[Mne_analysis] Mne_analysis Digest, Vol 117, Issue 3
Dirk van Moorselaar
dirkvanmoorselaar at gmail.com
Tue Oct 3 05:50:59 EDT 2017
Dear Alexandre,
I probably do something wrong but it does not seem to work. In the final step of preprocessing I interpolate channels like this
epochs.interpolate_bads(reset_bads=True, mode ='accurate’) and then save them as a -epo.fif file
When I try to combine multiple sessions, I read in the different files and store them in a list, which I try to concatenate with the following code:
mne.concatenate_epochs(all_epochs) #where all_epochs is a list of epoched data data. However, this does seem to work and gives me the following error:
/Users/dirk/mne-python/mne/epochs.py in concatenate_epochs(epochs_list)
2737 .. versionadded:: 0.9.0
2738 """
-> 2739 return _finish_concat(*_concatenate_epochs(epochs_list))
2740
2741
/Users/dirk/mne-python/mne/epochs.py in _finish_concat(info, data, events, event_id, tmin, tmax, baseline, selection, drop_log, verbose)
2716 selection=selection, drop_log=drop_log, proj=False,
2717 on_missing='ignore', verbose=verbose)
-> 2718 out.drop_bad()
2719 return out
2720
/Users/dirk/mne-python/mne/epochs.py in drop_bad(self, reject, flat, verbose)
/Users/dirk/mne-python/mne/utils.py in verbose(function, *args, **kwargs)
724 with use_log_level(verbose_level):
725 return function(*args, **kwargs)
--> 726 return function(*args, **kwargs)
727
728
/Users/dirk/mne-python/mne/epochs.py in drop_bad(self, reject, flat, verbose)
964 raise ValueError('reject and flat, if strings, must be "existing"')
965 self._reject_setup(reject, flat)
--> 966 self._get_data(out=False)
967 return self
968
/Users/dirk/mne-python/mne/epochs.py in _get_data(self, out, verbose)
/Users/dirk/mne-python/mne/utils.py in verbose(function, *args, **kwargs)
724 with use_log_level(verbose_level):
725 return function(*args, **kwargs)
--> 726 return function(*args, **kwargs)
727
728
/Users/dirk/mne-python/mne/epochs.py in _get_data(self, out, verbose)
1129 good_idx = []
1130 n_out = 0
-> 1131 assert n_events == len(self.selection)
1132 for idx, sel in enumerate(self.selection):
1133 if self.preload: # from memory
AssertionError:
I checked and in both epoch objects self.info <http://self.info/>[‘bads’] = [].
Hope that this is helpful,
Dirk
> On 3 Oct 2017, at 11:30, mne_analysis-request at nmr.mgh.harvard.edu wrote:
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> Today's Topics:
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> 1. Re: trying to use ica.plot_overlay (Alexandre Gramfort)
> 2. Concatenate preprocessed epochs (Dirk van Moorselaar)
> 3. Re: Concatenate preprocessed epochs (Alexandre Gramfort)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 3 Oct 2017 10:15:19 +0200
> From: Alexandre Gramfort <alexandre.gramfort at inria.fr>
> Subject: Re: [Mne_analysis] trying to use ica.plot_overlay
> To: Discussion and support forum for the users of MNE Software
> <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
> <CADeotZo_27h_S08iMPO2E4DRsYLW3QN_tDfmVAH765OjxY_F4w at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> hi Megan,
>
> can you try with:
>
> ica.plot_sources(epoch_avg, exclude=[35])
>
>
> exclude should be in an int not a string.
>
>
> Alex
>
>
>
> On Tue, Oct 3, 2017 at 12:55 AM, Megan Schendel <mschendel at mrn.org> wrote:
>
>> Hi all,
>> I'm having trouble following the tutorial for Artifact Correction with ICA.
>> http://martinos.org/mne/stable/auto_tutorials/plot_
>> artifacts_correction_ica.html?highlight=ica%20fit
>>
>> I have epoched data where my artifact is timed to the event; I'm not
>> investigating EOG artifact. I am able to use ica.plot_properties and
>> ica.plot_sources fine. But when I try to do ica.plot_overlay, it looks
>> like it's not excluding my bad component. Since artifact is timed to
>> event, average is just the averaged epochs.
>>
>> Attached: images from ica.plot_properties, ica.plot_sources, and
>> ica.plot_overlay. I'm not exactly clear on what picks and exclude expects
>> (list, array, int?).
>>
>> Commands used are below.
>> Thanks very much for any help!
>>
>> Megan
>>
>> random_state = 23
>> n_components =50 # if float, select n_components by explained variance of PCA
>> method = 'fastica' # for comparison with EEGLAB try "extended-infomax" here
>> decim = 3 # we need sufficient statistics, not all time points -> saves time
>> reject=None # artifact is rather large, so don't want to reject it...
>>
>> ica = ICA(n_components=n_components, method=method, random_state=random_state)
>> ica.fit(epochs, picks=picks_meg, decim=decim, reject=reject)
>>
>> ica.plot_sources(epochs)
>>
>> epoch_avg= epochs.average()
>>
>> ica.plot_sources(epoch_avg, exclude=['35'])
>>
>> ica.plot_properties(epochs, picks=35, psd_args={'fmax': 35.},
>> image_args={'sigma': 1.})
>>
>>
>> # Following lines included with input and output:
>>
>> In [72]: ica.plot_overlay(epoch_avg, exclude=['35'], show=False)
>> Transforming to ICA space (50 components)
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/lib/python3.5/site-packages/numpy/lib/arraysetops.py:375: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
>> mask &= (ar1 != a)
>> Zeroing out 0 ICA components
>> Out[72]: <matplotlib.figure.Figure at 0x7f8c469d55c0>
>>
>>
>> In [74]: mne.__version__
>> Out[74]: '0.14.dev0'
>>
>>
>> MEG Technician
>> The Mind Research Network
>> 1101 Yale Blvd. NE
>> Albuquerque, New Mexico 87106
>>
>>
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> Message: 2
> Date: Tue, 3 Oct 2017 11:25:53 +0200
> From: Dirk van Moorselaar <dirkvanmoorselaar at gmail.com>
> Subject: [Mne_analysis] Concatenate preprocessed epochs
> To: mne_analysis at nmr.mgh.harvard.edu
> Message-ID: <A4177DA8-5BB1-4E8A-845F-8553D6A405B6 at gmail.com>
> Content-Type: text/plain; charset=us-ascii
>
> Hello,
>
> I have a follow up question on a question that I asked previously.
> In my experiment I have collected data into seperate sessions, on separate days. I apply preprocessing (artefact detection, Ica, bad electrode selection) on these sessions separately and after preprocessing and spline interpolation to correct bad channels I would like to combine these separate sessions int a single -epo.fif file.
>
> To do this I use mne.concatenate_epochs(). However, this fails and gives me an assertion error. I understood from my previous question that to get this to work I need to remove the bad channels from both sessions (even if we are dealing with separate channels in the two sessions) and then use interpolation on the concatenated data before further processing.
>
> At first sight I do not necessarily like this solution as in some cases I have to remove perfectly fine channels from one session, even though their signal was good in that session. Is there a workaround that still allows you to concatenate epochs, but does not force you to have the same channels marked as bad in both sessions?
>
> Thank you again,
>
> Dirk
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 3 Oct 2017 11:30:14 +0200
> From: Alexandre Gramfort <alexandre.gramfort at inria.fr>
> Subject: Re: [Mne_analysis] Concatenate preprocessed epochs
> To: Discussion and support forum for the users of MNE Software
> <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
> <CADeotZoDBnCBX+dDE2hrkatDWUeE=w6DSwUwKSDoqBRoV=pkLQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Dirk,
>
> if you interpolate the bads so you end up with only good channels it should
> work no?
>
> Alex
>
>
> On Tue, Oct 3, 2017 at 11:25 AM, Dirk van Moorselaar <
> dirkvanmoorselaar at gmail.com> wrote:
>
>> Hello,
>>
>> I have a follow up question on a question that I asked previously.
>> In my experiment I have collected data into seperate sessions, on separate
>> days. I apply preprocessing (artefact detection, Ica, bad electrode
>> selection) on these sessions separately and after preprocessing and spline
>> interpolation to correct bad channels I would like to combine these
>> separate sessions int a single -epo.fif file.
>>
>> To do this I use mne.concatenate_epochs(). However, this fails and gives
>> me an assertion error. I understood from my previous question that to get
>> this to work I need to remove the bad channels from both sessions (even if
>> we are dealing with separate channels in the two sessions) and then use
>> interpolation on the concatenated data before further processing.
>>
>> At first sight I do not necessarily like this solution as in some cases I
>> have to remove perfectly fine channels from one session, even though their
>> signal was good in that session. Is there a workaround that still allows
>> you to concatenate epochs, but does not force you to have the same channels
>> marked as bad in both sessions?
>>
>> Thank you again,
>>
>> Dirk
>>
>>
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
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