[Mne_analysis] Resampling with TMS artifacts

Rockhill, Alexander P. AROCKHILL at mgh.harvard.edu
Wed Feb 14 14:11:41 EST 2018
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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__
  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')

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?


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


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


On Wed, Feb 14, 2018 at 3:49 PM, Rockhill, Alexander P. <AROCKHILL at mgh.harvard.edu<mailto: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?



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