Using mne-bids to convert CTF data to bids format

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22

Now I upgraded to mne_bids: 0.11.dev0, there’s an error with the BIDSPath:

from mne_bids import BIDSPath, write_raw_bids

output_path = r'Z:\MEG_data\MNE-pilot-data-bids'
bids_path = BIDSPath(subject=subject, session=session,
                     task=task, run=run, root=output_path)


write_raw_bids(raw, bids_path, events_data=events_data, 
               event_id=events_id, overwrite=True)
Traceback (most recent call last):

  File "C:\Users\ghafarit\AppData\Local\Temp\ipykernel_23084\1508003131.py", line 1, in <module>
    write_raw_bids(raw, bids_path, events_data=events_data,

  File "<decorator-gen-611>", line 12, in write_raw_bids

  File "C:\Users\ghafarit\Anaconda3\envs\mne\lib\site-packages\mne_bids\write.py", line 1504, in write_raw_bids
    raise RuntimeError('"bids_path" must be a BIDSPath object. Please '

RuntimeError: "bids_path" must be a BIDSPath object. Please instantiate using mne_bids.BIDSPath().

What do you suggest I do now?

23

No idea :person_shrugging: from what you shared it’s not clear what the error could be. Progress with one error message at a time … anyhow, if this is a different issue, I suggest you investigate first and try to solve it. If you really hit a wall and cannot progress further or if you think you have identified a bug, please open a new report either here or on Issues · mne-tools/mne-bids · GitHub

1 Like
24

In order to convert the ctf data to bids format, I upgraded mne_bids and that was the only thing I changed, everything else was the same as before (there was no error regarding BIDSPath when I was using mne_bids:0.10). Basically the MWE is still the same as the one I shared with you before.

This error is the reason I can’t try the developer’s version of mne_bids to see if on windows I can convert CTF data to bids format. and I could not solve it unfortunately.

That’s why I asked if you have any ideas how to solve it and move forward in converting ctf data to bids.

25

Can you insert these lines directly above the call to write_raw_bids() please, and tell us the output it produces?

print(type(bids_path))
print(bids_path)

Thanks!

26

Hi Richard,

Thanks for your reply.
below please find the output and error:

<class 'mne_bids.path.BIDSPath'>
Z:/MEG_data/MNE-pilot-data-bids/sub-02/ses-01/meg/sub-02_ses-01_task-SpAtt_run-01_meg.ds
Traceback (most recent call last):

  File "C:\Users\ghafarit\AppData\Local\Temp\ipykernel_23084\1067814209.py", line 3, in <module>
    write_raw_bids(raw, bids_path, events_data=events_data,

  File "<decorator-gen-611>", line 12, in write_raw_bids

  File "C:\Users\ghafarit\Anaconda3\envs\mne\lib\site-packages\mne_bids\write.py", line 1504, in write_raw_bids
    raise RuntimeError('"bids_path" must be a BIDSPath object. Please '

RuntimeError: "bids_path" must be a BIDSPath object. Please instantiate using mne_bids.BIDSPath().

thanks,
Tara

27

@tghafari Thank you!

@sappelhoff The type of the BIDSPath object looks kinda weird, no? Why does it have an entire “path to the namespace” (sorry, idk how to properly call this) prepended? I’ve never seen anything like this… this probably also explains why the check fails. I wonder if there are multiple MNE-BIDS installations interacting with each other in unforeseen ways?

28

@tghafari Could you please share the output of:

import mne_bids
print(mne_bids.__file__)

Thank you so much!

29

Could it also be some Windows specific stuff that we are not testing appropriately? :thinking:

I couldn’t reproduce this issue on Ubuntu 18.04

30

thanks for following this up @richard

here’s the output:

import mne_bids
print(mne_bids.__file__)
C:\Users\ghafarit\Anaconda3\envs\mne\lib\site-packages\mne_bids\__init__.py
1 Like
31

@sappelhoff

In any case:

  • we should raise a TypeError instead of a RuntimeError here
  • we should print what which type we actually received when we expected the BIDSPath
1 Like
32

Thank you, I will look into this.

33

Actually this is not correct; I get the same behavior on macOS:

In [9]: from mne_bids import BIDSPath

In [10]: BIDSPath
Out[10]: mne_bids.path.BIDSPath

So this is not it.

@tghafari I suspect something with your installation is broken … I’d suggest you wait for the MNE-BIDS 0.11 release and then do a fresh install of everything.

Sorry I cannot be of more help.

Richard

34

Thanks @richard,

I hope I don’t have to wait for long. I am making all my scripts BIDS compatible at the moment, I will continue to use mne-bids 0.10 for .fif data for now until the next version is released.

Just to be clear, by “fresh install of everything” you mean uninstalling and installing mne-bids, right?

Bests,
Tara