Python-MNE-源定位和逆问题03：使用MNE、dSPM、sLORETA和eLORETA进行源定位

最新推荐文章于 2024-09-26 19:15:00 发布

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最新推荐文章于 2024-09-26 19:15:00 发布

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分类专栏： MNE-Python 翻译版-中文官方文档文章标签： python 开发语言学习 numpy 笔记信息可视化

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本教程的目的是教你如何把线性最小范数逆方法计算和应用在evoked/raw/epoch数据上：

import matplotlib.pyplot as plt
import numpy as np

import mne
from mne.datasets import sample
from mne.minimum_norm import apply_inverse, make_inverse_operator

处理MEG数据：

data_path = sample.data_path()
raw_fname = 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"]  # mark known bad channels
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,
)

Opening raw data file /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis_filt-0-40_raw.fif...
    Read a total of 4 projection items:
        PCA-v1 (1 x 102)  idle
        PCA-v2 (1 x 102)  idle
        PCA-v3 (1 x 102)  idle
        Average EEG reference (1 x 60)  idle
    Range : 6450 ... 48149 =     42.956 ...   320.665 secs
Ready.
319 events found on stim channel STI 014
Event IDs: [ 1  2  3  4  5 32]
Not setting metadata
72 matching events found
Setting baseline interval to [-0.19979521315838786, 0.0] s
Applying baseline correction (mode: mean)
Created an SSP operator (subspace dimension = 3)
3 projection items activated

计算正则化噪声协方差

noise_cov = mne.compute_covariance(
    epochs, tmax=0.0, method=["shrunk", "empirical"], rank=None, verbose=True
)

fig_cov, fig_spectra = mne.viz.plot_cov(noise_cov, raw.info)

在这里插入图片描述

Loading data for 72 events and 106 original time points …
Rejecting epoch based on EOG : [‘EOG 061’]
Rejecting epoch based on EOG : [‘EOG 061’]
Rejecting epoch based on EOG : [‘EOG 061’]
Rejecting epoch based on EOG : [‘EOG 061’]
Rejecting epoch based on EOG : [‘EOG 061’]
Rejecting epoch based on MAG : [‘MEG 1711’]
Rejecting epoch based on EOG : [‘EOG 061’]
Rejecting epoch based on EOG : [‘EOG 061’]
Rejecting epoch based on EOG : [‘EOG 061’]
Rejecting epoch based on EOG : [‘EOG 061’]
Rejecting epoch based on EOG : [‘EOG 061’]
Rejecting epoch based on EOG : [‘EOG 061’]
Rejecting epoch based on EOG : [‘EOG 061’]
Rejecting epoch based on EOG : [‘EOG 061’]
Rejecting epoch based on EOG : [‘EOG 061’]
Rejecting epoch based on EOG : [‘EOG 061’]
Rejecting epoch based on EOG : [‘EOG 061’]
17 bad epochs dropped
Created an SSP operator (subspace dimension = 3)
Setting small MEG eigenvalues to zero (without PCA)
Reducing data rank from 305 -> 302
Estimating covariance using SHRUNK
Done.
Estimating covariance using EMPIRICAL
Done.
Using cross-validation to select the best estimator.
Number of samples used : 1705
log-likelihood on unseen data (descending order):
shrunk: -1466.545
empirical: -1574.608
selecting best estimator: shrunk
[done]
Computing rank from covariance with rank=None
Using tolerance 2.2e-14 (2.2e-16 eps * 102 dim * 0.97 max singular value)
Estimated rank (mag): 99
MAG: rank 99 computed from 102 data channels with 0 projectors
Computing rank from covariance with rank=None
Using tolerance 1.6e-13 (2.2e-16 eps * 203 dim * 3.5 max singular value)
Estimated rank (grad): 203
GRAD: rank 203 computed from 203 data channels with 0 projectors

计算evoked

只用MEG通道，简化一下提高速度：

evoked = epochs.average().pick("meg")
evoked.plot(time_unit="s")
evoked.plot_topomap(times=np.linspace(0.05, 0.15, 5), ch_type="mag")

在这里插入图片描述
查看白化后的数据：

evoked.plot_white(noise_cov, time_unit="s")
del epochs, raw  # to save memory

在这里插入图片描述

NOTE: pick_types() is a legacy function. New code should use inst.pick(…).
Computing rank from covariance with rank=None
Using tolerance 1.6e-13 (2.2e-16 eps * 203 dim * 3.5 max singular value)
Estimated rank (grad): 203
GRAD: rank 203 computed from 203 data channels with 0 projectors
Computing rank from covariance with rank=None
Using tolerance 2.2e-14 (2.2e-16 eps * 102 dim * 0.97 max singular value)
Estimated rank (mag): 99
MAG: rank 99 computed from 102 data channels with 3 projectors
Created an SSP operator (subspace dimension = 3)
Computing rank from covariance with rank={‘grad’: 203, ‘mag’: 99, ‘meg’: 302}
Setting small MEG eigenvalues to zero (without PCA)
Created the whitener using a noise covariance matrix with rank 302 (3 small eigenvalues omitted)

逆模型：在evoked和raw数据上应用MNE/dSPM

在这里，我们首先读取forward solution。你可能需要为自己的数据计算一个，参考正问题的教程。

fname_fwd = data_path / "MEG" / "sample" / "sample_audvis-meg-oct-6-fwd.fif"
fwd = mne.read_forward_solution(fname_fwd)

Reading forward solution from /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-meg-oct-6-fwd.fif…
Reading a source space…
Computing patch statistics…
Patch information added…
Distance information added…
[done]
Reading a source space…
Computing patch statistics…
Patch information added…
Distance information added…
[done]
2 source spaces read
Desired named matrix (kind = 3523 (FIFF_MNE_FORWARD_SOLUTION_GRAD)) not available
Read MEG forward solution (7498 sources, 306 channels, free orientations)
Source spaces transformed to the forward solution coordinate frame

然后，我们来造一个逆算子：

inverse_operator = make_inverse_operator(
    evoked.info, fwd, noise_cov, loose=0.2, depth=0.8
)
del fwd

Converting forward solution to surface orientation
Average patch normals will be employed in the rotation to the local surface coordinates…
Converting to surface-based source orientations…
[done]
info[“bads”] and noise_cov[“bads”] do not match, excluding bad channels from both
Computing inverse operator with 305 channels.
305 out of 306 channels remain after picking
Selected 305 channels
Creating the depth weighting matrix…
203 planar channels
limit = 7265/7498 = 10.037795
scale = 2.52065e-08 exp = 0.8
Applying loose dipole orientations to surface source spaces: 0.2
Whitening the forward solution.
Created an SSP operator (subspace dimension = 3)
Computing rank from covariance with rank=None
Using tolerance 2.9e-13 (2.2e-16 eps * 305 dim * 4.2 max singular value)
Estimated rank (mag + grad): 302
MEG: rank 302 computed from 305 data channels with 3 projectors
Setting small MEG eigenvalues to zero (without PCA)
Creating the source covariance matrix
Adjusting source covariance matrix.
Computing SVD of whitened and weighted lead field matrix.
largest singular value = 4.69812
scaling factor to adjust the trace = 8.80908e+18 (nchan = 305 nzero = 3)

你可以将逆算子写入：

from mne.minimum_norm import write_inverse_operator
write_inverse_operator(
    "sample_audvis-meg-oct-6-inv.fif", inverse_operator
)

计算逆问题

我们可以使用它来计算逆解并获得stc：

method = "dSPM"  # could choose MNE, sLORETA, or eLORETA instead
snr = 3.0
lambda2 = 1.0 / snr**2
stc, residual = apply_inverse(
    evoked,
    inverse_operator,
    lambda2,
    method=method,
    pick_ori=None,
    return_residual=True,
    verbose=True,
)

Preparing the inverse operator for use…
Scaled noise and source covariance from nave = 1 to nave = 55
Created the regularized inverter
Created an SSP operator (subspace dimension = 3)
Created the whitener using a noise covariance matrix with rank 302 (3 small eigenvalues omitted)
Computing noise-normalization factors (dSPM)…
[done]
Applying inverse operator to “aud_l”…
Picked 305 channels from the data
Computing inverse…
Eigenleads need to be weighted …
Computing residual…
Explained 66.0% variance
Combining the current components…
dSPM…
[done]

可视化

fig, ax = plt.subplots()
ax.plot(1e3 * stc.times, stc.data[::100, :].T)
ax.set(xlabel="time (ms)", ylabel=f"{method} value")

在这里插入图片描述
对原始数据和拟合后的残差进行检验：

fig, axes = plt.subplots(2, 1)
evoked.plot(axes=axes)
for ax in axes:
    for text in list(ax.texts):
        text.remove()
    for line in ax.lines:
        line.set_color("#98df81")
residual.plot(axes=axes)

在这里插入图片描述
在这里，我们使用peak getter将可视化移动到峰值出现的时间点，并在最大峰值顶点处画一个标记。

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)