jjlatval / meg-inverse-unet Goto Github PK

Hi,

When I run simulate_data.py, I get the error
No such file or directory: '/home/mne_data/MNE-sample-data/subjects/sample/bem/sample-ico-3-src.fif'

In fact, when I look through the appropriate /bem folder, I see corresponding .fif files for oct-6, and some other stuff, but not for ico-3. I am a newbie in MNE Python, but I wanted to reproduce your experiments, so I did this:

surf = mne.setup_source_space('sample', spacing='ico3', subjects_dir='/home/mne_data/MNE-sample-data/subjects/')
mne.write_source_spaces('/home/mne_data/MNE-sample-data/subjects/sample/bem/sample-ico-3-src.fif', surf)

Is it correct or did I miss something? Because after I ran simulate_data.py again, it went through "computing MEG and EEG at 1282 source locations, 305 out of 366 channels remain after picking", and then it failed after these stages:

Computing inverse operator with 305 channels.
Created an SSP operator (subspace dimension = 8)
estimated rank (mag + grad): 297
Setting small MEG eigenvalues to zero.
Not doing PCA for MEG.
Created the whitener using a noise covariance matrix with rank 297 (8 small eigenvalues omitted)
Creating the depth weighting matrix...
203 planar channels
limit = 1233/1282 = 10.026908
scale = 3.16883e-08 exp = 0.8
Computing inverse operator with 305 channels.
Creating the source covariance matrix
Applying loose dipole orientations. Loose value of 0.2.
Whitening the forward solution.
Adjusting source covariance matrix.
Computing SVD of whitened and weighted lead field matrix.
largest singular value = 16.5682
scaling factor to adjust the trace = 6.47565e+21

Traceback (most recent call last):
File "simulate_data.py", line 13, in
main()
File "simulate_data.py", line 10, in main
sim.save_simulated_data()
File "/home/MEG-inverse-UNet/simulation_model/simulation_model.py", line 167, in save_simulated_data
self.mne = self.calculate_inverse_solution(data, method='MNE')
File "/MEG-inverse-UNet/simulation_model/simulation_model.py", line 222, in calculate_inverse_solution
stc = apply_inverse_raw(data, inv, lambda2=self.lambda2, method=method)
File "", line 2, in apply_inverse_raw
File "/home/anaconda3/lib/python3.6/site-packages/mne/utils.py", line 952, in verbose
return function(*args, **kwargs)
File "/home/anaconda3/lib/python3.6/site-packages/mne/minimum_norm/inverse.py", line 1057, in apply_inverse_raw
_check_reference(raw, inverse_operator['info']['ch_names'])
File "/home/anaconda3/lib/python3.6/site-packages/mne/minimum_norm/inverse.py", line 808, in _check_reference
raise ValueError('Custom EEG reference is not allowed for inverse '
ValueError: Custom EEG reference is not allowed for inverse modeling.

There is not the config.py. Please upload it. Thank you！