[Mne_analysis] [concatenation of annotated epochs]

Sat Sep 3 07:05:33 EDT 2022

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Hi Eric,

Thank you and that is indeed one workaround. I changed my analytic approach
(for radically different reasons)  so I don't need this fix urgently
anymore :-)  I did open a github issue though (as feature enhancement) with
the same title for future pointers as you suggested.

Many thanks, and great w-e.
Best,

Virginie van Wassenhove <https://secure-web.cisco.com/1h6fmLteG2ehz2u3spEsRwBVGAFYFJuY9Pf7LtxhUp74rXkjYWxjbrxZ4ER4A-rYZ2xH2cFY78mBkR7teSjJZHQw9QJ87b6dc6_aelzLwu22tRr6CqSmR1RiERLaOWl1_FKyJZt3GHCp2xmiW_jPFosIDc_ITNxcZZpeU5mt3FMg2vU7_99trYl6pSaBRWDquGogwgg5OxXguM7LKjcmkD8I6GBcLCfDjgsJF4XnBmTl_wunml8zgF8plYeYp65cTRcq8UVyS_fAV1GkUtjRlW5jGLioSa23DDoRl-J-UFC9hUhUcT5KZS1n94h9k6LGU/https%3A%2F%2Fbrainthemind.com%2F>
*My working hours may not be yours, respond in your own time*

On Fri, Sep 2, 2022 at 6:38 PM Eric Larson <larson.eric.d at gmail.com> wrote:

>         External Email - Use Caution
>
> 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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>> _____________________________________
>> CEA NeuroSpin, INSERM, Univ Paris-Saclay
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