[WIP] Add bids converter #4128

jasmainak · 2017-03-30T05:19:47Z

The BIDS specification can be found here

The BIDS compatible MNE sample data can be found here. Let's see how much of this we can automate.

codecov-io · 2017-03-30T06:10:30Z

Codecov Report

Merging #4128 into master will decrease coverage by 1.87%.
The diff coverage is 21.05%.

@@            Coverage Diff             @@
##           master    #4128      +/-   ##
==========================================
- Coverage   86.05%   84.17%   -1.88%     
==========================================
  Files         354      355       +1     
  Lines       63734    63772      +38     
  Branches     9709     9711       +2     
==========================================
- Hits        54847    53683    -1164     
- Misses       6216     7380    +1164     
- Partials     2671     2709      +38

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choldgraf · 2017-03-30T14:34:37Z

maybe we should put this in mne.io? are you here today so we can chat?

teonbrooks · 2017-03-30T15:50:43Z

interested in this as well, let me know when you meet

dengemann · 2017-04-06T02:48:10Z

Funny PR that just adds code without calling it :)

choldgraf · 2017-04-06T02:53:36Z

It's wip ;-)

…

On Wed, Apr 5, 2017, 7:48 PM Denis A. Engemann ***@***.***> wrote: Funny PR that just adds code without calling it :) — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#4128 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABwSHSkdRhRKS1x8iDmBn7jjxaDSWwnHks5rtFJrgaJpZM4Mt4FZ> .

dengemann · 2017-04-06T02:55:01Z

I know. But maybe some provocations can help changing the status :) On Wed, Apr 5, 2017 at 10:53 PM Chris Holdgraf <notifications@github.com> wrote:

…

It's wip ;-) On Wed, Apr 5, 2017, 7:48 PM Denis A. Engemann ***@***.***> wrote: > Funny PR that just adds code without calling it :) > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > < #4128 (comment)>, > or mute the thread > < https://github.com/notifications/unsubscribe-auth/ABwSHSkdRhRKS1x8iDmBn7jjxaDSWwnHks5rtFJrgaJpZM4Mt4FZ > > . > — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#4128 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AB0figdjRHgTvqtIQPOwB_6yEHZTp26hks5rtFOxgaJpZM4Mt4FZ> .

choldgraf · 2017-04-06T16:22:53Z

I think some folks are still out of town etc, but I believe @jasmainak was going to iterate on this per the conversations we had at the sprint!

jasmainak · 2017-04-06T18:23:43Z

@dengemann you will see me next week. Perhaps a good opportunity to push for this ;)

dengemann · 2017-04-06T18:25:40Z

yes we can push together :D

…

On Thu, Apr 6, 2017 at 2:24 PM Mainak Jas ***@***.***> wrote: @dengemann <https://github.com/dengemann> you will see me next week. Perhaps a good opportunity to push for this ;) — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#4128 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AB0finkC_IcUNefbCCZj-1PlIpsswtVYks5rtS2vgaJpZM4Mt4FZ> .

jasmainak · 2017-04-22T22:23:09Z

I added a tiny example. Perhaps I could do with a round of reviews and words of encouragement to help me finish this PR ;)

dengemann · 2017-04-22T22:24:43Z

You mean the auto reject PR? I couldn't encourage you more :)

…

On Sat, Apr 22, 2017 at 6:23 PM Mainak Jas ***@***.***> wrote: I added a tiny example. Perhaps I could do with a round of reviews and words of encouragement to help me finish this PR ;) — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#4128 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AB0fiuPD1visy4iBIQYRVXdGX5VEMWVoks5ryn3OgaJpZM4Mt4FZ> .

choldgraf · 2017-04-22T22:31:17Z

examples/io/plot_bids.py

+
+fnames = dict(events='sample_audvis_raw-eve.fif',
+              raw='sample_audvis_raw.fif')
+


I think it'd be good to have a little more explanation about what kind of folder structure BIDS follows. Maybe we could add in some RST that gave a rough idea of what this folder structure would be, something w/ this structure:

root/ anat/ meg/ file1.fif

etc

yeah maybe eventually. For now, I'll try to provide a link to the BIDS draft ...

choldgraf · 2017-04-22T22:31:52Z

examples/io/plot_bids.py

+
+input_path = op.join(data_path, 'MEG', 'sample')
+output_path = op.join(data_path, '..', 'MNE-sample-data-bids')
+folder_to_bids(input_path=input_path, output_path=output_path,


Is there some minimal amount of information that each file must have, that is not absolutely required from MNE?

yeah, there is. You have required fields and you have optional fields. There has to be way to indicate to the user that these required fields are incomplete even after the automatic conversion

choldgraf · 2017-04-22T22:32:41Z

examples/io/plot_bids.py

+
+input_path = op.join(data_path, 'MEG', 'sample')
+output_path = op.join(data_path, '..', 'MNE-sample-data-bids')
+folder_to_bids(input_path=input_path, output_path=output_path,


How about metadata for time etc? Does it only pull this from a trigger channel? What if we added in support for an events array along with event_id, and it could build an events TSV file from this if it existed.

Metadata for time comes from raw.info. For the events, I'm reading it from an events file for now. Didn't want to do too much guessing about trigger channel etc. ...

agramfort · 2017-04-23T11:28:10Z

@jasmainak I would create a mne-bids repo in mne-tools to quickly make progress. Working in the mne-python code base will be more difficult.

wdyt?

choldgraf · 2017-04-23T15:57:07Z

@agramfort that's an interesting idea. What can we imagine would go in there other than just this PR? Maybe a place to host the MNE-BIDS data? I agree this might be a good offshoot project for now, just trying to envision what it'd look like.

agramfort · 2017-04-23T19:04:00Z

I don't know but MEG bids is still evolving fast and a PR is not ideal for quick collab without nitpicks.

jasmainak · 2017-04-23T20:04:05Z

yeah I agree. Let's make a mne-bids repo. @agramfort can you create it and give me access?

I think apart from the MNE sample data, I'd like to see how much of the conversion for the openfmri data we can easily automate. I feel that with bids a lot of the metadata is already available in fif files. Then perhaps presenting the user with what information is missing so they can fill it manually.

agramfort · 2017-04-23T20:29:31Z

here we go: https://github.com/mne-tools/mne-bids

choldgraf · 2017-04-23T23:46:50Z

sounds good to me - I'm working on a BIDS-iEEG draft w/ some colleagues as well, so I can push some of our sample data there too perhaps!

jasmainak · 2017-04-24T09:03:33Z

cool, I added what's in this PR to the repo. Let's iterate from there

Add bids converter

898a17d

jasmainak force-pushed the bids_converter branch 2 times, most recently from 07db06c to 53bc8c4 Compare April 22, 2017 22:06

Make example work

817af82

jasmainak force-pushed the bids_converter branch from 53bc8c4 to 817af82 Compare April 22, 2017 22:20

Move to io module

2b8db34

choldgraf reviewed Apr 22, 2017

View reviewed changes

Docstrings

5c4179f

ktavabi mentioned this pull request Jul 12, 2017

Channel TSV mne-tools/mne-bids#2

Closed

jasmainak closed this Feb 20, 2018

teonbrooks mentioned this pull request Aug 24, 2018

BIDS I/O Functionality #4127

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[WIP] Add bids converter #4128

[WIP] Add bids converter #4128

jasmainak commented Mar 30, 2017 •

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jasmainak commented Apr 23, 2017 •

edited

agramfort commented Apr 23, 2017 via email

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jasmainak commented Apr 24, 2017


		fnames = dict(events='sample_audvis_raw-eve.fif',
		raw='sample_audvis_raw.fif')

[WIP] Add bids converter #4128

[WIP] Add bids converter #4128

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jasmainak commented Mar 30, 2017 • edited

codecov-io commented Mar 30, 2017

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