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mne-tools / mne-bids

MNE-BIDS is a Python package that allows you to read and write BIDS-compatible datasets with the help of MNE-Python.
https://mne.tools/mne-bids/
BSD 3-Clause "New" or "Revised" License
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Documentation bug in quickstart guide #663

Closed hoechenberger closed 3 years ago

hoechenberger commented 3 years ago

@pchholak Actually there's a mistake in the example in the quickstart guide: BIDSPath doesn't accept a bids_root parameter – this should be root.

Originally posted by @hoechenberger in https://github.com/mne-tools/mne-bids/issues/661#issuecomment-747440629

adam2392 commented 3 years ago

@hoechenberger

I can fix this really quick. Any chance at releasing 0.7 as a quick fix after that regarding anonymization of EDF files / format='BrainVision' feature?

hoechenberger commented 3 years ago

We can make another release soon, alright. But we should fix #656 and #662 first

sappelhoff commented 3 years ago

We can make another release soon, alright. But we should fix #656 and #662 first

there'll also be a BIDS release soon, and there are two issues that may impact MNE-BIDS as well (in terms of features)

but of course that could also be included in mne-bids 0.8 ...

hoechenberger commented 3 years ago

there'll also be a BIDS release soon, and there are two issues that may impact MNE-BIDS as well (in terms of features)

Thanks @sappelhoff! I was aware of the EEGLAB change but not of the others changes.

Any gut feeling when the new BIDS release will be due?

sappelhoff commented 3 years ago

Any gut feeling when the new BIDS release will be due?

yes, we'll try to release 1.5.0 within the next two weeks to integrate the ASL (arterial spin labelling) and qMRI extensions ... but these won't impact mne-bids as far as I can tell.

Then we'll be working hard on integrating PET as a 1.6 release ... hopefully a maximum of 1 to 2 months later.

But the coordsystem PR and other "smaller" things that may impact mne-bids more will be integrated in these larger releases.

hoechenberger commented 3 years ago

I would say, then, we just proceed with MNE-BIDS at normal speed and fix the issues that were mentioned, and we'll decide ad-hoc whether it's worth supporting new BIDS features (if they've been released at that time) or whether we should simply schedule their support for the release after that. I don't think it's super important to support all BIDS changes within a few days or even weeks…

sappelhoff commented 3 years ago

agreed :-)

adam2392 commented 3 years ago

We can make another release soon, alright. But we should fix #656 and #662 first

there'll also be a BIDS release soon, and there are two issues that may impact MNE-BIDS as well (in terms of features)

but of course that could also be included in mne-bids 0.8 ...

Yeah I think overall there is a bit of "cleanup" work to do to support multiple coordsystems/electrodes json/tsv files. Even those can theoretically exist, I'm in favor of pushing that off for 0.8, since that's a very corner-case.

I've had one subject where i wanted to store multiple copies of the electrode coordinates, but didn't need to use mne-bids in that one.

For these 3 main issues @hoechenberger pointed out, looks like a quick and easy fix, so I submitted a PR #675.