[Mne_analysis] ValueError: The eigenspectrum of the leadfield at this voxel is complex. Consider reducing the rank of the leadfield by using reduce_rank=True.
Britta Westner
britta.wstnr at gmail.com
Fri Sep 13 07:29:01 EDT 2019
External Email - Use Caution
Hi Pooja,
I used your code with the MNE sample data (EEG) as input, however, I could
not recreate the problem, so it seems to be connected to your data ... Or
were you able to recreate the problem with any of the example data sets?
Some ideas: Did you inspect your head model for the case where this happens
in your data? Did you check whether the leadfield is [0., 0., 0.] anywhere?
Best,
Britta
On Tue, Sep 3, 2019 at 1:24 PM pooja prabhu <prabhuppooja at gmail.com> wrote:
> External Email - Use Caution
>
> Hai Alex,
> Thanks for help.
> Here is a snippet :
> ##creating volume source space
> src= setup_volume_source_space(subj, pos=5.0,mri=aseg_fname, bem=fname_model,mindist=7.0,
> subjects_dir=subjects_dir)
> ##forward model
> fwd = mne.make_forward_solution(info=raw.info, trans=None, src=src, bem=fname_bem,
> mindist=2.0, meg=False, eeg=True, n_jobs=1)
> ##computing noise covariance
> noise_cov = mne.compute_covariance(epochs, tmin=0, tmax=0.2,
> method='empirical', rank='full')
> ##computing data covariance
> data_cov = mne.compute_covariance(epochs, tmin=0.2, tmax=epochs.tmax, method='empirical',
> rank='full')
> ##
> filters = make_lcmv(info=epochs.info, forward=fwd, data_cov=data_cov,
> reg=0.05, noise_cov=noise_cov, pick_ori='max-power',
> weight_norm='nai',reduce_rank=True)
>
> Let me know anything more is required.
> Thank You
>
> On Tue, Sep 3, 2019 at 8:34 AM pooja prabhu <prabhuppooja at gmail.com>
> wrote:
>
>> Hai Eric,
>> I tried exclude=10 but no luck.
>> What else i can change to solve this error?
>>
>> On Sat, Aug 31, 2019 at 3:35 PM pooja prabhu <prabhuppooja at gmail.com>
>> wrote:
>>
>>> Hai group,
>>> I encountered the problem while executing the function make_lcmv. The
>>> error is ,
>>> ValueError: The eigenspectrum of the leadfield at this voxel is complex.
>>> Consider reducing the rank of the leadfield by using reduce_rank=True.
>>>
>>> As recommended i changed included the parameter reduce_rank=True in the
>>> function 'make_lcmv', even after that the code gives the same error.
>>> I am not sure what is the problem.
>>> This work uses 19 channel EEG signals.
>>> -------------------------------------
>>> Snippet of the code:
>>> src= setup_volume_source_space(subj, pos=5.0,mri=aseg_fname,
>>> bem=fname_model,mindist=7.0, subjects_dir=subjects_dir)
>>> fwd = mne.make_forward_solution(info=raw.info, trans=None, src=src,
>>> bem=fname_bem, mindist=2.0, meg=False, eeg=True, n_jobs=1)
>>> noise_cov = mne.compute_covariance(epochs, tmin=0, tmax=0.2,
>>> method='empirical',
>>> rank=None)
>>> data_cov = mne.compute_covariance(epochs, tmin=0.2, tmax=epochs.tmax,
>>> method='empirical', rank='full')
>>> filters = make_lcmv(info=epochs.info, forward=fwd, data_cov=data_cov,
>>> reg=0.05,
>>> noise_cov=noise_cov, pick_ori='max-power',
>>> weight_norm='nai',reduce_rank=True)
>>> ---------------------------------------
>>> --
>>> Thank You
>>> Pooja Prabhu
>>>
>>>
>>
>> --
>> Thank You
>> Pooja Prabhu
>>
>>
>
> --
> Thank You
> Pooja Prabhu
>
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