Note
Click here to download the full example code
Brainstorm CTF phantom dataset tutorial¶
Here we compute the evoked from raw for the Brainstorm CTF phantom tutorial dataset. For comparison, see 1 and:
References¶
- 1
François Tadel, Sylvain Baillet, John C. Mosher, Dimitrios Pantazis, and Richard M. Leahy. Brainstorm: a user-friendly application for MEG/EEG analysis. Computational Intelligence and Neuroscience, 2011:1–13, 2011. doi:10.1155/2011/879716.
# Authors: Eric Larson <larson.eric.d@gmail.com>
#
# License: BSD-3-Clause
import os.path as op
import warnings
import numpy as np
import matplotlib.pyplot as plt
import mne
from mne import fit_dipole
from mne.datasets.brainstorm import bst_phantom_ctf
from mne.io import read_raw_ctf
print(__doc__)
The data were collected with a CTF system at 2400 Hz.
data_path = bst_phantom_ctf.data_path(verbose=True)
# Switch to these to use the higher-SNR data:
# raw_path = op.join(data_path, 'phantom_200uA_20150709_01.ds')
# dip_freq = 7.
raw_path = op.join(data_path, 'phantom_20uA_20150603_03.ds')
dip_freq = 23.
erm_path = op.join(data_path, 'emptyroom_20150709_01.ds')
raw = read_raw_ctf(raw_path, preload=True)
Out:
ds directory : /home/circleci/mne_data/MNE-brainstorm-data/bst_phantom_ctf/phantom_20uA_20150603_03.ds
res4 data read.
hc data read.
Separate EEG position data file read.
Quaternion matching (desired vs. transformed):
-0.39 74.35 0.00 mm <-> -0.39 74.35 -0.00 mm (orig : -39.23 63.82 -204.07 mm) diff = 0.000 mm
0.39 -74.35 0.00 mm <-> 0.39 -74.35 0.00 mm (orig : 65.69 -41.53 -205.68 mm) diff = 0.000 mm
75.00 0.00 0.00 mm <-> 75.00 -0.00 0.00 mm (orig : 64.32 61.80 -226.08 mm) diff = 0.000 mm
Coordinate transformations established.
Polhemus data for 3 HPI coils added
Device coordinate locations for 3 HPI coils added
Measurement info composed.
Finding samples for /home/circleci/mne_data/MNE-brainstorm-data/bst_phantom_ctf/phantom_20uA_20150603_03.ds/phantom_20uA_20150603_03.meg4:
System clock channel is available, checking which samples are valid.
10 x 2400 = 24000 samples from 304 chs
Current compensation grade : 3
Reading 0 ... 23999 = 0.000 ... 10.000 secs...
The sinusoidal signal is generated on channel HDAC006, so we can use that to obtain precise timing.
sinusoid, times = raw[raw.ch_names.index('HDAC006-4408')]
plt.figure()
plt.plot(times[times < 1.], sinusoid.T[times < 1.])
Let’s create some events using this signal by thresholding the sinusoid.
The CTF software compensation works reasonably well:
raw.plot()
But here we can get slightly better noise suppression, lower localization bias, and a better dipole goodness of fit with spatio-temporal (tSSS) Maxwell filtering:
raw.apply_gradient_compensation(0) # must un-do software compensation first
mf_kwargs = dict(origin=(0., 0., 0.), st_duration=10.)
raw = mne.preprocessing.maxwell_filter(raw, **mf_kwargs)
raw.plot()
Out:
Compensator constructed to change 3 -> 0
Applying compensator to loaded data
Maxwell filtering raw data
No bad MEG channels
Processing 0 gradiometers and 299 magnetometers (of which 290 are actually KIT gradiometers)
Using origin 0.0, 0.0, 0.0 mm in the head frame
Processing data using tSSS with st_duration=10.0
Using 86/95 harmonic components for 0.000 (71/80 in, 15/15 out)
Using loaded raw data
Processing 1 data chunk
Projecting 8 intersecting tSSS components for 0.000 - 10.000 sec (#1/1)
[done]
Our choice of tmin and tmax should capture exactly one cycle, so we can make the unusual choice of baselining using the entire epoch when creating our evoked data. We also then crop to a single time point (@t=0) because this is a peak in our signal.
tmin = -0.5 / dip_freq
tmax = -tmin
epochs = mne.Epochs(raw, events, event_id=1, tmin=tmin, tmax=tmax,
baseline=(None, None))
evoked = epochs.average()
evoked.plot(time_unit='s')
evoked.crop(0., 0.)
Out:
Not setting metadata
Not setting metadata
460 matching events found
Setting baseline interval to [-0.021666666666666667, 0.021666666666666667] sec
Applying baseline correction (mode: mean)
0 projection items activated
Let’s use a sphere head geometry model and let’s see the coordinate alignment and the sphere location.
sphere = mne.make_sphere_model(r0=(0., 0., 0.), head_radius=0.08)
mne.viz.plot_alignment(raw.info, subject='sample',
meg='helmet', bem=sphere, dig=True,
surfaces=['brain'])
del raw, epochs
Out:
Equiv. model fitting -> RV = 0.00372821 %
mu1 = 0.943946 lambda1 = 0.139079
mu2 = 0.665521 lambda2 = 0.684839
mu3 = -0.0973038 lambda3 = -0.013548
Set up EEG sphere model with scalp radius 80.0 mm
Getting helmet for system CTF_275
To do a dipole fit, let’s use the covariance provided by the empty room recording.
raw_erm = read_raw_ctf(erm_path).apply_gradient_compensation(0)
raw_erm = mne.preprocessing.maxwell_filter(raw_erm, coord_frame='meg',
**mf_kwargs)
cov = mne.compute_raw_covariance(raw_erm)
del raw_erm
with warnings.catch_warnings(record=True):
# ignore warning about data rank exceeding that of info (75 > 71)
warnings.simplefilter('ignore')
dip, residual = fit_dipole(evoked, cov, sphere, verbose=True)
Out:
ds directory : /home/circleci/mne_data/MNE-brainstorm-data/bst_phantom_ctf/emptyroom_20150709_01.ds
res4 data read.
hc data read.
Separate EEG position data file read.
Quaternion matching (desired vs. transformed):
-0.00 74.50 0.00 mm <-> -0.00 74.50 -0.00 mm (orig : -50.17 57.61 -188.51 mm) diff = 0.000 mm
0.00 -74.50 0.00 mm <-> 0.00 -74.50 0.00 mm (orig : 60.49 -42.15 -190.81 mm) diff = 0.000 mm
74.66 0.00 0.00 mm <-> 74.66 -0.00 0.00 mm (orig : 53.03 61.29 -209.99 mm) diff = 0.000 mm
Coordinate transformations established.
Polhemus data for 3 HPI coils added
Device coordinate locations for 3 HPI coils added
Measurement info composed.
Finding samples for /home/circleci/mne_data/MNE-brainstorm-data/bst_phantom_ctf/emptyroom_20150709_01.ds/emptyroom_20150709_01.meg4:
System clock channel is available, checking which samples are valid.
100 x 600 = 60000 samples from 304 chs
Current compensation grade : 3
Compensator constructed to change 3 -> 0
Maxwell filtering raw data
No bad MEG channels
Processing 0 gradiometers and 299 magnetometers (of which 290 are actually KIT gradiometers)
Using origin 0.0, 0.0, 0.0 mm in the meg frame (1.3, -8.8, -2.8 mm in the head frame)
Processing data using tSSS with st_duration=10.0
Using 90/95 harmonic components for 0.000 (75/80 in, 15/15 out)
Loading raw data from disk
Processing 10 data chunks
Projecting 8 intersecting tSSS components for 0.000 - 9.998 sec (#1/10)
Projecting 8 intersecting tSSS components for 10.000 - 19.998 sec (#2/10)
Projecting 8 intersecting tSSS components for 20.000 - 29.998 sec (#3/10)
Projecting 8 intersecting tSSS components for 30.000 - 39.998 sec (#4/10)
Projecting 9 intersecting tSSS components for 40.000 - 49.998 sec (#5/10)
Projecting 8 intersecting tSSS components for 50.000 - 59.998 sec (#6/10)
Projecting 7 intersecting tSSS components for 60.000 - 69.998 sec (#7/10)
Projecting 9 intersecting tSSS components for 70.000 - 79.998 sec (#8/10)
Projecting 9 intersecting tSSS components for 80.000 - 89.998 sec (#9/10)
Projecting 8 intersecting tSSS components for 90.000 - 99.998 sec (#10/10)
[done]
Using up to 500 segments
Number of samples used : 60000
[done]
BEM : <ConductorModel | Sphere (3 layers): r0=[0.0, 0.0, 0.0] R=80 mm>
MRI transform : identity
Sphere model : origin at ( 0.00 0.00 0.00) mm, rad = 0.1 mm
Guess grid : 20.0 mm
Guess mindist : 5.0 mm
Guess exclude : 20.0 mm
Using normal MEG coil definitions.
Coordinate transformation: MRI (surface RAS) -> head
1.000000 0.000000 0.000000 0.00 mm
0.000000 1.000000 0.000000 0.00 mm
0.000000 0.000000 1.000000 0.00 mm
0.000000 0.000000 0.000000 1.00
Coordinate transformation: MEG device -> head
0.999939 -0.002039 -0.010868 -2.00 mm
-0.001115 0.959234 -0.282612 -20.74 mm
0.011001 0.282607 0.959173 9.38 mm
0.000000 0.000000 0.000000 1.00
0 bad channels total
Read 273 MEG channels from info
Read 26 MEG compensation channels from info
105 coil definitions read
Coordinate transformation: MEG device -> head
0.999939 -0.002039 -0.010868 -2.00 mm
-0.001115 0.959234 -0.282612 -20.74 mm
0.011001 0.282607 0.959173 9.38 mm
0.000000 0.000000 0.000000 1.00
5 compensation data sets in info
MEG coil definitions created in head coordinates.
Decomposing the sensor noise covariance matrix...
Removing 5 compensators from info because not all compensation channels were picked.
Computing rank from covariance with rank=None
Using tolerance 1.9e-15 (2.2e-16 eps * 273 dim * 0.031 max singular value)
Estimated rank (mag): 75
MAG: rank 75 computed from 273 data channels with 0 projectors
Setting small MAG eigenvalues to zero (without PCA)
Created the whitener using a noise covariance matrix with rank 75 (198 small eigenvalues omitted)
---- Computing the forward solution for the guesses...
Making a spherical guess space with radius 72.0 mm...
Filtering (grid = 20 mm)...
Surface CM = ( 0.0 0.0 0.0) mm
Surface fits inside a sphere with radius 72.0 mm
Surface extent:
x = -72.0 ... 72.0 mm
y = -72.0 ... 72.0 mm
z = -72.0 ... 72.0 mm
Grid extent:
x = -80.0 ... 80.0 mm
y = -80.0 ... 80.0 mm
z = -80.0 ... 80.0 mm
729 sources before omitting any.
178 sources after omitting infeasible sources not within 20.0 - 72.0 mm.
170 sources remaining after excluding the sources outside the surface and less than 5.0 mm inside.
Go through all guess source locations...
[done 170 sources]
---- Fitted : 0.0 ms
No projector specified for this dataset. Please consider the method self.add_proj.
1 time points fitted
Compare the actual position with the estimated one.
expected_pos = np.array([18., 0., 49.])
diff = np.sqrt(np.sum((dip.pos[0] * 1000 - expected_pos) ** 2))
print('Actual pos: %s mm' % np.array_str(expected_pos, precision=1))
print('Estimated pos: %s mm' % np.array_str(dip.pos[0] * 1000, precision=1))
print('Difference: %0.1f mm' % diff)
print('Amplitude: %0.1f nAm' % (1e9 * dip.amplitude[0]))
print('GOF: %0.1f %%' % dip.gof[0])
Out:
Actual pos: [18. 0. 49.] mm
Estimated pos: [18.5 -2.2 44.6] mm
Difference: 4.9 mm
Amplitude: 10.0 nAm
GOF: 96.5 %
Total running time of the script: ( 0 minutes 26.677 seconds)
Estimated memory usage: 501 MB