Sphinx Gallery Site

[JohnGriffiths]

Pages we want to have:

These will become pages = .py scripts in examples folder (see below)

• [ ] General commentary page
• [ ] Data fetchers - PO
• [ ] Snirf events - JG, DM
• [ ] Snirf epoching - JG, DM
• [ ] Snirf glm - JG, DM
• [ ] Nifti events - AC, JG
• [ ] Nifti volumetric glm - AC, JG
• [ ] Nifti volumetric FC - AC, JG
• [ ] Nifti surface glm - HA, JG
• [ ] Nifti surface FC - HA, JG
• [ ] EEG rest power spectra - TM
• [ ] EEG epoched - KK
• [ ] Homer surface projection and viz
• [ ] Homer surface GLM
• [ ] Homer surface FC
• [ ] Montage things - JG
• [ ] Homer pipeline script -
• [ ] Custom psychopy task - TM
• [ ] Data quality summary

Approach:

1. Review relevant colab code
2. Make a sketch outline of the example page contents. ( Major sections, analyses done, images shown)
3. Decide what the functions should be and write them
4. Make the script work
5. Start running on github CI

[JohnGriffiths]

Sphinx gallery example repos (there are many)

https://github.com/nilearn/nilearn
https://github.com/mne-tools/mne-python
https://github.com/NeuroTechX/eeg-notebooks

Four main folders in a CI- integrated sphinx gallery site hosting github repo:

• library folder - contains core functions
• doc folder - organized and manages website compilation and structure
• examples folder - core executable scripts that make core example pages
• hidden .github folder - defined github CI processes

The files corresponding to the executable

[JohnGriffiths]

Reference colab nbs that we have so far.

The above will be based on these.

Snirf GLMs: https://colab.research.google.com/drive/1nsRpXiEWPvUiIA-au_w5fsUrHvSVSHyO?usp=sharing

Montages: https://colab.research.google.com/drive/1BBtGmR6SyJUqkJEZPR-L4qwX1a8a8H9M?usp=sharing

Nifti GLMs: https://colab.research.google.com/drive/1V4A6vUJC2am2nUn9jeLcIdveEm8rftUa?usp=sharing https://colab.research.google.com/drive/12TPwZe2qSsbwSAD4SFgVJaifOrtF49uG?usp=sharing

Nifti FC: https://colab.research.google.com/drive/1MnJoamNqFJtHA8hQGvvqEi3rJHjpT3cW?usp=sharing

Surface FC: https://colab.research.google.com/drive/1JMhBRXlSw2s96ymF-Es_74_WNchWZ73d?usp=sharing https://colab.research.google.com/drive/1zVv75Yl5_L4TChAnYEOOPSSKI98sys6S?usp=sharing

[tmorshed]

• [ ] Reading the .snirf file into raw_intensity @kevinkadak

• [ ] Reading EEG from the raw_intensity/H5Py @kevinkadak

• [ ] Monitor EEG quality @tmorshed:

  • [ ] Find out where it's zero:
  • [ ] w_avg
  • [ ] coupling?
  • [ ] Find artefacts
  • [ ] notch @ 60 Hz power line

• [ ] Power spectra: [@FrankMazza]

  • [ ] Lowpass 45 > Hamming, 1p
  • [ ] Welch's Method (mne.time_frequency.psd_welch()): 0-45

Colab notebook: https://drive.google.com/file/d/1wC1qsYH5jVRjuqASL5JgSzVB43_iDQbq/view?usp=sharing