[Mne_analysis] autoreject

[Mainak Jas]

        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)
>
>
>
>
>
>
>
>
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