[Mne_analysis] Simulate activity in subcortical structures using MNE python?

[Christopher Bailey]

Hi Lori,

Based on the error, your label_ts-variable isn’t what mne is expecting. From the docstring of simulate_sparse_stc:

    labels : None | list of Labels
        The labels. The default is None, otherwise its size must be n_dipoles.

How did you create label_ts? Generally speaking, a little more context would be helpful to determine where the problem lies. I strongly recommend using ‘gist’s for this (https://gist.github.com)—you can copy-paste code in there and send the link to a mailing list like this one.

/Chris

On 23 Oct 2017, at 23.39, Lori Sanfratello <lsanfratello at mrn.org<mailto:lsanfratello at mrn.org>> wrote:

Hi Alex, thanks, I do have that part worked out. I have everything set up (mixed source space, fwd, inv, labels) and was trying to use:

stc = simulate_sparse_stc(fwd['src'], n_dipoles=1, times=times, labels=label_ts[0][69, :])

  and get the error message:

  File "/export/mialab/users/lsanfratello/python_anaconda/anaconda2/lib/python2.7/site-packages/mne/simulation/source.py", line 73, in select_source_in_label
    if label.hemi == 'lh':
AttributeError: 'numpy.float64' object has no attribute 'hemi'

Any chance there is a simple remedy?
Thanks,
Lori



On Sun, Oct 22, 2017 at 9:29 AM, Alexandre Gramfort <alexandre.gramfort at inria.fr<mailto:alexandre.gramfort at inria.fr>> wrote:
hi Lori,

yes it should be possible but there is no such example.

a good place to start is:

https://martinos.org/mne/stable/auto_examples/inverse/plot_mixed_source_space_inverse.html

to make a source space

then you need to simulate.

sorry I don't have enough time to help you more right now

Alex

On Thu, Oct 19, 2017 at 12:44 AM, Lori Sanfratello <lsanfratello at mrn.org<mailto:lsanfratello at mrn.org>> wrote:
Hello, I would like to simulate activity in amygdala using MNE.  I have not been able to find a method to do this in the documentation.  Is this possible at this time?
Many thanks,
Lori

--
Dr. L. Sanfratello, PhD
Assistant Professor of Trans. Neuroscience
The Mind Research Network,
1101 Yale Blvd NE
Albuquerque, NM 87106
505 272-5557<tel:(505)%20272-5557>

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--
Dr. L. Sanfratello, PhD
Assistant Professor of Trans. Neuroscience
The Mind Research Network,
1101 Yale Blvd NE
Albuquerque, NM 87106
505 272-5557
_______________________________________________
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The information in this e-mail is intended only for the person to whom it is
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