content: """
  .. _tut-inverse-methods:
  
  Source localization with MNE/dSPM/sLORETA/eLORETA
  =================================================
  
  The aim of this tutorial is to teach you how to compute and apply a linear
  minimum-norm inverse method on evoked/raw/epochs data.
  """
  
  import os.path as op
  
  import numpy as np
  import matplotlib.pyplot as plt
  
  import mne
  from mne.datasets import sample
  from mne.minimum_norm import make_inverse_operator, apply_inverse
  
  ###############################################################################
  # Process MEG data
  
  data_path = sample.data_path()
  raw_fname = op.join(data_path, 'MEG', 'sample',
                      'sample_audvis_filt-0-40_raw.fif')
  
  raw = mne.io.read_raw_fif(raw_fname)  # already has an average reference
  events = mne.find_events(raw, stim_channel='STI 014')
  
  event_id = dict(aud_l=1)  # event trigger and conditions
  tmin = -0.2  # start of each epoch (200ms before the trigger)
  tmax = 0.5  # end of each epoch (500ms after the trigger)
  raw.info['bads'] = ['MEG 2443', 'EEG 053']
  baseline = (None, 0)  # means from the first instant to t = 0
  reject = dict(grad=4000e-13, mag=4e-12, eog=150e-6)
  
  epochs = mne.Epochs(raw, events, event_id, tmin, tmax, proj=True,
                      picks=('meg', 'eog'), baseline=baseline, reject=reject)
  
  ###############################################################################
  # Compute regularized noise covariance
  # ------------------------------------
  # For more details see :ref:`tut-compute-covariance`.
  
  noise_cov = mne.compute_covariance(
      epochs, tmax=0., method=['shrunk', 'empirical'], rank=None, verbose=True)
  
  fig_cov, fig_spectra = mne.viz.plot_cov(noise_cov, raw.info)
  
  ###############################################################################
  # Compute the evoked response
  # ---------------------------
  # Let's just use the MEG channels for simplicity.
  
  evoked = epochs.average().pick('meg')
  evoked.plot(time_unit='s')
  evoked.plot_topomap(times=np.linspace(0.05, 0.15, 5), ch_type='mag',
                      time_unit='s')
  
  ###############################################################################
  # It's also a good idea to look at whitened data:
  
  evoked.plot_white(noise_cov, time_unit='s')
  del epochs, raw  # to save memory
  
  ###############################################################################
  # Inverse modeling: MNE/dSPM on evoked and raw data
  # -------------------------------------------------
  # Here we first read the forward solution. You will likely need to compute
  # one for your own data -- see :ref:`tut-forward` for information on how
  # to do it.
  
  fname_fwd = data_path + '/MEG/sample/sample_audvis-meg-oct-6-fwd.fif'
  fwd = mne.read_forward_solution(fname_fwd)
  
  ###############################################################################
  # Next, we make an MEG inverse operator.
  
  inverse_operator = make_inverse_operator(
      evoked.info, fwd, noise_cov, loose=0.2, depth=0.8)
  del fwd
  
  # You can write it to disk with::
  #
  #     >>> from mne.minimum_norm import write_inverse_operator
  #     >>> write_inverse_operator('sample_audvis-meg-oct-6-inv.fif',
  #                                inverse_operator)
  
  ###############################################################################
  # Compute inverse solution
  # ------------------------
  # We can use this to compute the inverse solution and obtain source time
  # courses:
  
  method = "dSPM"
  snr = 3.
  lambda2 = 1. / snr ** 2
  stc, residual = apply_inverse(evoked, inverse_operator, lambda2,
                                method=method, pick_ori=None,
                                return_residual=True, verbose=True)
  
  ###############################################################################
  # Visualization
  # -------------
  # We can look at different dipole activations:
  
  fig, ax = plt.subplots()
  ax.plot(1e3 * stc.times, stc.data[::100, :].T)
  ax.set(xlabel='time (ms)', ylabel='%s value' % method)
  
  ###############################################################################
  # Examine the original data and the residual after fitting:
  
  fig, axes = plt.subplots(2, 1)
  evoked.plot(axes=axes)
  for ax in axes:
      ax.texts = []
      for line in ax.lines:
          line.set_color('#98df81')
  residual.plot(axes=axes)
  
  ###############################################################################
  # Here we use peak getter to move visualization to the time point of the peak
  # and draw a marker at the maximum peak vertex.
  
  # sphinx_gallery_thumbnail_number = 9
  
  vertno_max, time_max = stc.get_peak(hemi='rh')
  
  subjects_dir = data_path + '/subjects'
  surfer_kwargs = dict(
      hemi='rh', subjects_dir=subjects_dir,
      clim=dict(kind='value', lims=[8, 12, 15]), views='lateral',
      initial_time=time_max, time_unit='s', size=(800, 800), smoothing_steps=10)
  brain = stc.plot(**surfer_kwargs)
  brain.add_foci(vertno_max, coords_as_verts=True, hemi='rh', color='blue',
                 scale_factor=0.6, alpha=0.5)
  brain.add_text(0.1, 0.9, 'dSPM (plus location of maximal activation)', 'title',
                 font_size=14)
  
  # The documentation website's movie is generated with:
  # brain.save_movie(..., tmin=0.05, tmax=0.15, interpolation='linear',
  #                  time_dilation=20, framerate=10, time_viewer=True)
  
  ###############################################################################
  # There are many other ways to visualize and work with source data, see
  # for example:
  #
  # - :ref:`tut-viz-stcs`
  # - :ref:`ex-morph-surface`
  # - :ref:`ex-morph-volume`
  # - :ref:`ex-vector-mne-solution`
  # - :ref:`tut-dipole-orientations`
  # - :ref:`tut-mne-fixed-free`
  # - :ref:`examples using apply_inverse
  #   <sphx_glr_backreferences_mne.minimum_norm.apply_inverse>`.
  