture and text

Tutorial 13: Artifact cleaning with SSP

• Francois: Fix process_ssp2:

  • Filters are not used correctly: The code must be updated to add the transient length to the segments that are read, then filter, then remove the transients before computing the SSP

  • New filters (bst_hfilter) are too slow compared to the the old ones (bst_fft_fir)

• Francois: Fix documentation: Section SSP Algorithm

Tutorial 22: Source estimation

• Francois: Update screen capture in section Averaging in source space

Tutorial 24: Time-Frequency

• Francois: Update definition of the filters (using 60dB attenuation)

Tutorial 25: Difference

• Francois: Update screen captures for band-pass filter

Tutorial 28: Scripting

• Francois: Update screen captures for band-pass filter

Tutorial epilepsy

• Francois: Update screen captures for band-pass filter

Tutorial visual group

• Francois: Update screen captures for band-pass filter

Tutorial Yokogawa

• Francois: Update screen captures for band-pass filter

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: Check that all the TODO blocks have been properly handled
• Francois: Remove useless images from all tutorials
• Francois: Update page count on the main tutorials page

• 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, Sylvain: How to deal with unconstrained sources?
  http://neuroimage.usc.edu/forums/showthread.php?2401

• Richard: How to assess significance from connectivity matrices?

• Richard, Hossein, Francois: Preparation of a tutorial

• All the functions using bandpass filters must be updated to use the new filters