problem of lemon_dataset.py

[ScarletVV]

When I ran this code, it output:
sub-032333 : **********************
sub-032333 : * PROCESSING FAILED! *
sub-032333 : **********************
sub-032333 : import_data : <function import_data at 0x7fd210b71900>
sub-032333 : <class 'FileNotFoundError'>
sub-032333 : [Errno 2] No such file or directory: '/home/uais1/Echo/OSL/DataPrepare/dataset/lemon/raw/sub-032333/RSEEG/sub-010041.vmrk'
sub-032333 : None

How can I fix this?

[cgohil8]

The problem is it can't find this file:

/home/uais1/Echo/OSL/DataPrepare/dataset/lemon/raw/sub-032333/RSEEG/sub-010041.vmrk

Seems like there's a mismatch between the filename and subject directory. It's trying to find the file sub-010041.vmrk in the directory for sub-032333.

[ScarletVV]

Yes it is, but my question is why the program wants to find the sub-010041.vmrk in the directory for sub-032333 ?
I just download the data from https://fcon_1000.projects.nitrc.org/indi/retro/MPI_LEMON/downloads/download_EEG.html and use one of them(sub-032333) to test the code and 124 line of code deleted

subjects = subjects[:2]

There is no subject named sub-010041 here, and no obvious reading of the .vmrk file code snippet in the code.

[cgohil8]

Where did you get lemon_dataset.py from? Can you send the contents of the script or a link.

[ScarletVV]

It should call 1_preprocess.py in osl/examples/lemon. https://github.com/OHBA-analysis/osl/blob/main/examples/lemon/1_preprocess.py

[ScarletVV]

This is the result of Jupyter Notebook running https://github.com/ScarletVV/lemon_process.git.

[cgohil8]

What version of MNE are you using?

[ScarletVV]

MNE 1.3.1

[cgohil8]

Do get the same error if you do:

import mne

raw = mne.io.read_raw_brainvision("/home/uais1/Echo/OSL/DataPrepare/dataset/lemon/raw/sub-032333/RSEEG/sub-032333.vhdr")

[ScarletVV]

yes

[cgohil8]

ah, it's an error in MNE then. You can try upgrade MNE:

conda activate osl
pip install --upgrade mne

Although OSL hasn't been tested against versions above MNE 1.3.1, so you might run into new bugs. If you update MNE does the following work:

import mne

raw = mne.io.read_raw_brainvision("/home/uais1/Echo/OSL/DataPrepare/dataset/lemon/raw/sub-032333/RSEEG/sub-032333.vhdr")

[ScarletVV]

Same error after upgrading MNE. Can I solve this problem if I install a lower version of MNE?

[ScarletVV]

Thank you for your patient guidance and answers. I will try similar work directly on MNE.

[cgohil8]

It's unlikely a lower version would fix this, but you can try.

You might be able to load it if you change the directory structure of the data. What happens if you create a new directory and copy only the .vhdr file into it. E.g. you can try something like:

mkdir ~/test
cp /home/uais1/Echo/OSL/DataPrepare/dataset/lemon/raw/sub-032333/RSEEG/sub-032333.vhdr ~/test
python
>> import mne
>> raw = mne.io.read_raw_brainvision("~/test/sub-032333.vhdr")

What happens then?

[ScarletVV]

Still same error...

[cgohil8]

Can you try again downloading the data from here instead:
https://ftp.gwdg.de/pub/misc/MPI-Leipzig_Mind-Brain-Body-LEMON/

[ScarletVV]

I try the data from your link then the mismatch error gone, but a new error :

sub-010005 : **********************
sub-010005 : * PROCESSING FAILED! *
sub-010005 : **********************
sub-010005 : set_eeg_reference : functools.partial(<function run_mne_anonymous at 0x7fda3b84f9a0>, method='set_eeg_reference')
sub-010005 : <class 'OSError'>
sub-010005 : could not get source code
sub-010005 : None
Computation complete
OSL osl_logger: handler 'console' level set to 'INFO'
logging to file: /home/uais1/Echo/OSL/DataPrepare/dataset/lemon/test_preproc/logs/osl_batch.log
Processed 0/1 files successfully

/home/uais1/Echo/osl/osl/preprocessing/mne_wrappers.py:67: RuntimeWarning: No bad channels to interpolate. Doing nothing...
getattr(dataset[target], method)(**userargs)
File "/home/uais1/Echo/osl/osl/preprocessing/batch.py", line 791, in run_proc_chain
dataset = append_preproc_info(dataset, config, extra_funcs)
File "/home/uais1/Echo/osl/osl/preprocessing/batch.py", line 367, in append_preproc_info
preproc_info += f"%% extra_funcs start %% \n{inspect.getsource(func)}\n%% extra_funcs end %%"
File "/home/uais1/anaconda3/envs/echo/lib/python3.10/inspect.py", line 1139, in getsource
lines, lnum = getsourcelines(object)
File "/home/uais1/anaconda3/envs/echo/lib/python3.10/inspect.py", line 1121, in getsourcelines
lines, lnum = findsource(object)
File "/home/uais1/anaconda3/envs/echo/lib/python3.10/inspect.py", line 958, in findsource
raise OSError('could not get source code')

[cgohil8]

What version of MNE are you using?

[ScarletVV]

1.7.0 then down to 1.3.1 still same error.

[cgohil8]

Can you:

• Re-install OSL from scratch to make sure you have the latest code.
• Try commenting out the set_eeg_reference line in the config.