mne-tools / mne-tools/mne-python
Problem converting NIRx fNIRS data
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Description
Dear experts,
We are trying to convert NIRx fNIRS data using MNE-BIDS mainly following the extremely nice documentation https://mne.tools/mne-bids/stable/auto_examples/convert_nirs_to_bids.html (thanks for that!!). However, when trying to write_raw_bids, we get an error saying 'head' coordinate frame must contain nasion and left and right pre-auricular point landmarks, and its missing the nasion. Attempting to solve this, we came across mne.io.read_raw_nirx, which seems to read the (meta)data correctly. However, because we do not specify the file extension, the write function fails because Found no extension for raw file, assuming "BTi" format and appending extension .pdf. So it seems that I can either read in the data via mne.io.read_raw_snirf but then the meta data is incomplete or I can use mne.io.read_raw_nirx but then the write function fails because I cannot specify the file extension. This is the first fNIRS dataset we are converting though, so we are very likely not getting something... Do you have any advise on how to handle this?
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
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Research direction
Start with the linked MNE-BIDS NIRx conversion example and reproduce the behavior using mne.io.read_raw_nirx, mne.io.read_raw_snirf, and write_raw_bids. Compare the resulting landmarks, metadata, and file-extension handling; done means establishing a reliable conversion path or documenting the remaining limitation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100