[Mne_analysis] autoreject

Tue Jul 10 10:27:44 EDT 2018

        External Email - Use Caution        

Hi Nathan,

The code and the version look good. I am wondering if there may be any
Salzburg peculiarities with the fif file. Could you share some of the data
with us? (also privately).

Best,
Denis
On Tue 10 Jul 2018 at 16:08, Nathan Weisz <nathanweisz at me.com> wrote:

>         External Email - Use Caution
>
> Hi Mainak,
>
> thanks for the reply.
>
> i am indeed not experienced in python. i mindlessly copy-pasted
> instructions from here:
> http://autoreject.github.io
>
> >>> pip install -U autoreject
> Requirement already up-to-date: autoreject in
> ./anaconda3/lib/python3.6/site-packages (0.1)
>
> is this the most recent version?
>
> regarding your other question:
> >>> epochs.info['bads']
> []
>
> best,
> nathan
>
>
> Am 10.07.2018 um 15:45 schrieb Mainak Jas <mainakjas at gmail.com>:
>
>         External Email - Use Caution
>
> Hi Nathan,
>
> It appears you do not have the latest version of autoreject. Could you try
> upgrading to the latest version from pip
> and trying again? Also what do you have in epochs.info['bads'] before you
> apply autoreject?
>
> Mainak
>
> On Tue, Jul 10, 2018 at 5:47 AM, Nathan Weisz <nathanweisz at me.com> wrote:
>
>>         External Email - Use Caution
>>
>> Hi,
>>
>> i am trying to explore a little the "autoreject" tools. specifically i am
>> trying to apply following example:
>>
>> https://autoreject.github.io/auto_examples/plot_auto_repair.html#sphx-glr-auto-examples-plot-auto-repair-py
>>
>> to a dataset recorded in salzburg.
>>
>> i adapted the code to chop out 2s epochs from the fif file. the rest
>> should be the same as in the tutorial example (which works great btw). code
>> below.
>>
>> however i am getting an error message that is over the top of my head.
>> >>> (executing lines 34 to 36 of "<tmp 1>")
>> Running autoreject on ch_type=grad
>> Traceback (most recent call last):
>> File "<tmp 1>", line 36, in <module>
>> ar.fit(epochs)
>> File
>> "/Users/b1019548/anaconda3/lib/python3.6/site-packages/autoreject/autoreject.py",
>> line 878, in fit
>> self.consensus, self.verbose)
>> File
>> "/Users/b1019548/anaconda3/lib/python3.6/site-packages/autoreject/autoreject.py",
>> line 683, in _run_local_reject_cv
>> local_reject.fit(epochs)
>> File
>> "/Users/b1019548/anaconda3/lib/python3.6/site-packages/autoreject/autoreject.py",
>> line 600, in fit
>> epochs.copy(), picks=self.picks_, verbose=self.verbose)
>> File
>> "/Users/b1019548/anaconda3/lib/python3.6/site-packages/autoreject/autoreject.py",
>> line 367, in compute_thresholds
>> verbose=verbose)
>> File
>> "/Users/b1019548/anaconda3/lib/python3.6/site-packages/autoreject/utils.py",
>> line 231, in clean_by_interp
>> interpolate_bads(inst_clean, picks=picks, reset_bads=True, mode='fast')
>> File
>> "/Users/b1019548/anaconda3/lib/python3.6/site-packages/autoreject/utils.py",
>> line 279, in interpolate_bads
>> _interpolate_bads_meg_fast(inst, picks=meg_picks_interp, mode=mode)
>> File
>> "/Users/b1019548/anaconda3/lib/python3.6/site-packages/autoreject/utils.py",
>> line 392, in _interpolate_bads_meg_fast
>> assert ch_names_a == ch_names_b
>> AssertionError
>>
>> this is likely due to my ignorance in the proper use of autoreject. but
>> the error message makes it difficult for me to infer what the problem might
>> be. i would appreciate any pointers.
>>
>> best,
>> nathan
>>
>> import numpy as np
>>
>> n_interpolates = np.array([1, 4, 32])
>> consensus_percs = np.linspace(0, 1.0, 11)
>>
>> ##
>>
>> import mne # noqa
>> from mne.utils import check_random_state # noqa
>>
>> from autoreject import (AutoReject, set_matplotlib_defaults) # noqa
>>
>> check_random_state(42)
>>
>> data_path = '/Users/b1019548/Desktop/Data_Sternberg/'
>> raw_fname = data_path + 'jens_H.fif'
>> raw = mne.io.read_raw_fif(raw_fname, preload=True)
>>
>>
>>
>> events = mne.make_fixed_length_events(raw, id=1, duration=2)
>>
>> raw.info['bads'] = []
>> picks = mne.pick_types(raw.info, meg='grad', eeg=False, stim=False,
>> eog=False, include=[], exclude=[])
>>
>> raw.info['projs'] = list()
>>
>> epochs = mne.Epochs(raw, events, tmin=0, tmax=2,
>> baseline=(None, 0), reject=None,
>> verbose=False, detrend=0, preload=True)
>>
>>
>> ##
>> ar = AutoReject(n_interpolates, consensus_percs, picks=picks,
>> thresh_method='random_search', random_state=42)
>> ar.fit(epochs)
>> epochs_clean = ar.transform(epochs)
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> 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.
>>
>>
> _______________________________________________
> 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.
>
>
> _______________________________________________
> 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.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20180710/afd223b5/attachment-0001.html 