Writting .mff files into BIDS, problems with write_raw_bids

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1

Hello, new to mne-python and could use some help. I’m currently trying to convert raw data from mff files into BIDS. At the moment I can read in and create a BIDS data structure with raw mff data, but I cannot convert a .bin file (from the mff file) into fif format.

At the moment my program looks like this:

import matplotlib
import pathlib

import mne
import mne_bids

matplotlib.use('Qt5Agg')
mne.set_log_level('warning') 

raw_fname = pathlib.Path('subject_data') / 'WM_1_isi0_s1c_20191110_020011.mff'
raw = mne.io.read_raw_egi(raw_fname)

out_path = pathlib.Path('out_data2/sample_BIDS') #Into which directory the data should go

bids_path = mne_bids.BIDSPath(subject='01',
                              session='01',
                              task='WM1 isi0',
                              datatype='eeg',
                              root=out_path) 

mne_bids.write_raw_bids(raw, bids_path=bids_path, events_data=events, format='FIF', allow_preload=True,
                        event_id=event_id, overwrite=True)

And spits out this error:

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
Input In [6], in <cell line: 9>()
      1 out_path = pathlib.Path('out_data2/sample_BIDS') #Into which directory the data should go
      3 bids_path = mne_bids.BIDSPath(subject='01',
      4                               session='01',
      5                               task='WM1 isi0',
      6                               datatype='eeg',
      7                               root=out_path) #An object that specifies the location of BIDS files
----> 9 mne_bids.write_raw_bids(raw, bids_path=bids_path, events_data=events, format='FIF', allow_preload=True,
     10                         event_id=event_id, overwrite=True)

File <decorator-gen-585>:12, in write_raw_bids(raw, bids_path, events_data, event_id, anonymize, format, symlink, empty_room, allow_preload, montage, acpc_aligned, overwrite, verbose)

File ~\anaconda3\envs\mne\lib\site-packages\mne_bids\write.py:1668, in write_raw_bids(***failed resolving arguments***)
   1663 make_dataset_description(bids_path.root, name=" ", overwrite=False)
   1665 _sidecar_json(raw, task=bids_path.task, manufacturer=manufacturer,
   1666               fname=sidecar_path.fpath, datatype=bids_path.datatype,
   1667               emptyroom_fname=associated_er_path, overwrite=overwrite)
-> 1668 _channels_tsv(raw, channels_path.fpath, overwrite)
   1670 # create parent directories if needed
   1671 _mkdir_p(os.path.dirname(data_path))

File ~\anaconda3\envs\mne\lib\site-packages\mne_bids\write.py:110, in _channels_tsv(raw, fname, overwrite)
    108 # get the manufacturer from the file in the Raw object
    109 _, ext = _parse_ext(raw.filenames[0])
--> 110 manufacturer = MANUFACTURERS[ext]
    112 ignored_channels = IGNORED_CHANNELS.get(manufacturer, list())
    114 status, ch_type, description = list(), list(), list()

KeyError: '.bin'

-----------------------------------

It appears that write_raw_bids is having problems converting .bin files into an fif format, though it could definitely be something else.

2

Hello, I’m not familiar with this file format, is that generated by EGI systems?

Because there’s currently a pull request to add support for EGI to MNE-BIDS, meaning it’s not yet officially supported:

Also pinging @sappelhoff and @mscheltienne who probably followed this development more closely than I did! Also I think I remember @cbrnr was once dealing with MFF files, but I might be mistaken.

Handing out tags here like candy!!! :lollipop:

In any case,
best of luck!

Richard

1 Like
3

Sorry, I never worked with MFF (at least as far as I can remember :laughing:).

1 Like
4

Hello,

EEG datasets have to be converted to one of the formats for BIDS. Quoting the write_raw_bids page:

The original file is simply copied over if the original file format is BIDS-supported for that datatype. Otherwise, this function will convert to a BIDS-supported file format while warning the user. For EEG and iEEG data, conversion will be to BrainVision format; for MEG, conversion will be to FIFF.

And at the moment, mne-bids does not recognize what the .bin extension corresponds to and how to convert it to BrainVision format. I’m adding support in the PR linked by @richard but I still have to fix a couple of bugs… I’ll try to find time this week.

Best,
Mathieu

1 Like