Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Don't silently apply the BIDS datatype's channel type to channels for which we don't have a proper BIDS -> MNE mapping #1048

Closed
hoechenberger opened this issue Aug 10, 2022 · 1 comment · Fixed by #1052
Closed

Don't silently apply the BIDS datatype's channel type to channels for which we don't have a proper BIDS -> MNE mapping #1048

hoechenberger opened this issue Aug 10, 2022 · 1 comment · Fixed by #1052
Assignees
@hoechenberger

Comments

@hoechenberger
Copy link
Member

hoechenberger commented Aug 10, 2022 •
edited
Loading

Originally posted by @hoechenberger in #1046 (comment)

We currently use the following channel type mapping from BIDS to MNE:

mne-bids/mne_bids/utils.py

Lines 77 to 83 in 16a7b0c

elif fro == 'bids' and to == 'mne':
mapping = dict(EEG='eeg', MISC='misc', TRIG='stim', EMG='emg',
ECOG='ecog', SEEG='seeg', EOG='eog', ECG='ecg',
RESP='resp', NIRS='fnirs_cw_amplitude',
# No MEG channels for now
# Many to one mapping
VEOG='eog', HEOG='eog', DBS='dbs')

Apparently, we silently apply the BIDS datatype's channel type to channels for which we don't have a proper BIDS -> MNE mapping defined here. I don't think we should do this. Instead, we should default to misc.
@sappelhoff
Copy link
Member

agreed

@hoechenberger hoechenberger self-assigned this Aug 19, 2022
@hoechenberger hoechenberger mentioned this issue Aug 19, 2022
Merged
7 tasks
hoechenberger added a commit to hoechenberger/mne-bids that referenced this issue Aug 19, 2022
@hoechenberger
Set channel type to misc if we cannot perform a proper conversion fro…
79a87a4 
…m BIDS to MNE channel types

Previously, e.g. GSR and temperature channels could end up as "eeg" channels, for example.

Fixes mne-tools#1048
hoechenberger added a commit to hoechenberger/mne-bids that referenced this issue Aug 19, 2022
@hoechenberger
Set channel type to misc if we cannot perform a proper conversion fro…
52edb4d 
…m BIDS to MNE channel types

Previously, e.g. GSR and temperature channels could end up as "eeg" channels, for example.

Fixes mne-tools#1048
hoechenberger added a commit that referenced this issue Aug 19, 2022
@hoechenberger
MRG: Set channel type to misc if we cannot perform a proper conversio…
d98128a 
…n from BIDS to MNE channel types (#1052)

* Set channel type to misc if we cannot perform a proper conversion from BIDS to MNE channel types

Previously, e.g. GSR and temperature channels could end up as "eeg" channels, for example.

Fixes #1048

* Fix test

* Fix NIRS
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@hoechenberger hoechenberger

Labels
None yet
Projects
None yet
Milestone
No milestone
2 participants
@hoechenberger @sappelhoff