I don’t know what is my issue. Montage type? or missing fsaverage folder in data. As is not installed. Is this typical or is there something to install ?
python3 /Users/andraderenew/Downloads/TUH_EEG/convert_eeg_to_bids.py
Extracting EDF parameters from /Users/andraderenew/Downloads/TUH_EEG/aaaaaaac-s002_2002_12_23-02_tcp_le/aaaaaaac_s002_t000.edf…
EDF file detected
Setting channel info structure…
Creating raw.info structure…
Traceback (most recent call last):
File “/Users/andraderenew/Downloads/TUH_EEG/convert_eeg_to_bids.py”, line 104, in
montage = mne.channels.make_standard_montage(‘standard_1020’)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/Users/andraderenew/Applications/MNE-Python/1.6.0_0/.mne-python/lib/python3.11/site-packages/mne/channels/montage.py”, line 1824, in make_standard_montage
return standard_montage_look_up_tablekind
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/Users/andraderenew/Applications/MNE-Python/1.6.0_0/.mne-python/lib/python3.11/site-packages/mne/channels/_standard_montage_utils.py”, line 112, in _mgh_or_standard
lpa, nasion, rpa = [x[“r”].copy() for x in get_mni_fiducials(“fsaverage”)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “”, line 12, in get_mni_fiducials
File “/Users/andraderenew/Applications/MNE-Python/1.6.0_0/.mne-python/lib/python3.11/site-packages/mne/_freesurfer.py”, line 467, in get_mni_fiducials
fids, coord_frame = read_fiducials(fname_fids_fs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “”, line 12, in read_fiducials
File “/Users/andraderenew/Applications/MNE-Python/1.6.0_0/.mne-python/lib/python3.11/site-packages/mne/_fiff/meas_info.py”, line 1977, in read_fiducials
fname = _check_fname(fname=fname, overwrite=“read”, must_exist=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “”, line 12, in _check_fname
File “/Users/andraderenew/Applications/MNE-Python/1.6.0_0/.mne-python/lib/python3.11/site-packages/mne/utils/check.py”, line 261, in _check_fname
raise FileNotFoundError(f’{name} does not exist: “{fname}”')
FileNotFoundError: File does not exist: “/Users/andraderenew/Applications/MNE-Python/1.6.0_0/.mne-python/lib/python3.11/site-packages/mne/data/fsaverage/fsaverage-fiducials.fif”
It seems like 1.6 should not have this problem because we switched to hatchafter releasing 1.6. @andraderenew did you install a dev version of MNE-Python on top of 1.6, or is this on 1.6? If you are latest dev we fixed this bug in the past few days so please update to an even newer one
Downloading the 1.6 sdist from PyPI I also see that the files are included:
$ ls mne-1.6.0/mne/data/fsaverage/
fsaverage-fiducials.fif ...
But I can look at the conda package, too, if you are indeed on vanilla 1.6.
python3 /Users/andraderenew/Downloads/TUH_EEG/convert_eeg_to_bids.py
Traceback (most recent call last):
File “/Users/andraderenew/Downloads/TUH_EEG/convert_eeg_to_bids.py”, line 37, in
from mne_bids import write_raw_bids, BIDSPath, print_dir_tree
ModuleNotFoundError: No module named ‘mne_bids’
And with version 1.5 for installer I don’t know where to find it.
I also have another script I want to run. But with dev version this happens.
(mne) andraderenew@Renes-MacBook-Air ~ % python3 /Users/andraderenew/Library/CloudStorage/OneDrive-UniversidaddeAlcala/research-Rene’s\ MacBook\ Air/2.\ processing_image/real\ code/mri/connectome\ circle\ mne.py
Traceback (most recent call last):
File “/Users/andraderenew/Library/CloudStorage/OneDrive-UniversidaddeAlcala/research-Rene’s MacBook Air/2. processing_image/real code/mri/connectome circle mne.py”, line 4, in
from mne_connectivity.viz import plot_connectivity_circle
ModuleNotFoundError: No module named ‘mne_connectivity’
This is the code.
import mne
import numpy as np
import os
from mne_connectivity.viz import plot_connectivity_circle
labels =
node_colors =
unknown_found = None
with open(‘/path/to/fs_default.txt’) as f:
for x in f.readlines():
if unknown_found and x.split():
labels.append(x.split()[2])
node_colors.append(tuple([float(color)/255 for color in x.split()[3:6]]))
if ‘Unknown’ in x:
unknown_found = True
I just tried our 1.6.0 installer on macOS arm64 and it looks to have the original missing file so I’m a bit stumped:
$ ls ~/Applications/MNE-Python/1.6.0_0/.mne-python/lib/python3.11/site-packages/mne/data/fsaverage/
fsaverage-fiducials.fif fsaverage-head.fif fsaverage-inner_skull-bem.fif fsaverage-trans.fif
For this I think you can pip install mne_connectivity. But it’s weird that your MNE installation did not come with this package because it’s supposed to. Perhaps something went wrong during your installation – I’d try removing the ~/Applications/MNE-Python directory and re-running the installer after making sure you have enough hard drive space available (looks like ~6GB is needed).
pip install mne-connectivity and pip install mne-bids did the trick. Although I don’t know why I have to install this. Isn’t it supposed to be in dev version?
about mac apple silicon installer I have reinstalled it and the files are there. So all that is fixed. Thank you so much.
mne_connectivity and mne_bids are separate packages from MNE-Python. If you use our standalone installers then they’re included, but if you just install MNE-Python (either dev version or stable) from pip, you won’t get them automatically.
