Twelveth week of GSoC: Getting ready for the final week of GSoC

sappelhoff
Published: 08/19/2019

My GSoC is soon coming to an end so I took some time to write down what still needs to be done:

Making a release of MNE-BIDS

In the past months, there were substantial additions, fixes, and cosmetic changes made to the codebase and documentation of MNE-BIDS. The last release has happened in April (about 4 months ago) and we were quite happy to observe some issues and pull requests raised and submitted by new users. With the next release we can provide some new functionality for this growing user base.

Handling coordinates for EEG and iEEG in MNE-BIDS

In MNE-BIDS, the part of the code that handles the writing of sensor positions in 3D space (=coordinates) is so far restricted to MEG data. Extending this functionality to EEG and iEEG data has been on the to do list for a long time now. Fortunately, I have been learning a bit more about this topic during my GSoC, and Mainak has provided some starting points in an unrelated PR that I can use to finish this issue. (After the release of MNE-BIDS though, to avoid cramming in too much last-minute content before the release)

Writing a data fetcher for OpenNeuro to be used in MNE-Python

While working with BIDS and M/EEG data, the need for good testing data has come up time and time again. For the mne-study-template we solved this issue with a combination of DataLad and OpenNeuro. Meanwhile, MNE-BIDS has its own dataset.py module ... however, we all feel like this module is duplicating the datasets module of MNE-Python and not advancing MNE-BIDS. Rather, it is confusing the purpose of MNE-BIDS.

As a solution, we want to write a generalized data fetching function for MNE-Python that works with OpenNeuro ... without adding the DataLad (and hence Git-Annex) dependency). Once this fetching function is implemented, we can import it in MNE-BIDS and finally deprecate MNE-BIDS' dataset.py module.

Make a PR in MNE-Python that will support making Epochs for duplicate events (will fix ds001971 PR)

In MNE-Python, making data epochs is not possible, if two events share the same time. This became apparent with the dataset ds001971 that we wanted to add to the mne-study-template pipeline: https://github.com/mne-tools/mne-study-template/pull/41. There was a suggestion on how to solve this issue by merging the event codes that occurred at the same time. Once this fix is implemented in MNE-Python, we can use this to finish the PR in the mne-study-template.

Salvage / close the PR on more "read_raw_bids" additions

Earlier in this GSoC, I made a PR intended to improve the reading functionality of MNE-BIDS (https://github.com/mne-tools/mne-bids/pull/244). However, the PR was controversially discussed, because it was not leveraging BIDS and instead relying on introducing a dictionary as a container for keyword arguments.

After lots of discussion, we agreed to solve the situation in a different way (by leveraging BIDS) and Mainak made some initial commits into that direction. However in the further progress, the PR was dropped because other issues had higher priority.

Before finishing my GSoC, I want to salvage what's possible from this PR and then close it ... and improving the original issue report so that the next attempt at this PR can rely on a more detailed objective.

1000 characters left