Epileptogenicity tutorial: minor documentation issues

Bugs
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1

Hi-

These are some instances where minor changes are required for the documentation, many presumably due to changes in brainstorm.

  1. Display the depth electrodes / panel IEEG
    There is no option for "project on electrode" as indicated.

  2. Display the SEEG recordings / SEEG time series
    R clicking on "Link to raw file" now has a menu for ECOG > Display time series (not SEEG > Display time series, as indicated).

  3. Display the SEEG recordings / SEEG time series
    Behavior of "3D electrodes" appears to have changed, as I get a view of the electrodes embedded in the 3d cortical model, which hides many of the contacts.

  4. Review recordings / power spectrum
    The channel file has sensor type set to ECOG but the pipeline editor defaults to look for SEEG. Running the Welch PSD with that that default in place generates a "no sensors selected" error. The user needs either to clear the sensor type field or edit the channel file.

  5. Review recordings / bad channels
    Would fix writing here: “We will now to review the recordings of...”

  6. Review recordings / seizure onset
    Looks to me like seizure #2 onset is at 141.303.

  7. Import epochs of interest / bipolar montage
    Montage name currently shown is Subject01: ECOG (bipolar 2)
    (SEEG in existing documentation is replaced with ECOG.)

  8. Time-frequency analysis
    In setting up multitaper analysis, need to switch sensor type to ECOG.

  9. Time-frequency analysis
    For multitaper analysis, the "time step" field (defaulted to 99.6 ms) is not described.

  10. Time-frequency analysis
    Setting colormap maximum with the specified matlab syntax does not work for me.

  11. Epileptogenicity maps / Surface: seizure 2/3
    Fix typo: "epiptogenicity"

  12. Epileptogenicity maps / create a movie
    Fix typo: "can be viewed on any computed"

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2

Thanks for the detailed report!

Display the depth electrodes / panel IEEG
There is no option for "project on electrode" as indicated.

This a menu that appears only for sEEG:
brainstorm3/toolbox/gui/panel_ieeg.m at master · brainstorm-tools/brainstorm3 · GitHub

R clicking on "Link to raw file" now has a menu for ECOG > Display time series (not SEEG > Display time series, as indicated).

If you are reading the Epileptogenicity tutorial, there is no ECOG in it...

Behavior of "3D electrodes" appears to have changed, as I get a view of the electrodes embedded in the 3d cortical model, which hides many of the contacts.

You have menus to display the 3D electrodes on the head, cortex or MRI.
It is just not explained how to change the transparency and other surface properties in these advanced tutorials. If you need help with this, get back to the introduction tutorials:
https://neuroimage.usc.edu/brainstorm/Tutorials/ExploreAnatomy

In general: The advanced tutorials are written for users who are already quite familiar with the Brainstorm interface and have followed all the introduction tutorials.

The channel file has sensor type set to ECOG but the pipeline editor defaults to look for SEEG. Running the Welch PSD with that that default in place generates a "no sensors selected" error. The user needs either to clear the sensor type field or edit the channel file.

The pipeline editor always prompts for the last value that was used, not for the types of sensors in the file.
This is an offline analysis tool, to build generic batch scripts, not an interactive interface.
Therefore: yes, you need edit the file "sensor types" of all the processes when you change modality of data to process.

Would fix writing here: “We will now to review the recordings of...”

Changed to "We will now review"

Looks to me like seizure #2 onset is at 141.303.

You can set the beginning of the seizure at many different places, depending on what your target is. In this specific case, we look at "the beginning of the fast gamma activity, which is the main feature used in the computation of the epileptogenicity maps".
No matter what the instructions are, I observed that different neurologists often mark different onsets on the same datasets. The latencies indicated here are the ones provided by the authors of the articles cited in reference, so I can't contradict them.
Feel free to adjust the timings depending on your data and expertise.

Montage name currently shown is Subject01: ECOG (bipolar 2)
(SEEG in existing documentation is replaced with ECOG.)

I don't understand this comment.

In setting up multitaper analysis, need to switch sensor type to ECOG.

If you are working with ECOG, of course.
But this is a SEEG dataset.

For multitaper analysis, the "time step" field (defaulted to 99.6 ms) is not described.

Fixed.

Setting colormap maximum with the specified matlab syntax does not work for me.

What syntax do you refer to?

Fix typo: "epiptogenicity"

Fixed.

Fix typo: "can be viewed on any computed"

Fixed.

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