Supporting CNTs (Neuroscan) files

[yjmantilla]

Describe the problem

Hi mne-bids team. I was wondering if there was any reason for not supporting CNTs. I have run into some problems when using write_raw_bids and I noticed it was not on the list of eeg extensions:

mne-bids/mne_bids/config.py

Lines 49 to 55 in 4c0755c

	eeg_manufacturers = {'.vhdr': 'BrainProducts', '.eeg': 'BrainProducts',
	'.edf': 'n/a', '.EDF': 'n/a', '.bdf': 'Biosemi',
	'.BDF': 'Biosemi',
	'.set': 'n/a', '.fdt': 'n/a',
	'.lay': 'Persyst', '.dat': 'Persyst',
	'.EEG': 'Nihon Kohden'}

Is there a reason for not supporting it beyond not being included on this dictionary?

[welcome]

Hello! 👋 Thanks for opening your first issue here! ❤️ We will try to get back to you soon. 🚴🏽‍♂️

[agramfort]

.cnt is not a format parf of the BIDS standard https://bids-specification.readthedocs.io/en/bep-009/04-modality-specific-files/03-electroencephalography.html

[yjmantilla]

Thanks @agramfort , I meant as an input format (that is, I want to convert from cnt to any of the accepted bids formats).

Right now I think it is giving an error when it extracts the .cnt extesion and is not able to pass the ALLOWED_INPUT_EXTENSIONS check:

mne-bids/mne_bids/write.py

Lines 1365 to 1383 in 4c0755c

	if not allow_preload:
	raw_fname = raw.filenames[0]
	if '.ds' in op.dirname(raw.filenames[0]):
	raw_fname = op.dirname(raw.filenames[0])
	# point to file containing header info for multifile systems
	raw_fname = raw_fname.replace('.eeg', '.vhdr')
	raw_fname = raw_fname.replace('.fdt', '.set')
	raw_fname = raw_fname.replace('.dat', '.lay')
	_, ext = _parse_ext(raw_fname)
	# force all EDF/BDF files with upper-case extension to be written as
	# lower case
	if ext == '.EDF':
	ext = '.edf'
	elif ext == '.BDF':
	ext = '.bdf'
	if ext not in ALLOWED_INPUT_EXTENSIONS:
	raise ValueError(f'Unrecognized file format {ext}')

Maybe I'm doing something wrong, Im just opening the file with the read_raw mne function and passing the Raw object to the write_raw_bids function .

[yjmantilla]

Here is a colab with the replication of the error I get:

https://colab.research.google.com/drive/1cKaSnQglJwdLL-isNBlN6z5p_LixvkJN?usp=sharing

[hoechenberger]

@sappelhoff WDYT?

[sappelhoff]

Hi @yjmantilla :)

I think if we are supporting Nihon Kohden and Persyst, we might as well support CNT ... as long as all of these non-supported file formats get auto-converted into a BIDS supported format. Could be an added feature in a PR?

[agramfort]

sounds like a plan !

…

[yjmantilla]

@sappelhoff Thanks!

I could test what happens if one naively just adds the .cnt format to the MANUFACTURERS dictionary, and start from there what would be required to accept support cnt .