Getting xml.etree.ElementTree.ParseErro when opening egi file

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1

When reading a raw egi file, the compiler return an error

xml.etree.ElementTree.ParseError: not well-formed (invalid token): line 1, column 0

Surprisingly, this only happen on certain file. But, the same file can open using Matlab eeglab.

My machine setup:

  • MNE version: 1.3.1
  • operating system: Windows 11

The code to reproduce the above runtime error

import mne
fname = 'P.mff'
raw = mne.io.read_raw_egi(fname, preload=True)

The file .mff is accessable via the following link

https://drive.google.com/drive/folders/1-18gaDSoPzVH2tKncCEIyvg6_QN6KK3-?usp=sharing

The full traceback is as below:

Traceback (most recent call last):
  File "C:\Users\userx\IdeaProjects\dproject\issue_mne.py", line 5, in <module>
    raw = mne.io.read_raw_egi(fname, preload=True)
  File "<decorator-gen-260>", line 12, in read_raw_egi
  File "C:\Users\userx\anaconda3\envs\dproject\lib\site-packages\mne\io\egi\egi.py", line 156, in read_raw_egi
    return _read_raw_egi_mff(input_fname, eog, misc, include,
  File "<decorator-gen-257>", line 12, in _read_raw_egi_mff
  File "C:\Users\userx\anaconda3\envs\dproject\lib\site-packages\mne\io\egi\egimff.py", line 389, in _read_raw_egi_mff
    return RawMff(input_fname, eog, misc, include, exclude,
  File "<decorator-gen-258>", line 12, in __init__
  File "C:\Users\userx\anaconda3\envs\dproject\lib\site-packages\mne\io\egi\egimff.py", line 412, in __init__
    egi_events, egi_info = _read_events(input_fname, egi_info)
  File "C:\Users\userx\anaconda3\envs\dproject\lib\site-packages\mne\io\egi\events.py", line 26, in _read_events
    mff_events, event_codes = _read_mff_events(input_fname, info['sfreq'])
  File "C:\Users\userx\anaconda3\envs\dproject\lib\site-packages\mne\io\egi\events.py", line 49, in _read_mff_events
    orig[xml_type] = _parse_xml(xml_file)
  File "C:\Users\userx\anaconda3\envs\dproject\lib\site-packages\mne\io\egi\events.py", line 81, in _parse_xml
    xml = parse(xml_file)
  File "C:\Users\userx\anaconda3\envs\dproject\lib\xml\etree\ElementTree.py", line 1222, in parse
    tree.parse(source, parser)
  File "C:\Users\userx\anaconda3\envs\dproject\lib\xml\etree\ElementTree.py", line 580, in parse
    self._root = parser._parse_whole(source)
xml.etree.ElementTree.ParseError: not well-formed (invalid token): line 1, column 0

This issue seem related to Unable to load MFF files : ParseError: not well-formed(invalid token) - #7 by ometett as highlighted by @drammock . But, I do not find any suspicious xml reside under the .mff.

Appreciate for any help

2

it looks like subject.xml is corrupted. That is the file that causes the ParseError and I can’t open it with my text editor (well, I can, but it complains “this file is either binary or uses an unsupported text encoding”). Either way, it’s not valid XML.

1 Like
3

Thanks for your time entertaining this issue @drammock