The source localization results can be seen from another window or something like that.
Actual results
0 files missing from /Users/masarusasaki/.pyenv/versions/anaconda3-5.3.1/lib/python3.7/site-packages/mne/datasets/_fsaverage/root.txt in /Users/masarusasaki/mne_data/MNE-fsaverage-data
0 files missing from /Users/masarusasaki/.pyenv/versions/anaconda3-5.3.1/lib/python3.7/site-packages/mne/datasets/_fsaverage/bem.txt in /Users/masarusasaki/mne_data/MNE-fsaverage-data/fsaverage
Reading /Users/masarusasaki/Documents/GitHub/Script/sasakidata/output_rest/2020-6-10/asrnc/rest1_f2t30_ave_ref_asrnc_interp_averef_ica_dipole_icbrain.fdt
Reading 0 ... 154623 = 0.000 ... 309.246 secs...
Adding average EEG reference projection.
1 projection items deactivated
Average reference projection was added, but has not been applied yet. Use the apply_proj method to apply it.
Source space : /Users/masarusasaki/mne_data/MNE-fsaverage-data/fsaverage/bem/fsaverage-ico-5-src.fif
MRI -> head transform : /Users/masarusasaki/.pyenv/versions/anaconda3-5.3.1/lib/python3.7/site-packages/mne/data/fsaverage/fsaverage-trans.fif
Measurement data : instance of Info
Conductor model : /Users/masarusasaki/mne_data/MNE-fsaverage-data/fsaverage/bem/fsaverage-5120-5120-5120-bem-sol.fif
Accurate field computations
Do computations in head coordinates
Free source orientations
Reading /Users/masarusasaki/mne_data/MNE-fsaverage-data/fsaverage/bem/fsaverage-ico-5-src.fif...
Read 2 source spaces a total of 20484 active source locations
Coordinate transformation: MRI (surface RAS) -> head
0.999994 0.003552 0.000202 -1.76 mm
-0.003558 0.998389 0.056626 31.09 mm
-0.000001 -0.056626 0.998395 39.60 mm
0.000000 0.000000 0.000000 1.00
Read 29 EEG channels from info
Head coordinate coil definitions created.
Source spaces are now in head coordinates.
Setting up the BEM model using /Users/masarusasaki/mne_data/MNE-fsaverage-data/fsaverage/bem/fsaverage-5120-5120-5120-bem-sol.fif...
Loading surfaces...
Three-layer model surfaces loaded.
Loading the solution matrix...
Loaded linear_collocation BEM solution from /Users/masarusasaki/mne_data/MNE-fsaverage-data/fsaverage/bem/fsaverage-5120-5120-5120-bem-sol.fif
Employing the head->MRI coordinate transform with the BEM model.
BEM model fsaverage-5120-5120-5120-bem-sol.fif is now set up
Source spaces are in head coordinates.
Checking that the sources are inside the surface and at least 5.0 mm away (will take a few...)
Skipping interior check for 2433 sources that fit inside a sphere of radius 47.7 mm
Skipping solid angle check for 0 points using Qhull
Skipping interior check for 2241 sources that fit inside a sphere of radius 47.7 mm
Skipping solid angle check for 0 points using Qhull
Setting up for EEG...
Computing EEG at 20484 source locations (free orientations)...
Finished.
<Forward | MEG channels: 0 | EEG channels: 29 | Source space: Surface with 20484 vertices | Source orientation: Free>
Using up to 1500 segments
Number of samples used : 150000
[done]
Converting forward solution to surface orientation
No patch info available. The standard source space normals will be employed in the rotation to the local surface coordinates....
Converting to surface-based source orientations...
[done]
Computing inverse operator with 29 channels.
29 out of 29 channels remain after picking
Selected 29 channels
Creating the depth weighting matrix...
29 EEG channels
limit = 20485/20484 = 2.709372
scale = 54673.7 exp = 0.8
Applying loose dipole orientations. Loose value of 0.2.
Whitening the forward solution.
Created an SSP operator (subspace dimension = 1)
Computing rank from covariance with rank=None
Using tolerance 3.3e-14 (2.2e-16 eps * 29 dim * 5.1 max singular value)
Estimated rank (eeg): 6
EEG: rank 6 computed from 29 data channels with 1 projector
Setting small EEG 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 = 1.90195
scaling factor to adjust the trace = 3.18336e+18
Traceback (most recent call last):
File "/Users/masarusasaki/Documents/GitHub/Script/Python/EEG_analysis/sloreta.py", line 49, in <module>
stc = apply_inverse(raw, inverse_operator, verbose=True)
File "<decorator-gen-302>", line 20, in apply_inverse
File "/Users/masarusasaki/.pyenv/versions/anaconda3-5.3.1/lib/python3.7/site-packages/mne/minimum_norm/inverse.py", line 877, in apply_inverse
method_params, return_residual, use_cps)
File "/Users/masarusasaki/.pyenv/versions/anaconda3-5.3.1/lib/python3.7/site-packages/mne/minimum_norm/inverse.py", line 891, in _apply_inverse
nave = evoked.nave
AttributeError: 'RawEEGLAB' object has no attribute 'nave'
[Finished in 34.809s]
Additional information
I have another problem with read_raw_eeglab because this function doesn't reflect the re-reference data in Python script.
So, I need to add the set_eeg_reference before computing the inverse_operator and apply_inverse function.
Describe the bug
I am faced with the error message as you see in the title when I tried to run the source localization script I made below.
The preprocessing to remove the noise with ICA was done by Matlab before running this script.
The EEG headset is Quick 30 made by Cognionics.
Thank you in advance.
Steps to reproduce
I attached here the script I run.
Expected results
The source localization results can be seen from another window or something like that.
Actual results
Additional information
I have another problem with read_raw_eeglab because this function doesn't reflect the re-reference data in Python script. So, I need to add the set_eeg_reference before computing the inverse_operator and apply_inverse function.