Read montage from a .bvef file

[WilliamLabCea]

Hi,

I meet some difficulties when I want to load a .bvef (montage files with mne 0.19.2). With previous version of mne (0.18.2) I used 'mne.channels.read_montage' function to load .bvef

With the new function 'mne.channels.read_custom_montage' mne report an value error:

Montage_fname = "/MontageAntneuro2.bvef" ...Montage = mne.channels.read_custom_montage(Montage_fname, head_size=None, unit='auto') raw = mne.io.read_raw_brainvision(vhdr_fname, montage=Montage, misc='auto', scale=1.0, preload=True, ... verbose=None) Extracting parameters from /media/258884/VERBATIM HD/EEG_Data/EEG_SoundTTC_2sp/Pilote-EEG2_YN_2019-12-04_14-54-58.vhdr... Setting channel info structure... Reading 0 ... 481250 = 0.000 ... 939.941 secs... <input>:2: RuntimeWarning: Limited 1 annotation(s) that were expanding outside the data range. Traceback (most recent call last): File "<input>", line 2, in <module> File "/home/258884/anaconda3/envs/NewPycharm/lib/python3.7/site-packages/mne/io/brainvision/brainvision.py", line 825, in read_raw_brainvision verbose=verbose) File "</home/258884/anaconda3/envs/NewPycharm/lib/python3.7/site-packages/mne/externals/decorator.py:decorator-gen-151>", line 2, in __init__ File "/home/258884/anaconda3/envs/NewPycharm/lib/python3.7/site-packages/mne/utils/_logging.py", line 90, in wrapper return function(*args, **kwargs) File "/home/258884/anaconda3/envs/NewPycharm/lib/python3.7/site-packages/mne/io/brainvision/brainvision.py", line 100, in __init__ _deprecate_montage(self, "read_raw_brainvision", montage) File "/home/258884/anaconda3/envs/NewPycharm/lib/python3.7/site-packages/mne/io/utils.py", line 32, in _deprecate_montage raw.set_montage(montage, **kwargs) File "</home/258884/anaconda3/envs/NewPycharm/lib/python3.7/site-packages/mne/externals/decorator.py:decorator-gen-30>", line 2, in set_montage File "/home/258884/anaconda3/envs/NewPycharm/lib/python3.7/site-packages/mne/utils/_logging.py", line 90, in wrapper return function(*args, **kwargs) File "/home/258884/anaconda3/envs/NewPycharm/lib/python3.7/site-packages/mne/channels/channels.py", line 488, in set_montage set_dig=set_dig, raise_if_subset=raise_if_subset) File "/home/258884/anaconda3/envs/NewPycharm/lib/python3.7/site-packages/mne/channels/montage.py", line 1545, in _set_montage _mnt = _get_montage_in_head(montage) File "/home/258884/anaconda3/envs/NewPycharm/lib/python3.7/site-packages/mne/channels/montage.py", line 1356, in _get_montage_in_head return transform_to_head(montage.copy()) File "/home/258884/anaconda3/envs/NewPycharm/lib/python3.7/site-packages/mne/channels/montage.py", line 935, in transform_to_head native_head_t = get_ras_to_neuromag_trans(nasion, lpa, rpa) File "/home/258884/anaconda3/envs/NewPycharm/lib/python3.7/site-packages/mne/transforms.py", line 650, in get_ras_to_neuromag_trans raise ValueError("Points have to be provided as one dimensional " ValueError: Points have to be provided as one dimensional arrays of length 3.

Thanks for your help

[larsoner]

@WilliamLabCea can you upload the .bvef file somewhere so we can take a look?

[WilliamLabCea]

here is the link for the .bvef file

https://drive.google.com/open?id=1aETFbIJKFnlkPJykF8jt_xCubKqFZneg

[larsoner]

@WilliamLabCea can you see if #7118 or #7119 fixes it for you?

[agramfort]

@WilliamLabCea https://github.com/WilliamLabCea in what coordinate system are these points? do you use these points as channel locations for source imaging?

[WilliamLabCea]

It is a spherical coordinate system for EEG file. I use this file for channel location (no source imaging reconstruction)

[agramfort]

our other standard montages do not do the job for you?

[WilliamLabCea]

Unfortunately no, the cap is an waveguard64 and doesn't fit with biosemi64 montage

[agramfort]

@WilliamLabCea this is now fixed in master and in the maint/0.19 branch. You appear in 0.19.3 is a few days