[Mne_analysis] Resampling with TMS artifacts

[Alexandre Gramfort]

to interpolate the artifact you need to load the data from disk.

it seems that your data are big and you cannot load them in memory.

how big are your data? How much RAM do you have on your machine?

Alex

On Wed, Feb 14, 2018 at 8:11 PM, Rockhill, Alexander P. <
AROCKHILL at mgh.harvard.edu> wrote:

> Hi Mainak,
>
>     Thank you for the suggestion. When I load in the raw data using the
> string preload option, there isn't a problem, but when try giving a string
> for preload to the epochs, I get:
>
> Traceback (most recent call last):
>   File "<stdin>", line 4, in <module>
>   File "<string>", line 2, in __init__
>   File "/autofs/space/karima_001/users/alex/software/anaconda2.
> 7/lib/python2.7/site-packages/mne-0.16.dev0-py2.7.egg/mne/utils.py", line
> 728, in verbose
>     return function(*args, **kwargs)
>   File "/autofs/space/karima_001/users/alex/software/anaconda2.
> 7/lib/python2.7/site-packages/mne-0.16.dev0-py2.7.egg/mne/epochs.py",
> line 1960, in __init__
>     verbose=verbose)
>   File "/autofs/space/karima_001/users/alex/software/anaconda2.
> 7/lib/python2.7/site-packages/mne-0.16.dev0-py2.7.egg/mne/epochs.py",
> line 386, in __init__
>     self.load_data()  # this will do the projection
>   File "/autofs/space/karima_001/users/alex/software/anaconda2.
> 7/lib/python2.7/site-packages/mne-0.16.dev0-py2.7.egg/mne/epochs.py",
> line 448, in load_data
>     self._data = self._get_data()
>   File "<string>", line 2, in _get_data
>   File "/autofs/space/karima_001/users/alex/software/anaconda2.
> 7/lib/python2.7/site-packages/mne-0.16.dev0-py2.7.egg/mne/utils.py", line
> 728, in verbose
>     return function(*args, **kwargs)
>   File "/autofs/space/karima_001/users/alex/software/anaconda2.
> 7/lib/python2.7/site-packages/mne-0.16.dev0-py2.7.egg/mne/epochs.py",
> line 1212, in _get_data
>     dtype=epoch_out.dtype, order='C')
> MemoryError
>
>
>
> In order to interpolate the artifact and downsample the data, I am
> following recommendations that the data be in epochs. Is there any
> suggestions for how to avoid this?
>
> Thanks,
>
> Alex
> ------------------------------
> *From:* mne_analysis-bounces at nmr.mgh.harvard.edu [
> mne_analysis-bounces at nmr.mgh.harvard.edu] on behalf of Mainak Jas [
> mainakjas at gmail.com]
> *Sent:* Wednesday, February 14, 2018 11:29 AM
> *To:* Discussion and support forum for the users of MNE Software
> *Subject:* Re: [Mne_analysis] Resampling with TMS artifacts
>
> Hi,
>
> How long is the artifact? Probably you could use fix_stim_artifact for
> this: https://mne-tools.github.io/dev/generated/mne.
> preprocessing.fix_stim_artifact.html
>
> or use decim parameter when epoching
>
> Mainak
>
> On Wed, Feb 14, 2018 at 3:49 PM, Rockhill, Alexander P. <
> AROCKHILL at mgh.harvard.edu> wrote:
>
>> Hi all,
>>
>>     I was wondering about the best way to resample data with a
>> high-frequency TMS artifact. I first epoched the raw data so that the TMS
>> events would be kept but when I resample the epochs, a low-pass filter is
>> applied which makes sense but causes a large filter artifact from the TMS
>> pulse. Is there any way to not apply this filter?
>>
>> Thanks,
>>
>> Alex
>>
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