epoching of sensor data in the experiment pipeline

[giadaan]

Hello all,

I defined my epochs parameters in the experiment file and I am now trying to actual epoch my sensor data. When running the function

e.make_epoch_selection(data='mag')

I get the following output:

{
"name": "ValueError",
"message": "'MEG0111' is not in list",
"stack": "---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
/export/home/gantonicelli/public/PROTRACK_MEG/Code/Untitled-1.ipynb Cell 5 line 1
----> 1 e.make_epoch_selection(data='mag')

File /opt/anaconda3/envs/eelbrain/lib/python3.11/site-packages/eelbrain/_experiment/mne_experiment.py:5004, in MneExperiment.make_epoch_selection(self, samplingrate, data, auto, overwrite, decim, **state)
5002 else:
5003 y_name = data
-> 5004 ds[data] = load.mne.epochs_ndvar(ds['epochs'], data=data)
5006 if auto is not None:
5007 if isinstance(auto, dict):

File /opt/anaconda3/envs/eelbrain/lib/python3.11/site-packages/eelbrain/io/fiff.py:1187, in epochs_ndvar(epochs, name, data, exclude, mult, info, sensors, vmax, sysname, connectivity, proj)
1184 if mult != 1:
1185 x *= mult
-> 1187 sensor = sensors or sensor_dim(epochs, picks, sysname, connectivity)
1188 time = UTS(epochs.times[0], 1. / epochs.info['sfreq'], len(epochs.times))
1189 return NDVar(x, ('case', sensor, time), info=info, name=name)

File /opt/anaconda3/envs/eelbrain/lib/python3.11/site-packages/eelbrain/_io/fiff.py:830, in sensor_dim(info, picks, sysname, connectivity)
828 if names != ch_names:
829 try:
--> 830 index = np.array([names.index(name) for name in ch_names])
831 c_matrix = c_matrix[index][:, index]
832 except IndexError:

File /opt/anaconda3/envs/eelbrain/lib/python3.11/site-packages/eelbrain/_io/fiff.py:830, in (.0)
828 if names != ch_names:
829 try:
--> 830 index = np.array([names.index(name) for name in ch_names])
831 c_matrix = c_matrix[index][:, index]
832 except IndexError:

ValueError: 'MEG0111' is not in list"
}

Any idea on how I could fix this issue? Thank you very much in advance

[proloyd]

@giadaan which eelbrain version are you using? Did you check if your files have channels with that name, manually (i.e. via opening them with mne.io.load_raw)? Can you try e.load_epochs(data='mag') and check if you can load the epochs?

[giadaan]

Hi! Yes, the channel is actually among my channels and no, I cannot do load.epochs (when running it, the program tells me to run make epoch selection first). Giada Antonicelli Predoctoral Researcher BCBL - Neurolinguistics and Aphasia group www.bcbl.eu Tel: +34 943 309 300 Ext #307 Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer We are working flexibly at BCBL. I am sending this message at a time that suits me. Please feel comfortable knowing that I do not expect you to read, respond to or action it outside of regular working hours. From: "Proloy Das" ***@***.***> To: "christianbrodbeck/Eelbrain" ***@***.***> Cc: "Giada Antonicelli" ***@***.***>, "Mention" ***@***.***> Sent: Thursday, February 22, 2024 8:33:22 AM Subject: Re: [christianbrodbeck/Eelbrain] epoching of sensor data in the experiment pipeline (Discussion #66) [ https://urldefense.com/v3/__https://github.com/giadaan__;!!D9dNQwwGXtA!R01VYwQuCzV70RqframAninyG2VvKht-yETtcdLJIL2VXSvewIZTKHlODrZen7B3ugWAJ6u0MLBNohHQDdlwjrqhtwMg$ | @giadaan ] which eelbrain version are you using? Did you check if your files have channels with that name, manually (i.e. via opening them with mne.io.load_raw )? Can you try e.load_epochs(data='mag') and check if you can load the epochs? — Reply to this email directly, [ https://urldefense.com/v3/__https://github.com/christianbrodbeck/Eelbrain/discussions/66*discussioncomment-8553068__;Iw!!D9dNQwwGXtA!R01VYwQuCzV70RqframAninyG2VvKht-yETtcdLJIL2VXSvewIZTKHlODrZen7B3ugWAJ6u0MLBNohHQDdlwjsdsOAKX$ | view it on GitHub ] , or [ https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/A4LXSXOOM67V7D55CH6XLPTYU3YEFAVCNFSM6AAAAABDSV4J7KVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4DKNJTGA3DQ__;!!D9dNQwwGXtA!R01VYwQuCzV70RqframAninyG2VvKht-yETtcdLJIL2VXSvewIZTKHlODrZen7B3ugWAJ6u0MLBNohHQDdlwjumUB6Ff$ | unsubscribe ] . You are receiving this because you were mentioned. Message ID: ***@***.***>

[giadaan]

eelbrain version 0.39.8

[christianbrodbeck]

The error happens when automatically trying to load the sensor connectivity (information about which sensor is adjacent to which other sensor).

Does the issue only occur with MneExperiment.make_epoch_selection() or also in other contexts like MneExperiment.load_epochs() (use reject=False)? If the former, could you re-try with Eelbrain 0.40a7 (https://github.com/christianbrodbeck/Eelbrain/wiki/Installing#pre-release-versions)? Otherwise, can you share a short segment of data?

[giadaan]

If I set reject=False in load_epochs() it works! Thank you!