[Mne_analysis] plot_label_from_stc.py: Exception: The source space does not appear to be an ico surface

[Alexandre Gramfort]

hi David,

how do you generate your source spaces? To use this tool, you should
use the -ico option.

Something like:

mne_setup_source_space --oct 6 --subject sample

for an oct 6 source space with approx 8000 locations or

mne_setup_source_space --ico 5 --subject sample

for an ico 5 source space with approx 20000 locations.

If you have an old MNE version use:

mne_setup_source_space --ico -6 --subject sample

for the oct 6.

Hope this helps,

Alex



On Sun, Jan 5, 2014 at 2:02 PM, David I Leitman
<leitman at mail.med.upenn.edu> wrote:
> Hi all
>
> I have been trying to run portions of the code contained in the example
> "plot_label_from_stc.py" going through line by line thing are well until
> this command:
>
> func_labels, _ = mne.stc_to_label(stc_mean_label, src=src, smooth=5,
>                                  subjects_dir=subjects_dir, connected=True)
>
> at this point i get the following output errors:
>
>
>
>
>
> Reading labels from parcellation..
> Triangle file: created by neuromag on Wed Feb 20 19:45:05 2013 nvert =
> 136162 ntri = 272320
>   read 34 labels from
> /mnt/thothdisk1/K_AWARD/K_DATA/MEG_DATA/L7689/label/lh.aparc.annot
> Triangle file: created by neuromag on Wed Feb 20 22:57:01 2013 nvert =
> 138400 ntri = 276796
>   read 34 labels from
> /mnt/thothdisk1/K_AWARD/K_DATA/MEG_DATA/L7689/label/rh.aparc.annot
> [done]
> ---------------------------------------------------------------------------
> Exception                                 Traceback (most recent call last)
> <ipython-input-223-de7294e7cf08> in <module>()
>      6
>      7 func_labels, _ = mne.stc_to_label(stc_mean_label, src=src, smooth=5,
> ----> 8                                   subjects_dir=subjects_dir,
> connected=True)
>      9
>
> /home/leitman/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/mne-0.7.1-py2.7.egg/mne/label.pyc
> in stc_to_label(stc, src, smooth, connected, subjects_dir)
>    642         rr = [1e3 * src[0]['rr'], 1e3 * src[1]['rr']]
>    643         tris = [src[0]['tris'], src[1]['tris']]
> --> 644         src_conn = spatial_src_connectivity(src).tocsr()
>    645
>    646     labels = []
>
> /home/leitman/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/mne-0.7.1-py2.7.egg/mne/utils.pyc
> in dec(*args, **kwargs)
>    378             return ret
>    379         else:
> --> 380             return function(*args, **kwargs)
>    381
>    382     # set __wrapped__ attribute so ?? in IPython gets the right
> source
>
> /home/leitman/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/mne-0.7.1-py2.7.egg/mne/source_estimate.pyc
> in spatial_src_connectivity(src, dist, verbose)
>   2216         The connectivity matrix describing the spatial graph
> structure.
>   2217     """
> -> 2218     return spatio_temporal_src_connectivity(src, 1, dist)
>   2219
>   2220
>
> /home/leitman/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/mne-0.7.1-py2.7.egg/mne/utils.pyc
> in dec(*args, **kwargs)
>    378             return ret
>    379         else:
> --> 380             return function(*args, **kwargs)
>    381
>    382     # set __wrapped__ attribute so ?? in IPython gets the right
> source
>
> /home/leitman/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/mne-0.7.1-py2.7.egg/mne/source_estimate.pyc
> in spatio_temporal_src_connectivity(src, n_times, dist, verbose)
>   2072     if dist is None:
>   2073         if src[0]['use_tris'] is None:
> -> 2074             raise Exception("The source space does not appear to be
> an ico "
>   2075                             "surface. Connectivity cannot be
> extracted from "
>   2076                             "non-ico source spaces.")
>
> Exception: The source space does not appear to be an ico surface.
> Connectivity cannot be extracted from non-ico source spaces.
>
>
> Do you have any suggestions when query
> inverse_operator['src']
> Out[227]: <SourceSpaces: [<'surf', n_vertices=136162, n_used=5759>, <'surf',
> n_vertices=138400, n_used=5838>]>
>
> so I think the space should be an ico surface
>
> thanks //dave
> David I. Leitman PhD
>
> Research Assistant Professor
> Department of Psychiatry-
> Neuropsychiatry program
> Perelman School of Medicine
> University of Pennsylvania
> Gates Pavilion 10th floor room 1042
> 3400 Spruce St
> Philadelphia, PA 19104-4283
> P: (215) 662-7389
> F: (215) 662-7903
> E: leitman at mail.med.upenn.edu
> Faculty page: http://www.med.upenn.edu/apps/faculty/index.php/g275/p8174343
> Lab website:
>  http://davidileitman.com
>
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