[Mne_analysis] [concatenation of annotated epochs]

Eric Larson larson.eric.d at gmail.com
Fri Sep 2 12:36:21 EDT 2022
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Is it possible for you instead to baseline correct, concatenate, then crop
out the baseline?

If not, it seems like in principle we might be able to concatenate even
with the epochs that you have. It might be worth opening an MNE-Python
issue on GitHub about it.

Eric


On Wed, Aug 31, 2022 at 5:10 AM Virginie van Wassenhove <
virginie.van.wassenhove at gmail.com> wrote:

>         External Email - Use Caution
>
> Hi folks,
>
> I am getting the error pasted below when trying to concatenate epochs that
> have been baselined and then cropped. Richard which included the
> annotation "(baseline period was cropped after baseline correction)" when
> doing so:
>
> [<EpochsFIF |  45 events (all good), 0 - 1 sec, baseline -0.2 – 0 sec
> (baseline period was cropped after baseline correction), ~42.5 MB, data
> loaded, with metadata,
>   '11': 45>,
>
> The limitation appears known in the error so my question is this an easy
> fix or should I find a work around?
>
> Many thanks,
> Virginie
>
> __________________________________________________
> Adding metadata with 39 columns
> 224 matching events found
>
> C:\Users\vv221713\AppData\Local\Temp\ipykernel_1360\3541098965.py:1:
> RuntimeWarning: Concatenation of Annotations within Epochs is not supported
> yet. All annotations will be dropped.
>   data_epo = mne.concatenate_epochs([epos_list[ei] for ei, e in
> enumerate(epos_list)
> Traceback (most recent call last):
>
>   File
> "C:\Users\vv221713\AppData\Local\Temp\ipykernel_1360\3541098965.py", line
> 1, in <cell line: 1>
>     data_epo = mne.concatenate_epochs([epos_list[ei] for ei, e in
> enumerate(epos_list)
>
>   File "<decorator-gen-267>", line 12, in concatenate_epochs
>
>   File
> "C:\Users\vv221713\AppData\Local\mne-python\1.1.1_0\lib\site-packages\mne\epochs.py",
> line 3544, in concatenate_epochs
>     return _finish_concat(*_concatenate_epochs(epochs_list,
>
>   File
> "C:\Users\vv221713\AppData\Local\mne-python\1.1.1_0\lib\site-packages\mne\epochs.py",
> line 3505, in _finish_concat
>     out = BaseEpochs(
>
>   File "<decorator-gen-247>", line 12, in __init__
>
>   File
> "C:\Users\vv221713\AppData\Local\mne-python\1.1.1_0\lib\site-packages\mne\epochs.py",
> line 557, in __init__
>     self.baseline = _check_baseline(baseline, times=self.times,
>
>   File
> "C:\Users\vv221713\AppData\Local\mne-python\1.1.1_0\lib\site-packages\mne\baseline.py",
> line 192, in _check_baseline
>     raise ValueError(msg)
>
> ValueError: Baseline interval [-0.2, 0.0] sec is outside of epochs data
> [0.0, 1.0] sec. Epochs were probably cropped.
> ______________________________
>
>
> Kind regards,
>
> *Virginie van Wassenhove*
> Dr. HDR.  [she/her] | Director, Cognition & Brain Dynamics
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